Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

[1] 2076
File a4/inst/extdata/esetExampleTimeCourse.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File a4Base/data/nlcvTT.rda: load().. ok [1 object(s)]; updateObject(nlcv, check=FALSE).. no match, no-op; nothing to update ==> 0
File ABAEnrichment/R/sysdata.rda: load().. ok [13 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ABSSeq/data/simuN5.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File acde/data/phytophthora.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File acde/vignettes/resVignette.rda: load().. ok [2 object(s)]; updateObject(STP, check=FALSE).. no match, no-op; updateObject(TC, check=FALSE).. no match, no-op; nothing to update ==> 0
File ACE/data/copyNumbersSegmented.rda: load().. ok [1 object(s)]; updateObject(QDNAseqCopyNumbers, check=FALSE).. returned an error ==> -1
File aCGH/data/colorectal.rda: load().. ok [2 object(s)]; updateObject(aCGH, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ACME/data/example.agff.rda: load().. ok [1 object(s)]; updateObject(ACMESet, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADaCGH2/data/inputEx.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADAM/data/ExpressionAedes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADAM/data/KeggPathwaysAedes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADAMgui/data/DiffAedes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADAMgui/data/GeneFunctionAedes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADAMgui/data/ResultAnalysisAedes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADImpute/Meta/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File ADImpute/data/demo_data.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADImpute/data/demo_net.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADImpute/data/demo_sce.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADImpute/data/network.coefficients.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ADImpute/data/transcript_length.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File adSplit/data/golubKEGGSplits.rda: load().. ok [1 object(s)]; updateObject(splitSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File AffiXcan/inst/extdata/testing.tba.toydata.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File AffiXcan/inst/extdata/training.tba.toydata.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File AffiXcan/data/exprMatrix.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File AffiXcan/data/regionAssoc.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AffiXcan/data/trainingCovariates.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File affy/data/cdfenv.example.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File affy/data/mapCdfName.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File affy/data/SpikeIn.rda: load().. ok [1 object(s)]; updateObject(ProbeSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File affycomp/data/dilution.phenodata.rda: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File affycomp/data/hgu133a.spikein.phenodata.rda: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File affycomp/data/hgu133a.spikein.xhyb.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File affycomp/data/mas5.assessment.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File affycomp/data/spikein.phenodata.rda: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AffyCompatible/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File affycoretools/vignettes/abatch.Rdata: load().. ok [1 object(s)]; updateObject(AffyBatch, check=FALSE).. no match, no-op; nothing to update ==> 0
File affycoretools/vignettes/exprSet.Rdata: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File affycoretools/vignettes/exprSet2.Rdata: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File AGDEX/data/agdex.res.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AGDEX/data/gset.data.rda: load().. ok [1 object(s)]; updateObject(GeneSetCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File AGDEX/data/human.data.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File AGDEX/data/map.data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AGDEX/data/mouse.data.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File aggregateBioVar/data-raw/ASE_integrated_sub.Rda: load().. ok [1 object(s)]; updateObject(Seurat, check=FALSE).. no match, no-op; nothing to update ==> 0
File aggregateBioVar/data/small_airway.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File AgiMicroRna/data/dd.micro.rda: load().. ok [1 object(s)]; updateObject(uRNAList, check=FALSE).. no match, no-op; nothing to update ==> 0
File AgiMicroRna/data/ddPROC.rda: load().. ok [1 object(s)]; updateObject(uRNAList, check=FALSE).. no match, no-op; nothing to update ==> 0
File AgiMicroRna/data/targets.micro.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AIMS/data/AIMSmodel.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AIMS/data/mcgillExample.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AllelicImbalance/data/ASEset.rdata: load().. ok [1 object(s)]; updateObject(ASEset, check=FALSE).. no match, no-op; nothing to update ==> 0
File AllelicImbalance/data/ASEset.sim.rdata: load().. ok [1 object(s)]; updateObject(ASEset, check=FALSE).. no match, no-op; nothing to update ==> 0
File AllelicImbalance/data/genomatrix.rdata: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File AllelicImbalance/data/GRvariants.rdata: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File AllelicImbalance/data/reads.rdata: load().. ok [1 object(s)]; updateObject(GAlignmentsList, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlphaBeta/inst/extdata/dm/output.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File AlphaBeta/inst/extdata/soma/outputSoma.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File AlphaBeta/inst/extdata/dm/Col_CG_global_estimates_ABneutral.Rdata: load().. failed! ==> -2
File AlphaBeta/inst/extdata/models/ABneutral_Boot_CG_global_estimates.Rdata: load().. failed! ==> -2
File AlphaBeta/inst/extdata/models/ABneutral_CG_global_estimates.Rdata: load().. failed! ==> -2
File AlphaBeta/inst/extdata/models/ABneutralSOMA_CG_Boot_global_estimates.Rdata: load().. failed! ==> -2
File AlphaBeta/inst/extdata/models/ABneutralSOMA_CG_global_estimates.Rdata: load().. failed! ==> -2
File AlphaBeta/inst/extdata/models/ABnull_CG_global_estimates.Rdata: load().. failed! ==> -2
File AlphaBeta/inst/extdata/models/ABselectMM_CG_global_estimates.Rdata: load().. failed! ==> -2
File AlphaBeta/inst/extdata/models/ABselectMMSOMA_CG_global_estimates.Rdata: load().. failed! ==> -2
File AlphaBeta/inst/extdata/models/ABselectUU_CG_global_estimates.Rdata: load().. failed! ==> -2
File AlphaBeta/inst/extdata/models/ABselectUUSOMA_CG_global_estimates.Rdata: load().. failed! ==> -2
File alpine/data/preprocessedData.rda: load().. ok [7 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(DFrame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlpsNMR/inst/extdata/nmr_dataset.rds: readRDS().. ok; updateObject(nmr_dataset_1D, check=FALSE).. no match, no-op ==> 0
File AlpsNMR/data/HMDB_blood.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlpsNMR/data/HMDB_cell.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlpsNMR/data/HMDB_urine.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlpsNMR/data/hmdb.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlpsNMR/data/Parameters_blood.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlpsNMR/data/Parameters_cell.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlpsNMR/data/Parameters_urine.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlpsNMR/data/ROI_blood.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlpsNMR/data/ROI_cell.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AlpsNMR/data/ROI_urine.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File altcdfenvs/data/cdfenvEx.rda: load().. ok [1 object(s)]; updateObject(CdfEnvAffy, check=FALSE).. no match, no-op; nothing to update ==> 0
File altcdfenvs/inst/exampleData/slamf_targets.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File AMARETTO/data/BatchData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AMARETTO/data/Driver_Genes.rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AMARETTO/data/MsigdbMapping.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AMARETTO/data/ProcessedDataLIHC.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AMARETTO/inst/extdata/MethylStates.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File amplican/inst/extdata/results/alignments/AlignmentsExperimentSet.rds: readRDS().. ok; updateObject(AlignmentsExperimentSet, check=FALSE).. no match, no-op ==> 0
File Anaquin/data/RnaQuinGeneMixture.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Anaquin/data/RnaQuinIsoformMixture.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Anaquin/data/UserGuideData_5.4.5.1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Anaquin/data/UserGuideData_5.4.6.3.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Anaquin/data/UserGuideData_5.6.3.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AneuFinder/tests/testthat/euploid_HB150318_1_003.bam_binsize_500000.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File AneuFinder/tests/testthat/trisomy_BB150803_IV_003.bam_binsize_500000.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File animalcules/inst/extdata/animalcules.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File animalcules/inst/extdata/asthma_example_dataset.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File animalcules/inst/extdata/biom_example.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File animalcules/inst/extdata/MAE.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op ==> 0
File animalcules/inst/extdata/TB_example_dataset.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File animalcules/inst/extdata/toy_data.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File annaffy/data/aafExpr.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File annmap/inst/rdata/HG-U133Plus2.tp53.expr.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File annmap/inst/rdata/HuEx-1_0.tp53.expr.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File annotate/data/hgByChroms.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File annotate/data/hgCLengths.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File annotate/data/hgu95Achroloc.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File annotate/data/hgu95Achrom.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File annotate/data/hgu95All.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File annotate/data/hgu95AProbLocs.rda: load().. ok [1 object(s)]; updateObject(chromLocation, check=FALSE).. no match, no-op; nothing to update ==> 0
File annotate/data/hgu95Asym.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File AnnotationDbi/inst/extdata/manyToOneBlackList.Rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File AnnotationDbi/inst/extdata/resultTable.Rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File AnnotationForge/inst/extdata/viableIDs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File AnnotationHubData/inst/extdata/badUCSCTracks/allBadTracks.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AnnotationHubData/inst/extdata/badUCSCTracks/allPossibleTracks.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AnnotationHubData/inst/extdata/badUCSCTracks/genomeTrackTable.Rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AnnotationHubData/inst/extdata/inpDrosPsuedo.rda: load().. ok [1 object(s)]; updateObject(AnnotationHubMetadata, check=FALSE).. returned an error ==> -1
File AnnotationHubData/inst/unitTests/cases/encodeDCCMetadata/tbl.parsedEncodeMetadata.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File annotationTools/data/orthologs_example.RData: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File annotatr/data/annotations.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File anota/data/anotaDataSet.RData: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File anota2seq/data/anota2seq_data.RData: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File AnVIL/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File AnVILBilling/data/demo_rec.rda: load().. ok [1 object(s)]; updateObject(avReckoning, check=FALSE).. no match, no-op; nothing to update ==> 0
File APAlyzer/inst/extdata/mm9_REF.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File APAlyzer/inst/extdata/mm9_TBX20.APAdiff_OUT.RData: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File APAlyzer/inst/extdata/mm9_TBX20.APAout.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File APAlyzer/inst/extdata/mm9_tissues_rawout.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/apEX.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/apEXG.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/gavin06FilteredEstimates.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/gavinBP2006.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/HMSPCI.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/HMSPCIgraph.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/Krogan.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/krogan06FilteredEstimates.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/kroganBPMat2006.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/MBMEcHMSPCI.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/MBMEcKrogan.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/MBMEcTAP.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/SBMHcHMSPCI.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/SBMHcTAP.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/TAP.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/TAPgraph.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/UnRBBcHMSPCI.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/UnRBBcTAP.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/yNameTAP.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File apComplex/data/yTAP.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File arrayMvout/data/afxsubDEG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File arrayMvout/data/fig3map.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File arrayMvout/data/ilmQA.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File arrayMvout/data/itnQA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File arrayMvout/data/maqcQA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File arrayMvout/data/s12cDEG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File arrayMvout/data/spikQA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File arrayMvout/inst/simpleaffy/afxsubQC.rda: load().. ok [1 object(s)]; updateObject(QCStats, check=FALSE).. returned an error ==> -1
File arrayMvout/inst/simpleaffy/s12cQC.rda: load().. ok [1 object(s)]; updateObject(QCStats, check=FALSE).. returned an error ==> -1
File arrayQuality/data/HsReferenceDB.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File arrayQuality/data/MmDEGenes.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File arrayQuality/data/MmReferenceDB.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ARRmNormalization/data/ProbesType.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_config.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_data_corum_mito_database.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_data_pathogen_LPN.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_data_pathogen_TB.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_data_ph_config.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_data_ph_contrast.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_data_ph_evidence.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_data_ph_keys.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_data_ph_msstats_modelqc.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_data_ph_msstats_results.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File artMS/data/artms_data_randomDF.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASAFE/data/adm_ancestries_test.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASAFE/data/adm_genotypes_test.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASGSCA/data/B0.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASGSCA/data/GenPhen.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASGSCA/data/QCAHS.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASGSCA/data/ResQCAHS.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASGSCA/data/W0.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASICS/data/sysdata.rda: load().. ok [1 object(s)]; updateObject(PureLibrary, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASpediaFI/data/GSE114922.fpkm.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASpediaFI/data/GSE114922.psi.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASpediaFI/R/sysdata.rda: load().. ok [2 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AssessORF/inst/extdata/MGAS5005_PreSaved_DataMapObj.rds: readRDS().. ok; updateObject(Assessment, check=FALSE).. no match, no-op ==> 0
File AssessORF/inst/extdata/MGAS5005_PreSaved_ResultsObj_GeneMarkS2.rds: readRDS().. ok; updateObject(Assessment, check=FALSE).. no match, no-op ==> 0
File AssessORF/inst/extdata/MGAS5005_PreSaved_ResultsObj_Prodigal.rds: readRDS().. ok; updateObject(Assessment, check=FALSE).. no match, no-op ==> 0
File ASSET/data/ex_fast_asset.rda: load().. ok [6 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASSET/data/ex_trait.rda: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASSET/data/ex_types.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASSET/inst/sampleData/vdata.rda: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASSIGN/data/excludegenes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASSIGN/data/geneList1.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASSIGN/data/gfrn_geneList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASSIGN/data/testData1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ASSIGN/data/trainingData1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ATACseqQC/inst/extdata/jolma2013.motifs.bindingList.95.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File atena/inst/extdata/Top28TEs.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File atena/inst/extdata/Top50genes.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File atSNP/data/default_par.rda: load().. ok [2 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File atSNP/data/encode_library.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File atSNP/data/example.rda: load().. ok [5 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File atSNP/data/jaspar_library.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File attract/data/exprs.dat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File attract/data/loring.eset.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File attract/data/samp.info.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File attract/data/subset.loring.eset.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File AUCell/inst/examples/cellsTsne.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Autotuner/inst/extdata/Autotuner.rds: readRDS().. ok; updateObject(Autotuner, check=FALSE).. returned an error ==> -1
File Autotuner/inst/extdata/AutotunerObj.rds: readRDS().. ok; updateObject(Autotuner, check=FALSE).. returned an error ==> -1
File Autotuner/inst/extdata/eicParamsEsts.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Autotuner/inst/extdata/header.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Autotuner/data/eicParamsEsts.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Autotuner/data/mzDb.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Autotuner/data/observedPeak.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AWFisher/data/data_mouseMetabolism.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File AWFisher/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
Skip package BaalChIP ==> -3
File BAC/data/ER.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BAC/vignettes/bac.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BAGS/data/AnnotationMFGO.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ballgown/data/bg.rda: load().. ok [1 object(s)]; updateObject(ballgown, check=FALSE).. no match, no-op; nothing to update ==> 0
File bambu/inst/extdata/annotateSpliceOverlapByDist_testQuery.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/annotateSpliceOverlapByDist_testSubject.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/annotateSpliceOverlapsByDist_refoutput.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/annotationGranges_txdbGrch38_91_chr9_1_1000000.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/defaultModels.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/extendedAnnotationGranges_txdbGrch38_91_chr9_1_1000000.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/readGrgList_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seIsoReCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seIsoReRef_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seOutput_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seOutputCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seOutputCombined2_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seOutputCombinedExtended_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seOutputExtended_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seReadClass_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seReadClassBS_Stranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seReadClassStranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/seReadClassUnstranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000_readClassSe.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/test_annotations.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/test_genomeSequence.rds: readRDS().. ok; updateObject(DNAStringSet, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/test_se_scored.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/inst/extdata/test_se.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File bambu/R/sysdata.rda: load().. ok [14 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bamsignals/inst/extdata/randomAnnot.Rdata: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File bamsignals/tests/testthat/randomReads.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BANDITS/data/gene_tr_id.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BANDITS/data/input_data.RData: load().. ok [1 object(s)]; updateObject(BANDITS_data, check=FALSE).. no match, no-op; nothing to update ==> 0
File BANDITS/data/precision.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BANDITS/data/results.RData: load().. ok [1 object(s)]; updateObject(BANDITS_test, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/data/compositions_hard_null.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/data/compositions_neg_spike.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/data/compositions_null.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/data/compositions_pos_spike.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/data/counts_hard_null.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/data/counts_neg_spike.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/data/counts_null.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/data/counts_pos_spike.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/tests/testthat/testthat_objects/banocc_model_test.RData: load().. ok [1 object(s)]; updateObject(stanmodel, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/tests/testthat/testthat_objects/sample_stan_data.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File banocc/tests/testthat/testthat_objects/sample_stan_fit.RData: load().. ok [1 object(s)]; updateObject(stanfit, check=FALSE).. no match, no-op; nothing to update ==> 0
File barcodetrackR/data/wu_subset.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File BaseSpaceR/data/aAuth.rda: load().. ok [1 object(s)]; updateObject(AppAuth, check=FALSE).. no match, no-op; nothing to update ==> 0
File Basic4Cseq/data/liverData.RData: load().. ok [1 object(s)]; updateObject(Data4Cseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File Basic4Cseq/data/liverDataRaw.RData: load().. ok [1 object(s)]; updateObject(Data4Cseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File BASiCS/data/ChainRNA.rda: load().. ok [1 object(s)]; updateObject(BASiCS_Chain, check=FALSE).. returned an error ==> -1
File BASiCS/data/ChainRNAReg.rda: load().. ok [1 object(s)]; updateObject(BASiCS_Chain, check=FALSE).. returned an error ==> -1
File BASiCS/data/ChainSC.rda: load().. ok [1 object(s)]; updateObject(BASiCS_Chain, check=FALSE).. returned an error ==> -1
File BASiCS/data/ChainSCReg.rda: load().. ok [1 object(s)]; updateObject(BASiCS_Chain, check=FALSE).. returned an error ==> -1
File BatchQC/data/example_batchqc_data.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BatchQC/data/protein_example_data.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BayesKnockdown/data/lincs.kd.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File BayesSpace/inst/testdata/maynard_151673_subset.metadata.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File bayNorm/data/EXAMPLE_DATA_list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File baySeq/data/CDPost.RData: load().. ok [1 object(s)]; updateObject(countData, check=FALSE).. no match, no-op; nothing to update ==> 0
File baySeq/data/CDPriors.RData: load().. ok [1 object(s)]; updateObject(countData, check=FALSE).. no match, no-op; nothing to update ==> 0
File baySeq/data/mobAnnotation.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File baySeq/data/mobData.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File baySeq/data/pairData.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File baySeq/data/simData.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File baySeq/data/zimData.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File BCRANK/data/BCRANKout.rda: load().. ok [1 object(s)]; updateObject(BCRANKresult, check=FALSE).. no match, no-op; nothing to update ==> 0
File BDMMAcorrect/data/L_mean.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File BDMMAcorrect/data/Microbiome_dat.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File beadarray/data/metaTemplate.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File beadarray/data/platformSigs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File beadarraySNP/data/chr17.260.rda: load().. ok [1 object(s)]; updateObject(SnpSetIllumina, check=FALSE).. no match, no-op; nothing to update ==> 0
File beadarraySNP/data/QC.260.rda: load().. ok [1 object(s)]; updateObject(QCIllumina, check=FALSE).. no match, no-op; nothing to update ==> 0
File BEARscc/data/analysis_examples.RData: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BEARscc/data/BEARscc_examples.RData: load().. ok [4 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BEAT/data/BEAT.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BEclear/data/BEclearCorrected.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BEclear/data/BEclearData.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File benchdamic/data/microbial_metabolism.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File benchdamic/data/ps_plaque_16S.RData: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File benchdamic/data/ps_stool_16S.RData: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File BgeeDB/data/geneList.RData: load().. ok [1 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File BicARE/data/sample.bicData.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File BicARE/data/sample.biclustering.RData: load().. ok [1 object(s)]; updateObject(biclustering, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiFET/inst/extdata/input_peak_motif.Rdata: load().. ok [2 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
Skip package BiGGR ==> -3
File bigmelon/data/cantaloupe.rda: load().. ok [1 object(s)]; updateObject(MethyLumiSet, check=FALSE).. returned an error ==> -1
File bigmelon/data/honeydew.rda: load().. ok [1 object(s)]; updateObject(MethyLumiSet, check=FALSE).. returned an error ==> -1
File bigPint/data/se_soybean_cn_sub.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/data/se_soybean_ir_sub.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/data/soybean_cn_metrics.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/data/soybean_cn_sub_metrics.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/data/soybean_cn_sub.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/data/soybean_cn.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/data/soybean_ir_metrics.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/data/soybean_ir_sub_metrics.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/data/soybean_ir_sub.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/data/soybean_ir.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/litre/soybean_ir_sub_metrics.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/litre/soybean_ir_sub.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/litrePresentation/add1_metrics.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/litrePresentation/kidneyLiver.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/litrePresentation/soybean_ir_sub_metrics.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/litrePresentation/soybean_ir_sub.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/pcplot/soybean_ir_sub_metrics.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/pcplot/soybean_ir_sub.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/smplot/soybean_cn_sub.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/volcano/soybean_ir_sub_metrics.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bigPint/inst/shiny-dashboards/volcano/soybean_ir_sub.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BindingSiteFinder/inst/extdata/gns.rds: readRDS().. failed! ==> -2
File BindingSiteFinder/inst/extdata/regions.rds: readRDS().. failed! ==> -2
File BindingSiteFinder/inst/extdata/bds.rda: load().. ok [1 object(s)]; updateObject(BSFDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File bioassayR/data/samplebioassay.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bioassayR/vignettes/getBM.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bioassayR/vignettes/getids.RData: load().. ok [1 object(s)]; updateObject(SDFset, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/data/geneCovariate.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/data/reporter.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/data/sample.ExpressionSet.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/data/sample.MultiSet.rda: load().. ok [1 object(s)]; updateObject(MultiSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/data/seD.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/data/SW.rda: load().. ok [1 object(s)]; updateObject(RGList, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/1.8/AnnotatedDataFrame.Rda: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/1.8/ExpressionSet.Rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/1.8/exprSet.Rda: load().. ok [1 object(s)]; updateObject(exprSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/1.8/MIAME.Rda: load().. ok [1 object(s)]; updateObject(MIAME, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/1.8/phenoData.Rda: load().. ok [1 object(s)]; updateObject(phenoData, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/aggregator.Rda: load().. ok [1 object(s)]; updateObject(aggregator, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/AnnotatedDataFrame.Rda: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/container.Rda: load().. ok [1 object(s)]; updateObject(container, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/ExpressionSet.Rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/exprSet.Rda: load().. ok [1 object(s)]; updateObject(exprSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/MIAME.Rda: load().. ok [1 object(s)]; updateObject(MIAME, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/MultiSet.Rda: load().. ok [1 object(s)]; updateObject(MultiSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/phenoData.Rda: load().. ok [1 object(s)]; updateObject(phenoData, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/ScalarCharacter.Rda: load().. ok [1 object(s)]; updateObject(ScalarCharacter, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/SnpSet.Rda: load().. ok [1 object(s)]; updateObject(SnpSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/Versioned.Rda: load().. ok [1 object(s)]; updateObject(Versioned, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/VersionedBiobase.Rda: load().. ok [1 object(s)]; updateObject(VersionedBiobase, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/Versions.Rda: load().. ok [1 object(s)]; updateObject(Versions, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/2.0/VersionsNull.Rda: load().. ok [1 object(s)]; updateObject(VersionsNull, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/aggregator.Rda: load().. ok [1 object(s)]; updateObject(aggregator, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/AnnotatedDataFrame.Rda: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/bbsym.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/container.Rda: load().. ok [1 object(s)]; updateObject(container, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/eset.rda: load().. ok [1 object(s)]; updateObject(exprSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/ExpressionSet.Rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/exprSet.Rda: load().. ok [1 object(s)]; updateObject(exprSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/golubMergeSub.rda: load().. ok [1 object(s)]; updateObject(exprSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/MIAME.Rda: load().. ok [1 object(s)]; updateObject(MIAME, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/MultiSet.Rda: load().. ok [1 object(s)]; updateObject(MultiSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/NChannelSet.Rda: load().. ok [1 object(s)]; updateObject(NChannelSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/sample.eSet.rda: load().. ok [1 object(s)]; updateObject(eSet, check=FALSE).. returned an error ==> -1
File Biobase/inst/unitTests/VersionedClass_data/devel/sample.exprSet.1.rda: load().. ok [1 object(s)]; updateObject(exprSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/sample.exprSet.rda: load().. ok [1 object(s)]; updateObject(exprSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/ScalarCharacter.Rda: load().. ok [1 object(s)]; updateObject(ScalarCharacter, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/ScalarInteger.Rda: load().. ok [1 object(s)]; updateObject(ScalarInteger, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/ScalarLogical.Rda: load().. ok [1 object(s)]; updateObject(ScalarLogical, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/ScalarNumeric.Rda: load().. ok [1 object(s)]; updateObject(ScalarNumeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/SnpSet.Rda: load().. ok [1 object(s)]; updateObject(SnpSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/SWPD.rda: load().. ok [1 object(s)]; updateObject(phenoData, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/swrep.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/Versioned.Rda: load().. ok [1 object(s)]; updateObject(Versioned, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/VersionedBiobase.Rda: load().. ok [1 object(s)]; updateObject(VersionedBiobase, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/Versions.Rda: load().. ok [1 object(s)]; updateObject(Versions, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biobase/inst/unitTests/VersionedClass_data/devel/VersionsNull.Rda: load().. ok [1 object(s)]; updateObject(Versions, check=FALSE).. no match, no-op; nothing to update ==> 0
File biobroom/data/hammer.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File bioCancer/inst/extdata/ReactomeFI2017.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File bioCancer/inst/extdata/ReactomeFI2018.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File bioCancer/data/epiGenomics.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bioCancer/data/user_CNA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bioCancer/data/user_MetHM27.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bioCancer/data/user_MetHM450.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bioCancer/data/user_mRNA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File bioCancer/data/user_Mut.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocCheck/inst/unitTests/IRangesParsedCode.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/annotTabs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/brcaMAE.rda: load().. ok [1 object(s)]; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BiocOncoTK/data/CCLE_DRUG_BROAD.rda: load().. ok [1 object(s)]; updateObject(DataFrame, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BiocOncoTK/data/cell_70138.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/darmGBMcls.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BiocOncoTK/data/dingMSI.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/fireMSI.rda: load().. ok [1 object(s)]; updateObject(DataFrame, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BiocOncoTK/data/icd10_c.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/k23sig.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/kang_DNArepair.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/map_tcga_ncit.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/molpo_3utr.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/molpo_5utr.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/molpo_CDS.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/molpo_WGS.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/MSIsensor.10k.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/pancan_sampTypeMap.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/pancan.clin.varnames.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/patient_to_tumor_code.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/pert_70138.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/data/small_msi.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/inst/mocks/ccleNRAS.rda: load().. ok [1 object(s)]; updateObject(DRTraceSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/inst/mocks/NRAS_AHR.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/inst/mocks/nrasdf.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/inst/MSIsensor/dingMSI.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocOncoTK/inst/pamphlets/blcaMAE.rda: load().. ok [1 object(s)]; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BioCor/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(GeneSetCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiocSklearn/inst/ban_6_17/se.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BiocSklearn/inst/hdf5/tenx_750/se.rds: readRDS().. ok; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File biocViews/data/biocViewsVocab.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File biodb/longtests/testthat/testthat-problems.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File BioMM/inst/extdata/cpgAnno.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File BioMM/inst/extdata/expData.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File BioMM/inst/extdata/goDB.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File BioMM/inst/extdata/keggDB.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File BioMM/inst/extdata/keggID2name202008.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File BioMM/inst/extdata/methylData.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File biomvRCNS/data/coriell.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File biomvRCNS/data/encodeTP53.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File biomvRCNS/data/variosm.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioNERO/data/filt.se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioNERO/data/og.zma.osa.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioNERO/data/osa.se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioNERO/data/zma.interpro.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioNERO/data/zma.se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioNERO/data/zma.tfs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioNet/data/pvaluesExample.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioNetStat/data/labels.rda: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioNetStat/data/varFile.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioQC/inst/extdata/GSE20113.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioQC/inst/extdata/kidney_example.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioQC/vignettes/simulation-benchmark.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File biosigner/data/diaplasma.rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/BLOSUM100.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/BLOSUM45.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/BLOSUM50.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/BLOSUM62.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/BLOSUM80.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/HNF4alpha.rda: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/PAM120.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/PAM250.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/PAM30.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/PAM40.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/PAM70.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/phiX174Phage.rda: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/srPhiX174.rda: load().. ok [3 object(s)]; updateObject(BStringSet, check=FALSE).. no match, no-op; updateObject(DNAStringSet, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File Biostrings/data/yeastSEQCHR1.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioTIP/data/cod.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioTIP/data/gencode.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioTIP/data/GSE6136_cli.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioTIP/data/GSE6136_matrix.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioTIP/data/ILEF.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioTIP/data/intron.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioTIP/data/membersL.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BioTIP/data/subcounts.optimize_80per.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File biovizBase/data/CRC.rda: load().. ok [3 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biovizBase/data/crc1.GeRL.rda: load().. ok [1 object(s)]; updateObject(SimpleGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File biovizBase/data/darned_hg19_subset500.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biovizBase/data/genesymbol.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biovizBase/data/hg19Ideogram.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biovizBase/data/hg19IdeogramCyto.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biovizBase/data/ideo.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File biovizBase/data/ideoCyto.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiRewire/data/BRCA_binary_matrix.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiRewire/data/test_dsg.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/clocks.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/ENSR_subset.hg19.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/ENSR_subset.hg38.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/GRCh37.chromArm.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/GRCh38.chromArm.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/H9state23unmeth.hg19.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/H9state23unmeth.hg38.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/hg19.chromArm.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/hg38.chromArm.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/HMM_CpG_islands.hg19.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/HMM_CpG_islands.hg38.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/seqinfo.hg19.rda: load().. ok [1 object(s)]; updateObject(Seqinfo, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/seqinfo.hg38.rda: load().. ok [1 object(s)]; updateObject(Seqinfo, check=FALSE).. no match, no-op; nothing to update ==> 0
File biscuiteer/data/seqinfo.mm10.rda: load().. ok [1 object(s)]; updateObject(Seqinfo, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiSeq/data/betaResults.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiSeq/data/betaResultsNull.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BiSeq/data/DMRs.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BiSeq/data/predictedMeth.RData: load().. ok [1 object(s)]; updateObject(BSrel, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BiSeq/data/promoters.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BiSeq/data/rrbs.RData: load().. ok [1 object(s)]; updateObject(BSraw, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BiSeq/data/vario.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File blacksheepr/data/sample_annotationdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File blacksheepr/data/sample_phosphodata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File blacksheepr/data/sample_rnadata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BLMA/data/GSE17054.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BLMA/data/GSE33223.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BLMA/data/GSE42140.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BLMA/data/GSE57194.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BloodGen3Module/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File bnbc/data/cgEx.rda: load().. ok [1 object(s)]; updateObject(ContactGroup, check=FALSE).. no match, no-op; nothing to update ==> 0
File bnem/data/bcr.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BOBaFIT/data/TCGA_BRCA_CN_segments.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BOBaFIT/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File BPRMeth/data/bernoulli_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BPRMeth/data/beta_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BPRMeth/data/binomial_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BPRMeth/data/encode_expr.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File BPRMeth/data/encode_met.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BPRMeth/data/gaussian_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BPRMeth/data/gex_data.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File BPRMeth/data/meth_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File brainflowprobes/data/four_panels_example_cov.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File brainflowprobes/data/pd.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File branchpointer/R/sysdata.rda: load().. ok [6 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(train, check=FALSE).. no match, no-op; updateObject(dummyVars, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(preProcess, check=FALSE).. no match, no-op; nothing to update ==> 0
File breakpointR/tests/testthat/nobreaks_exampleFile.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File breakpointR/tests/testthat/withbreaks_exampleFile.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File brendaDb/data/acronyms.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File BRGenomics/data/PROseq_paired.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File BRGenomics/data/PROseq.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File BRGenomics/data/txs_dm6_chr4.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File bridge/data/hiv.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File bsseq/data/BS.chr22.rda: load().. ok [1 object(s)]; updateObject(BSseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File BubbleTree/data/all.somatic.lst.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BubbleTree/data/allCall.lst.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BubbleTree/data/allCNV.lst.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BubbleTree/data/allHetero.lst.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BubbleTree/data/allRBD.lst.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BubbleTree/data/cancer.genes.minus2.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BubbleTree/data/centromere.dat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BubbleTree/data/cnv.gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BubbleTree/data/cyto.gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BubbleTree/data/gene.uni.clean.gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BubbleTree/data/hg19.seqinfo.rda: load().. ok [1 object(s)]; updateObject(Seqinfo, check=FALSE).. no match, no-op; nothing to update ==> 0
File BubbleTree/data/snp.gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File BubbleTree/data/vol.genes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUMHMM/data/covFile.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUMHMM/data/docFile.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUMHMM/data/dorFile.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUMHMM/data/se.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUMHMM/data/seq.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File bumphunter/data/TT.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bumphunter/inst/unitTests/bumpsTest1.rda: load().. ok [1 object(s)]; updateObject(bumps, check=FALSE).. no match, no-op; nothing to update ==> 0
File bumphunter/inst/unitTests/bumpsTest2.rda: load().. ok [1 object(s)]; updateObject(bumps, check=FALSE).. no match, no-op; nothing to update ==> 0
File bumphunter/inst/unitTests/loessSmoothed.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bumphunter/inst/unitTests/loessSmoothed2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bumphunter/inst/unitTests/runmedSmoothed.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File bumphunter/inst/unitTests/runmedSmoothed2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUS/data/copasi.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUS/data/tumors.miRNA.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUS/data/tumors.mRNA.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUScorrect/data/BUSexample_data.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUSpaRse/data/cellranger_biotypes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUSpaRse/data/ensembl_gene_biotypes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUSpaRse/data/ensembl_gff_mcols.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUSpaRse/data/ensembl_gtf_mcols.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUSpaRse/data/ensembl_tx_biotypes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUSpaRse/data/refseq_gff_mcols.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUSpaRse/inst/testdata/toy_example.RData: load().. ok [8 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(dgCMatrix, check=FALSE).. no match, no-op; updateObject(dgCMatrix, check=FALSE).. no match, no-op; updateObject(dgCMatrix, check=FALSE).. no match, no-op; updateObject(dgCMatrix, check=FALSE).. no match, no-op; updateObject(dgCMatrix, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File BUSseq/data/BUSseqfits_example.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAEN/data/realData.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAFE/data/CAFE_data.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAGEfightR/data/exampleBidirectional.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAGEfightR/data/exampleCTSSs.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAGEfightR/data/exampleDesign.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAGEfightR/data/exampleGenes.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAGEfightR/data/exampleUnidirectional.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File cageminer/data/chr_length.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File cageminer/data/gcn.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cageminer/data/gene_ranges.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File cageminer/data/guides.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cageminer/data/hubs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cageminer/data/mine2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cageminer/data/mined_candidates.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cageminer/data/pepper_se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File cageminer/data/snp_pos.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File cageminer/data/tfs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAGEr/data/exampleCAGEexp.RData: load().. ok [1 object(s)]; updateObject(CAGEexp, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAGEr/data/exampleZv9_annot.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAGEr/data/FANTOM5humanSamples.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAGEr/data/FANTOM5mouseSamples.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File calm/data/pso.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAMERA/data/mm14.rda: load().. ok [1 object(s)]; updateObject(xcmsSet, check=FALSE).. returned an error ==> -1
File canceR/inst/extdata/rdata/brca_tcga73genes.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File canceR/inst/extdata/rdata/brca_tcgaClassifier223.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File canceR/inst/extdata/rdata/brca_tcgaGSEAlm1021.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File canceR/inst/extdata/rdata/Circos.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File canceR/inst/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File canceR/inst/extdata/rdata/prad_michPhenoTest1021.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File canceR/inst/extdata/rdata/ucec_tcga_pubGSEA1021.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File cancerclass/data/GOLUB.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File cancerclass/data/GOLUB1.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File CancerInSilico/data/ReferenceGeneExpression.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CancerInSilico/data/SampleModels.RData: load().. ok [6 object(s)]; updateObject(DrasdoHohmeModel, check=FALSE).. no match, no-op; updateObject(DrasdoHohmeModel, check=FALSE).. no match, no-op; updateObject(DrasdoHohmeModel, check=FALSE).. no match, no-op; updateObject(DrasdoHohmeModel, check=FALSE).. no match, no-op; updateObject(DrasdoHohmeModel, check=FALSE).. no match, no-op; updateObject(DrasdoHohmeModel, check=FALSE).. no match, no-op; nothing to update ==> 0
File CancerInSilico/data/SamplePathways.RData: load().. ok [4 object(s)]; updateObject(Pathway, check=FALSE).. no match, no-op; updateObject(Pathway, check=FALSE).. no match, no-op; updateObject(Pathway, check=FALSE).. no match, no-op; updateObject(Pathway, check=FALSE).. no match, no-op; nothing to update ==> 0
File CancerSubtypes/data/GeneExp.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CancerSubtypes/data/miRNAExp.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CancerSubtypes/data/Ranking.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CancerSubtypes/data/status.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File CancerSubtypes/data/time.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File CAnD/data/ancestries.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File caOmicsV/data/biomatrixPlotDemoData.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File caOmicsV/data/bionetPlotDemoData.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File caOmicsV/data/CNVDemoData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File caOmicsV/data/methylDemoData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File caOmicsV/data/miRNA.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File caOmicsV/data/miRNADemoData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File caOmicsV/data/RNA2miRNA.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File caOmicsV/data/RNASeq.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File caOmicsV/data/RNASeqDemoData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File caOmicsV/data/sampleDemoData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/inst/progenyMembers.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/inst/toy_inputs_ex1.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/inst/toy_measurements_ex1.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/inst/toy_measurements_ex2.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/inst/toy_network_ex1.RData: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/inst/toy_network_ex2.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/inst/toy_parsed_data_ex1.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/inst/toy_perturbations_ex1.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/inst/toy_result_expected_ex1.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CARNIVAL/vignettes/toy_files_vignettes/parsedData_t18_01_53d28_04_2021n4.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File casper/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File casper/data/distrsGSE37704.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File casper/data/hg19DB.RData: load().. ok [1 object(s)]; updateObject(annotatedGenome, check=FALSE).. no match, no-op; nothing to update ==> 0
File casper/data/K562.r1l1.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CATALYST/data/isotope_list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CATALYST/data/merging_table.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File CATALYST/data/mp_cells.rda: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CATALYST/data/PBMC_fs.rda: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File CATALYST/data/PBMC_md.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CATALYST/data/PBMC_panel.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CATALYST/data/raw_data.rda: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File CATALYST/data/sample_ff.rda: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CATALYST/data/sample_key.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CATALYST/data/ss_exp.rda: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Category/inst/UnitTests/ghgans10.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File categoryCompare/data/ccData.RData: load().. ok [9 object(s)]; updateObject(ccOptions, check=FALSE).. no match, no-op; updateObject(ccCompareCollection, check=FALSE).. no match, no-op; updateObject(ccCompareResult, check=FALSE).. no match, no-op; updateObject(ccEnrichCollection, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(ccGeneList, check=FALSE).. returned an error ==> -1
File cbaf/inst/extdata/test/2ac417972df8_2ac417972df8.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test/2ac449ee43f7_2ac449ee43f7.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test/2ac44ede75ff_2ac44ede75ff.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test/2ac470695f1_2ac470695f1.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test/2ac4712b7f0e_2ac4712b7f0e.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test/2ac47eb35cad_2ac47eb35cad.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test/2ac47f9152b6_2ac47f9152b6.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test2/4490161f7a56_4490161f7a56.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test2/4490473b4435_4490473b4435.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test2/44904c54297a_44904c54297a.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test2/449055e968f2_449055e968f2.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test2/449063b8131f_449063b8131f.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test2/44906d6248a4_44906d6248a4.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/test2/4490a4e5e6a_4490a4e5e6a.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole/7f81bf44679_7f81bf44679.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole/7f81eec3217_7f81eec3217.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole/7f82a8a2a98_7f82a8a2a98.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole/7f85e6a86d_7f85e6a86d.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole/7f871617e02_7f871617e02.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole/7f874d137bc_7f874d137bc.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole/7f8c0e1af0_7f8c0e1af0.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole2/7f81bf44679_7f81bf44679.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole2/7f81eec3217_7f81eec3217.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole2/7f82a8a2a98_7f82a8a2a98.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole2/7f85e6a86d_7f85e6a86d.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole2/7f871617e02_7f871617e02.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole2/7f874d137bc_7f874d137bc.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cbaf/inst/extdata/Whole2/7f8c0e1af0_7f8c0e1af0.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cBioPortalData/inst/extdata/metadata_table.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File cBioPortalData/data/studiesTable.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File cBioPortalData/inst/extdata/api/api_build.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cBioPortalData/inst/extdata/api/err_api_info.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cBioPortalData/inst/extdata/api/err_api.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File cBioPortalData/inst/extdata/pack/err_pack_info.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cBioPortalData/inst/extdata/pack/err_pack.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File cBioPortalData/inst/extdata/pack/pack_build.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CCPROMISE/data/exmplESet.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File CCPROMISE/data/exmplGeneSet.rda: load().. ok [1 object(s)]; updateObject(GeneSetCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File CCPROMISE/data/exmplMSet.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File CCPROMISE/data/exmplPat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File celaref/data/de_table.demo_query.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File celaref/data/de_table.demo_ref.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File celaref/data/demo_cell_info_table.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File celaref/data/demo_counts_matrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File celaref/data/demo_gene_info_table.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File celaref/data/demo_microarray_expr.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File celaref/data/demo_microarray_sample_sheet.rda: load().. ok [1 object(s)]; updateObject(grouped_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File celaref/data/demo_query_se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File celaref/data/demo_ref_se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File celaref/inst/extdata/larger_doco_examples.rdata: load().. ok [3 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/celdaCGGridSearchRes.rda: load().. ok [1 object(s)]; updateObject(celdaList, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/celdaCGMod.rda: load().. ok [1 object(s)]; updateObject(celda_CG, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/celdaCGSim.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/celdaCMod.rda: load().. ok [1 object(s)]; updateObject(celda_C, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/celdaCSim.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/celdaGMod.rda: load().. ok [1 object(s)]; updateObject(celda_G, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/celdaGSim.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/contaminationSim.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/sampleCells.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/sceCeldaC.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/sceCeldaCG.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/sceCeldaCGGridSearch.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File celda/data/sceCeldaG.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellaRepertorium/data/ccdb_ex.rda: load().. ok [1 object(s)]; updateObject(ContigCellDB, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellaRepertorium/data/contigs_qc.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellaRepertorium/tests/testthat/out/pairing1.rda: load().. failed! ==> -2
File CellaRepertorium/tests/testthat/out/pairing2.rda: load().. failed! ==> -2
File CellaRepertorium/tests/testthat/out/pairing3.rda: load().. failed! ==> -2
File CellaRepertorium/tests/testthat/out/permutation1.rda: load().. failed! ==> -2
File CellBarcode/data/bc_obj.RData: load().. ok [1 object(s)]; updateObject(BarcodeObj, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellbaseR/cellbaseR.Rcheck/00_pkg_src/cellbaseR/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File cellbaseR/cellbaseR.Rcheck/cellbaseR/help/aliases.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File cellbaseR/cellbaseR.Rcheck/cellbaseR/help/paths.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File cellbaseR/cellbaseR.Rcheck/cellbaseR/Meta/features.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cellbaseR/cellbaseR.Rcheck/cellbaseR/Meta/hsearch.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cellbaseR/cellbaseR.Rcheck/cellbaseR/Meta/links.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File cellbaseR/cellbaseR.Rcheck/cellbaseR/Meta/nsInfo.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cellbaseR/cellbaseR.Rcheck/cellbaseR/Meta/package.rds: readRDS().. ok; updateObject(packageDescription2, check=FALSE).. no match, no-op ==> 0
File cellbaseR/cellbaseR.Rcheck/cellbaseR/Meta/Rd.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File cellbaseR/cellbaseR.Rcheck/cellbaseR/Meta/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File CellBench/inst/extdata/10x_sce_sample.rds: readRDS().. ok; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op ==> 0
File CellBench/inst/extdata/celseq_sce_sample.rds: readRDS().. ok; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op ==> 0
File CellBench/data/sample_sce_data.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellHTS2/data/bdgpbiomart.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellHTS2/data/dualCh.rda: load().. ok [1 object(s)]; updateObject(cellHTS, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellHTS2/data/KcViab.rda: load().. ok [1 object(s)]; updateObject(cellHTS, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellHTS2/data/KcViabSmall.rda: load().. ok [1 object(s)]; updateObject(cellHTS, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellHTS2/data/oldKcViabSmall.rda: load().. ok [1 object(s)]; updateObject(cellHTS, check=FALSE).. returned an error ==> -1
File CelliD/data/Hallmark.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CelliD/data/HgProteinCodingGenes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CelliD/data/MgProteinCodingGenes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CelliD/data/seuratPbmc.rda: load().. ok [1 object(s)]; updateObject(Seurat, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/extra_human_genes.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/extra_mouse_genes.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/feature_info.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/mES1_features.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/mES1_labels.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/param_mES_all.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/param_mES_common.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/sample_counts.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/sample_stats.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/training_mES_features.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellity/data/training_mES_labels.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellMapper/data/ExampleQueryGenes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellMapper/data/NegativeControlGenes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellMapper/data/PositiveControlGenes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellmigRation/data/preProcCellMig.rda: load().. ok [1 object(s)]; updateObject(CellMig, check=FALSE).. returned an error ==> -1
File cellmigRation/data/ThreeConditions.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. returned an error ==> -1
File cellmigRation/data/TrackCellsDataset.rda: load().. ok [1 object(s)]; updateObject(trackedCells, check=FALSE).. returned an error ==> -1
File cellmigRation/data/TrajectoryDataset.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellmigRation/data/WSADataset.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellMixS/inst/extdata/sim50.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File CellMixS/R/sysdata.rda: load().. ok [2 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellNOptR/data/CNOlist_ToyPB.RData: load().. ok [1 object(s)]; updateObject(CNOlist, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellNOptR/data/CNOlistDREAM.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellNOptR/data/CNOlistToy.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellNOptR/data/CNOlistToy2.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellNOptR/data/CNOlistToyMMB.RData: load().. ok [1 object(s)]; updateObject(CNOlist, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellNOptR/data/DreamModel.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellNOptR/data/PKN_ToyPB.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellNOptR/data/ToyModel.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellNOptR/data/ToyModel2.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellScore/inst/extdata/eset48.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File CellTrails/inst/exdata/bundle.rds: readRDS().. ok; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op ==> 0
File CellTrails/inst/exdata/th2.rds: readRDS().. ok; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op ==> 0
File CellTrails/data/exSCE.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File cellTree/data/HSMM_lda_model.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CEMiTool/data/cem.rda: load().. ok [1 object(s)]; updateObject(CEMiTool, check=FALSE).. returned an error ==> -1
File CEMiTool/data/expr0.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CEMiTool/data/sample_annot.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Cepo/data/cellbench.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File Cepo/data/sce_pancreas.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ceRNAnetsim/data/huge_example.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ceRNAnetsim/data/midsamp_new_counts.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ceRNAnetsim/data/midsamp.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ceRNAnetsim/data/minsamp.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ceRNAnetsim/data/mirtarbasegene.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ceRNAnetsim/data/new_counts.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ceRNAnetsim/data/TCGA_E9_A1N5_mirnanormal.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ceRNAnetsim/data/TCGA_E9_A1N5_mirnatumor.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ceRNAnetsim/data/TCGA_E9_A1N5_normal.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ceRNAnetsim/data/TCGA_E9_A1N5_tumor.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File CeTF/data/CeTFdemo.RData: load().. ok [1 object(s)]; updateObject(CeTF, check=FALSE).. returned an error ==> -1
File CeTF/data/enrichdemo.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CeTF/data/refGenes.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CeTF/data/RIF_input.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CeTF/data/simCounts.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CeTF/data/simNorm.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CeTF/data/TFs.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CGEN/inst/sampleData/SNPdata.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CGHbase/data/WiltingCalled.rda: load().. ok [1 object(s)]; updateObject(cghCall, check=FALSE).. no match, no-op; nothing to update ==> 0
File CGHbase/data/WiltingNorm.rda: load().. ok [1 object(s)]; updateObject(cghRaw, check=FALSE).. no match, no-op; nothing to update ==> 0
File CGHbase/data/WiltingRaw.rda: load().. ok [1 object(s)]; updateObject(cghRaw, check=FALSE).. no match, no-op; nothing to update ==> 0
File CGHbase/data/WiltingRegions.rda: load().. ok [1 object(s)]; updateObject(cghRegions, check=FALSE).. no match, no-op; nothing to update ==> 0
File CGHbase/data/WiltingSeg.rda: load().. ok [1 object(s)]; updateObject(cghSeg, check=FALSE).. no match, no-op; nothing to update ==> 0
File cghMCR/data/segData.rda: load().. ok [1 object(s)]; updateObject(DNAcopy, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChemmineR/data/apfp.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChemmineR/data/apset.rda: load().. ok [1 object(s)]; updateObject(APset, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChemmineR/data/atomprop.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChemmineR/data/pubchemFPencoding.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChemmineR/data/sdfsample.rda: load().. ok [1 object(s)]; updateObject(SDFset, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChemmineR/data/smisample.rda: load().. ok [1 object(s)]; updateObject(SMIset, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChemmineR/vignettes/launchCMTool.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChemmineR/vignettes/listCMTools.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChemmineR/vignettes/toolDetails.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHETAH/data/headneck_ref.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHETAH/data/input_mel.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File Chicago/data/cdUnitTest.rda: load().. ok [1 object(s)]; updateObject(chicagoData, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPanalyser/data/ChIPanalyserData.rda: load().. ok [4 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPanalyser/inst/unitTests/genomeWideScoringAccess.rda: load().. ok [1 object(s)]; updateObject(genomicProfileParameters, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPanalyser/inst/unitTests/genomeWideScoringNoAccess.rda: load().. ok [1 object(s)]; updateObject(genomicProfileParameters, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPanalyser/inst/unitTests/GPPWithPFM.rda: load().. ok [1 object(s)]; updateObject(genomicProfileParameters, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPanalyser/inst/unitTests/OccupancyAccess.rda: load().. ok [1 object(s)]; updateObject(genomicProfileParameters, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPanalyser/inst/unitTests/OccupancyNoAccess.rda: load().. ok [1 object(s)]; updateObject(genomicProfileParameters, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPanalyser/inst/unitTests/PWMScoreAccess.rda: load().. ok [1 object(s)]; updateObject(genomicProfileParameters, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPanalyser/inst/unitTests/PWMScoreNoAccess.rda: load().. ok [1 object(s)]; updateObject(genomicProfileParameters, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPComp/data/seqData.rda: load().. ok [1 object(s)]; updateObject(ChIPComp, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPexoQual/data/blacklists.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPexoQual/data/exoExample.RData: load().. ok [1 object(s)]; updateObject(ExoData, check=FALSE).. no match, no-op; nothing to update ==> 0
Skip package ChIPpeakAnno ==> -3
File ChIPQC/data/blacklist_hg19.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPQC/data/example_QCexperiment.RData: load().. ok [1 object(s)]; updateObject(ChIPQCexperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPQC/data/tamoxifen_QC.RData: load().. ok [1 object(s)]; updateObject(ChIPQCexperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPseeker/data/gsminfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPseeker/data/tagMatrixList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPseeker/data/ucsc_release.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPseeker/inst/extdata/processedGSM.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File chipseq/data/cstest.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File chipseq/inst/Scripts/abc.rda: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File chipseq/inst/Scripts/isochores.mm9.rda: load().. ok [1 object(s)]; updateObject(RangedData, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChIPXpress/data/Oct4ESC_ChIPgenes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File chopsticks/data/for.exercise.RData: load().. ok [3 object(s)]; updateObject(snp.matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File chopsticks/data/testdata.RData: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(snp.matrix, check=FALSE).. no match, no-op; updateObject(X.snp.matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChromHeatMap/data/cytobands.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChromHeatMap/data/demo.rda: load().. ok [2 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ChrStrandData, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromPlot/data/hg_cytoBandIdeo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromPlot/data/hg_gap.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromPlot/data/mm10_cytoBandIdeo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromPlot/data/mm10_gap.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChromSCape/data/hg38.chromosomes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChromSCape/data/hg38.cytoBand.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChromSCape/data/hg38.GeneTSS.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChromSCape/data/mm10.chromosomes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChromSCape/data/mm10.cytoBand.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChromSCape/data/mm10.GeneTSS.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ChromSCape/data/scExp.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromstaR/data/combined_mode-differential.RData: load().. ok [1 object(s)]; updateObject(combinedMultiHMM, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromstaR/data/genes_rn4.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromstaR/data/H3K27me3-BN-rep1.RData: load().. ok [1 object(s)]; updateObject(uniHMM, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromstaR/data/multivariate_mode-combinatorial_condition-SHR.RData: load().. ok [1 object(s)]; updateObject(multiHMM, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromstaR/tests/testthat/stateswap/H3K27Ac_GMP_Rep1_SRR1521798.bam_binsize_1000_chr_chr14.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromswitch/data/H3K4me3.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromVAR/data/example_counts.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromVAR/data/mini_counts.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromVAR/data/mini_dev.rda: load().. ok [1 object(s)]; updateObject(chromVARDeviations, check=FALSE).. no match, no-op; nothing to update ==> 0
File chromVAR/data/mini_ix.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_cel.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_cfa.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_dme.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_dre.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_gga.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_hsa.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_mmu.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_oar.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_rno.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CHRONOS/inst/extdata/Examples/data.RData: load().. ok [14 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File cicero/data/cell_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cicero/data/cicero_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cicero/data/gene_annotation_sample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cicero/data/human.hg19.genome.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cicero/tests/tsne_coord.Rdata: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CINdex/data/clin.crc.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CINdex/data/cnvgr.18.auto.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File CINdex/data/cyto.cin4heatmap.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CINdex/data/cytobands.cin.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CINdex/data/geneAnno.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CINdex/data/grl.data.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File CINdex/data/hg18.ucsctrack.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File CINdex/data/snpgr.18.auto.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File circRNAprofiler/data/ahChainFiles.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File circRNAprofiler/data/ahRepeatMasker.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File circRNAprofiler/data/attractSpecies.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File circRNAprofiler/data/backSplicedJunctions.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File circRNAprofiler/data/gtf.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File circRNAprofiler/data/gwasTraits.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File circRNAprofiler/data/iupac.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File circRNAprofiler/data/memeDB.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File circRNAprofiler/data/mergedBSJunctions.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File circRNAprofiler/data/miRspeciesCodes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CiteFuse/data/CITEseq_example.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CiteFuse/data/lr_pair_subset.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CiteFuse/data/sce_control_subset.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File CiteFuse/data/sce_ctcl_subset.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ClassifyR/data/asthma.RData: load().. ok [2 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ClassifyR/data/HuRI.RData: load().. ok [1 object(s)]; updateObject(Pairs, check=FALSE).. no match, no-op; nothing to update ==> 0
File cleanUpdTSeq/data/classifier.rda: load().. ok [1 object(s)]; updateObject(PASclassifier, check=FALSE).. returned an error ==> -1
File cleanUpdTSeq/data/data.NaiveBayes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cleanUpdTSeq/inst/extdata/test-predNaiveBayes.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(featureVector, check=FALSE).. returned an error ==> -1
File clippda/data/liver_pheno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clippda/data/liverdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clippda/data/liverRawData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clippda/data/pheno_urine.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cliProfiler/inst/extdata/test.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File cliqueMS/data/ex.cliqueGroups.RData: load().. ok [1 object(s)]; updateObject(anClique, check=FALSE).. no match, no-op; nothing to update ==> 0
File cliqueMS/data/negative.adinfo.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cliqueMS/data/positive.adinfo.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Clomial/data/breastCancer.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Clomial/data/Clomial1000.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Clonality/data/freqdata.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Clonality/data/lcis.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clst/data/actino.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clst/data/bvseqs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clst/data/strep.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clstutils/data/seqdat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clstutils/data/seqs.rda: load().. ok [1 object(s)]; updateObject(DNAbin, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterExperiment/data/fluidigmColData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterExperiment/data/fluidigmData.rda: load().. ok [1 object(s)]; updateObject(SimpleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterExperiment/data/rsecFluidigm.rda: load().. ok [1 object(s)]; updateObject(ClusterExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterExperiment/data/simData.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File ClusterJudge/data/mi.GO.Yeast.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ClusterJudge/data/Yeast.GO.assocs.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/data/DE_GSE8057.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/data/gcSample.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/data/kegg_species.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/D39/EG2ALLGO.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/D39/EG2GO.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/D39/geneTable.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/D39/GO2ALLEG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/D39/GO2EG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/D39/proteinTable.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/M5005/EG2ALLGO.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/M5005/EG2GO.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/M5005/geneTable.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/M5005/GO2ALLEG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterProfiler/outdated/M5005/GO2EG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterSeq/data/cD.ratThymus.RData: load().. ok [1 object(s)]; updateObject(countData, check=FALSE).. no match, no-op; nothing to update ==> 0
File clusterSeq/data/ratThymus.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ClusterSignificance/data/mlpMatrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ClusterSignificance/data/pcpMatrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/cbmc_m.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/cbmc_ref.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/downrefs.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/human_genes_10x.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/mouse_genes_10x.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/object_loc_lookup.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/pbmc_markers_M3Drop.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/pbmc_markers.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/pbmc_matrix_small.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/pbmc_meta.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/pbmc_vargenes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/s_small.rda: load().. ok [1 object(s)]; updateObject(seurat, check=FALSE).. returned an error ==> -1
File clustifyr/data/s_small3.rda: load().. ok [1 object(s)]; updateObject(Seurat, check=FALSE).. no match, no-op; nothing to update ==> 0
File clustifyr/data/sce_small.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File CMA/data/golub.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CMA/data/khan.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cmapR/tests/testthat/arr3d.rds: readRDS().. ok; updateObject(array, check=FALSE).. no match, no-op ==> 0
File cmapR/tests/testthat/distil_result.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cmapR/tests/testthat/extract.gct.res.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cmapR/tests/testthat/matrices.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cmapR/tests/testthat/rnorm_matrix.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File cmapR/tests/testthat/rnorm20.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File cmapR/tests/testthat/robust_zs_rnorm20.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File cmapR/data/cdesc_char.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cmapR/data/ds.RData: load().. ok [1 object(s)]; updateObject(GCT, check=FALSE).. no match, no-op; nothing to update ==> 0
File cmapR/data/gene_set.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cmapR/data/kd_gct.RData: load().. ok [1 object(s)]; updateObject(GCT, check=FALSE).. no match, no-op; nothing to update ==> 0
File cn.farms/inst/exampleData/annotation/pd.genomewidesnp.6/1.1.0/featureSet.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cn.farms/inst/exampleData/mlData.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File cn.farms/inst/exampleData/normData.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File cn.farms/inst/exampleData/slData.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File cn.farms/inst/exampleData/testSegments.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File cn.farms/R/sysdata.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cn.mops/data/cn.mops.RData: load().. ok [4 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNAnorm/data/CN.RData: load().. ok [1 object(s)]; updateObject(CNAnorm, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNAnorm/data/gPar.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNAnorm/data/hg19_hs_ideogr.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNAnorm/data/LS041.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNEr/data/axisTrack.rda: load().. ok [1 object(s)]; updateObject(GenomeAxisTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNEr/data/CNEDanRer10Hg38.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNEr/data/cneFinalListDanRer10Hg38.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNEr/data/CNEHg38DanRer10.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNEr/data/cpgIslands.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNEr/data/grangesPairsForDotplot.rda: load().. ok [1 object(s)]; updateObject(GRangePairs, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNEr/data/refGenes.rda: load().. ok [1 object(s)]; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORdt/data/CNOlistPB.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORdt/data/modelPB.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/CNOlistToy_Gene.RData: load().. ok [1 object(s)]; updateObject(CNOlist, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/database.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/feederObject_toy.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/indices.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/integratedModel_toy.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/PPINigraph.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/simData_toy.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/ToyModel_Gene.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/ToyModelPB.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/ToyModelPBCNOlist.RData: load().. ok [1 object(s)]; updateObject(CNOlist, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORfeeder/data/UniprotIDdream.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORode/data/CNOlist_ToyPB.RData: load().. ok [1 object(s)]; updateObject(CNOlist, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORode/data/MD-ToyPB.RData: load().. ok [1 object(s)]; updateObject(CNOlist, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORode/data/PKN_ToyPB.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORode/data/PKN-ToyPB.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORode/data/ToyCNOlist.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORode/data/ToyIndices.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNORode/data/ToyModel.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNTools/data/geneInfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNTools/data/sampleData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVgears/data/cohort_examples.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVgears/data/hg18_chr_arms.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVgears/data/hg18_start_end_centromeres.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVgears/data/hg19_chr_arms.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVgears/data/hg19_start_end_centromeres.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVgears/data/hg38_chr_arms.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVgears/data/hg38_start_end_centromeres.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVgears/data/markers_examples.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVgears/data/penn_22.rda: load().. ok [1 object(s)]; updateObject(CNVresults, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVgears/data/quanti_22.rda: load().. ok [1 object(s)]; updateObject(CNVresults, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNViz/data/gene_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNViz/data/meta_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNViz/data/probe_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNViz/data/segment_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNViz/data/variant_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNViz/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVPanelizer/data/referenceReadCounts.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVPanelizer/data/sampleReadCounts.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CNVRanger/inst/extdata/GBM_GISTIC_peaks.rda: load().. failed! ==> -2
File CNVrd2/data/fcgr3bMXL.RData: load().. ok [3 object(s)]; updateObject(CNVrd2, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/atf3_chr1.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/brcaATACCoord1.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/brcaATACData1.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/brcaMCoord1.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/brcaMetadata.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/brcaMethylData1.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/brcaPCScores.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/brcaPCScores657.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/esr1_chr1.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/gata3_chr1.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/nrf1_chr1.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File COCOA/data/rsScores.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File codelink/data/codelink.example.rda: load().. ok [1 object(s)]; updateObject(Codelink, check=FALSE).. no match, no-op; nothing to update ==> 0
File codelink/data/codset.rda: load().. ok [1 object(s)]; updateObject(CodelinkSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File CODEX/data/bambedObjDemo.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CODEX/data/coverageObjDemo.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CODEX/data/gcDemo.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File CODEX/data/mapp_ref.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CODEX/data/mappability.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CODEX/data/mappDemo.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File CODEX/data/normObjDemo.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CODEX/data/qcObjDemo.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File coexnet/data/info.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coexnet/data/net1.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File coexnet/data/net2.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoGAPS/data/GIST.RData: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(CogapsResult, check=FALSE).. returned an error ==> -1
File cogena/data/AllGeneSymbols.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File cogena/data/Psoriasis.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File Cogito/data/MurEpi.ChIP.small.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File Cogito/data/MurEpi.RNA.small.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File Cogito/data/MurEpi.RRBS.small.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File coGPS/data/human_c1.rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cola/inst/extdata/consensus_mat_list.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cola/data/cola_rl.rda: load().. ok [1 object(s)]; updateObject(ConsensusPartitionList, check=FALSE).. no match, no-op; nothing to update ==> 0
File cola/data/golub_cola_ds.rda: load().. ok [1 object(s)]; updateObject(DownSamplingConsensusPartition, check=FALSE).. no match, no-op; nothing to update ==> 0
File cola/data/golub_cola_rh.rda: load().. ok [1 object(s)]; updateObject(HierarchicalPartition, check=FALSE).. no match, no-op; nothing to update ==> 0
File cola/data/golub_cola.rda: load().. ok [1 object(s)]; updateObject(ConsensusPartitionList, check=FALSE).. no match, no-op; nothing to update ==> 0
File comapr/data/coCount.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File comapr/data/parents_geno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File comapr/data/snp_geno_gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File comapr/data/snp_geno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File comapr/data/twoSamples.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File combi/data/Zhang.RData: load().. ok [3 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File combi/inst/extdata/zhangFits.RData: load().. ok [3 object(s)]; updateObject(combi, check=FALSE).. no match, no-op; updateObject(combi, check=FALSE).. no match, no-op; updateObject(combi, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/allIG.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/allIGtrack.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/allimprintedIG.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/allimprintedIGtrack.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/BindingMotifAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/BindingMotifMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/bindingMotifsBiomartAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/bindingMotifsBiomartMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/bindingMotifsBiomartSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/BindingMotifSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/bindMotifsBiomartTrackAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/bindMotifsBiomartTrackMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/bindMotifsBiomartTrackSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chipTFtrack_old.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chipTFtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chromatinHMMRoadMapAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chromatinHMMRoadMapMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chromatinHMMRoadMapSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chromHMM_RoadMapAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chromHMM_RoadMapAllE063.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chromHMM_RoadMapMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chromHMM_RoadMapSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chromhmmNoPattern.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chromhmmPattern.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/chromhmmtrackone.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/ClinVarCnvTrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/clinVarMaintrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/CoreillCNVTrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/coreilVarianttrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/cosmicVarianttrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/cpgIslandsUCSC.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/cpgIslandtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/dgfootprints_RoadMapSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/DNaseI_RoadMapSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/dnasetrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/DupTrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/dyaRM.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/dyaRMtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/eGTexTrackall.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/eGTexTrackSNP.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/enhFANTOMtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/enhRM.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/enhRMtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/eQTLAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/eQTLMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/eQTLSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/eQTLTrackAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/eQTLTrackMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/eQTLTrackSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/gadtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/gcContent.rda: load().. ok [1 object(s)]; updateObject(DataTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/gctrack.rda: load().. ok [1 object(s)]; updateObject(DataTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/geneENSEMBLtrack.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/geneNameEnsembl.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/GeneReviewsTrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/GeneReviewTrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/genesENSEMBL.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/genesGencodetrack.rda: load().. ok [1 object(s)]; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/genesNameENSEMBL.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/genesUcsctrack.rda: load().. ok [1 object(s)]; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/genetrack4psiGTEX.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/genetrack4RM.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/grtrack4eGTex.rda: load().. ok [1 object(s)]; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/GWASTrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/histonalltrack.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/histoneonetrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/imprintedGenesGTEx.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/interestGenesENSEMBL.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/interestgenesENSEMBLtrack.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/interestgenesENSMBLtrack.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/interestTranscriptENSEMBL.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/interesttransENSMBLtrack.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/ISCAtrack_Grch38.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/ISCAtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/knownGenesUCSC.rda: load().. ok [1 object(s)]; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/matrix_HiC_Rao.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/metQTLSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/metQTLTrackAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/metQTLTrackMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/metQTLTrackSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/miRNATargetRegionsBiomart.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/miRNATargetRegionsBiomartTrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/OtherRegulatoryRegionsAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/OtherRegulatoryRegionsSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/otherRegulatoryRegionsTrackAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/otherRegulatoryRegionsTrackSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/PancreasIG.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/PancreasIGtrack.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/PancreasimprintedIG.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/PancreasimprintedIGtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/promRMtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/promRMtrackE063.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/psiGTex.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/psiGTexTrackall.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/psiGTexTrackSNP.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/refGenesUCSC.rda: load().. ok [1 object(s)]; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/regulationENSEMBLtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/RegulatoryEvidenceBiomartAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/RegulatoryEvidenceBiomartMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/RegulatoryEvidenceBiomartSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/regulatoryEvidenceBiomartTrackAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/regulatoryEvidenceBiomartTrackMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/regulatoryEvidenceBiomartTrackSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/RegulatoryFeaturesBiomartAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/RegulatoryFeaturesBiomartMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/RegulatoryFeaturesBiomartSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/regulatoryFeaturesBiomartTrackAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/regulatoryFeaturesBiomartTrackMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/regulatoryFeaturesBiomartTrackSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/RegulatorySegmentsBiomartAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/RegulatorySegmentsBiomartMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/RegulatorySegmentsBiomartSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/regulatorySegmentsBiomartTrackAll.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/regulatorySegmentsBiomartTrackMultiple.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/regulatorySegmentsBiomartTrackSingle.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/repeatMaskerTrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/SegmentalDupsUCSC.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/snpBiomart.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/snpBiomarttrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/snptrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/snpUCSCtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/StomachIG.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/StomachIGtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/strucBiomarttrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/structureBiomart.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/tfbsFANTOMtrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/transENSMBLtrack.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/xenogenestrack.rda: load().. ok [1 object(s)]; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMET/data/xenorefGenesUCSC.rda: load().. ok [1 object(s)]; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMethDMR/inst/extdata/450k_Gene_3_200.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File coMethDMR/inst/extdata/450k_InterGene_3_200.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File coMethDMR/inst/extdata/CpGislandsChr22_ex.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File coMethDMR/data/betaMatrix_ex1.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMethDMR/data/betaMatrix_ex2.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMethDMR/data/betaMatrix_ex3.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMethDMR/data/betaMatrix_ex4.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMethDMR/data/betasChr22_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coMethDMR/data/pheno_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File compartmap/data/hg19.gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File compartmap/data/hg38.gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File compartmap/data/k562_scatac_chr14.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File compartmap/data/k562_scrna_chr14.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File compartmap/data/k562_scrna_raw.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File compartmap/data/mm10.gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File compartmap/data/mm9.gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File compartmap/data/ss3_umi_sce.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File COMPASS/data/COMPASS.rda: load().. ok [2 object(s)]; updateObject(COMPASSContainer, check=FALSE).. no match, no-op; updateObject(COMPASSResult, check=FALSE).. no match, no-op; nothing to update ==> 0
File compcodeR/inst/extdata/Pickrell.Cheung.Mu.Phi.Estimates.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File compcodeR/vignettes/compcodeR_parameters_2014-04-02-11-00-28.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File compEpiTools/inst/extdata/CGIgr_mm9.Rdata: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File compEpiTools/inst/extdata/H3K4me1GR.Rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File compEpiTools/inst/extdata/H3K4me3GR.Rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File compEpiTools/inst/extdata/Pol2GR.Rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File ComplexHeatmap/inst/extdata/dmr_summary.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File ComplexHeatmap/inst/extdata/gene_expression.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File ComplexHeatmap/inst/extdata/gr.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File ComplexHeatmap/inst/extdata/measles.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File ComplexHeatmap/inst/extdata/meth.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File ComplexHeatmap/inst/extdata/rand_mat.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File ComplexHeatmap/inst/extdata/tcga_lung_adenocarcinoma_provisional_ras_raf_mek_jnk_signalling.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File ComplexHeatmap/inst/extdata/random_meth_expr_data.RData: load().. ok [10 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File condiments/data/toy_dataset.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/clu.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/estimates.2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/estimates.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/files.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/Results.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/step1.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/step2.1.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/step2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/step3.1.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/step3.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/step4.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONFESS/data/steps2_4.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensus/data/TCGA.RData: load().. ok [4 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusOV/data/GSE14764.eset.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusOV/R/sysdata.rda: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_CTCF_MYJ_NarrowPeaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_CTCF_MYJ_Peaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_CTCF_MYN_NarrowPeaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_CTCF_MYN_Peaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_FOSL2_01_NarrowPeaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_FOSL2_01_Peaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_FOXA1_01_NarrowPeaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_FOXA1_01_Peaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_NR3C1_CFQ_NarrowPeaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_NR3C1_CFQ_Peaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_NR3C1_CFR_NarrowPeaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_NR3C1_CFR_Peaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_NR3C1_CFS_NarrowPeaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/A549_NR3C1_CFS_Peaks_partial.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/NOrMAL_nucleosome_positions.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/NOrMAL_nucleosome_ranges.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/NucPosSimulator_nucleosome_positions.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/NucPosSimulator_nucleosome_ranges.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/PING_nucleosome_positions.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File consensusSeekeR/data/PING_nucleosome_ranges.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File CONSTANd/inst/extdata/organs_cleaned.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File contiBAIT/data/exampleChrTable.rda: load().. ok [1 object(s)]; updateObject(ChrTable, check=FALSE).. no match, no-op; nothing to update ==> 0
File contiBAIT/data/exampleContigOrder.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File contiBAIT/data/exampleCrickFreq.rda: load().. ok [1 object(s)]; updateObject(StrandReadMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File contiBAIT/data/exampleDividedChr.rda: load().. ok [1 object(s)]; updateObject(ChrTable, check=FALSE).. no match, no-op; nothing to update ==> 0
File contiBAIT/data/exampleLGList.rda: load().. ok [1 object(s)]; updateObject(LinkageGroupList, check=FALSE).. no match, no-op; nothing to update ==> 0
File contiBAIT/data/exampleLibList.rda: load().. ok [1 object(s)]; updateObject(LibraryGroupList, check=FALSE).. no match, no-op; nothing to update ==> 0
File contiBAIT/data/exampleReadCounts.rda: load().. ok [1 object(s)]; updateObject(StrandReadMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File contiBAIT/data/exampleStrandFreq.rda: load().. ok [1 object(s)]; updateObject(StrandFreqMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File contiBAIT/data/exampleWatsonFreq.rda: load().. ok [1 object(s)]; updateObject(StrandReadMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File contiBAIT/data/exampleWCMatrix.rda: load().. ok [1 object(s)]; updateObject(StrandStateMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File conumee/data/detail_regions.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File conumee/data/exclude_regions.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File conumee/data/tcgaBRCA.sentrix2name.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File conumee/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File copynumber/data/BAF.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File copynumber/data/logR.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File copynumber/data/lymphoma.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File copynumber/data/micma.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File copynumber/R/sysdata.rda: load().. ok [7 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coRdon/data/HD59_KO.rda: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coRdon/data/HD59_PATHWAYS.rda: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coRdon/data/HD59.rda: load().. ok [1 object(s)]; updateObject(codonTable, check=FALSE).. no match, no-op; nothing to update ==> 0
File coRdon/data/LD94_KO.rda: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coRdon/data/LD94_PATHWAYS.rda: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coRdon/data/LD94.rda: load().. ok [1 object(s)]; updateObject(codonTable, check=FALSE).. no match, no-op; nothing to update ==> 0
File coRdon/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; updateObject(data.table, check=FALSE).. no match, no-op; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoRegNet/data/CHEA_sub.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoRegNet/data/CIT_BLCA_CNV.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoRegNet/data/CIT_BLCA_EXP.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoRegNet/data/CIT_BLCA_Subgroup.RData: load().. ok [1 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoRegNet/data/ENCODE_sub.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoRegNet/data/HIPPIE_sub.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoRegNet/data/HumanTF_entrezgene.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoRegNet/data/HumanTF.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoRegNet/data/STRING_sub.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoreGx/data/clevelandSmall_cSet.rda: load().. ok [1 object(s)]; updateObject(CoreSet, check=FALSE).. returned an error ==> -1
File CoreGx/data/exampleDataMapper.rda: load().. ok [1 object(s)]; updateObject(LongTableDataMapper, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoreGx/data/merckLongTable.rda: load().. ok [1 object(s)]; updateObject(LongTable, check=FALSE).. no match, no-op; nothing to update ==> 0
File CORREP/data/gal_all.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CORREP/data/true.member.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File coseq/data/fietz.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File cosmosR/data/meta_network.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cosmosR/data/metabolite_to_pubchem.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File cosmosR/data/omnipath_ptm.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cosmosR/data/toy_metabolic_input.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File cosmosR/data/toy_network.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cosmosR/data/toy_RNA.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File cosmosR/data/toy_signaling_input.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File cosmosR/R/sysdata.rda: load().. ok [4 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File CountClust/data/AbundanceGoM.rda: load().. ok [1 object(s)]; updateObject(topics, check=FALSE).. no match, no-op; nothing to update ==> 0
File CountClust/data/ex.counts.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CountClust/data/GTExV6Brain.FitGoM.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CountClust/data/MouseDeng2014.FitGoM.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CountClust/data/MouseJaitinSpleen.FitGoM.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File countsimQC/data/countsimExample_dfmat.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File countsimQC/data/countsimExample.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoverageView/data/DF_H3K36me3_control.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoverageView/data/DF_H3K36me3.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoverageView/data/DF_H3K4me3_ctl.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoverageView/data/DF_H3K4me3_nopeaks_ratios.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoverageView/data/DF_H3K4me3.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CoverageView/data/FoxA1_chr19.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File covRNA/data/Baca.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File cpvSNP/data/geneSetAnalysis.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File cpvSNP/data/test_genesHg19.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File cpvSNP/data/test_snpsGSC.RData: load().. ok [1 object(s)]; updateObject(GeneSetCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File cqn/data/montgomery.subset.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File cqn/data/sizeFactors.subset.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File cqn/data/uCovar.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/data/AsCas12a.rda: load().. ok [1 object(s)]; updateObject(CrisprNuclease, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/data/CasRx.rda: load().. ok [1 object(s)]; updateObject(CrisprNuclease, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/data/enAsCas12a.rda: load().. ok [1 object(s)]; updateObject(CrisprNuclease, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/data/restrictionEnzymes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/data/SaCas9.rda: load().. ok [1 object(s)]; updateObject(CrisprNuclease, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/data/SpCas9.rda: load().. ok [1 object(s)]; updateObject(CrisprNuclease, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/data/SpGCas9.rda: load().. ok [1 object(s)]; updateObject(CrisprNuclease, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/inst/pams/cas12a/cas12a.pams.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/inst/pams/cas12a/doench/encas12a.scores.doench.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/inst/pams/cas9/cas9.pams.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprBase/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprScore/data/scoringMethodsInfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprScore/inst/cfd_cas9/cfd.mm.scores.cas9.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprScore/inst/cfd_cas9/cfd.mm.weights.cas9.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprScore/inst/cfd_cas9/cfd.pam.scores.cas9.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprScore/inst/cfd_cas9/cfd.pam.weights.cas9.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprScore/inst/mit/mit.weights.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File crisprScore/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File CRISPRseek/inst/extdata/all.gRNAs.df.RDS: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File CRISPRseek/inst/extdata/Cpf1Eff.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File CRISPRseek/inst/extdata/CRISPRscanEff.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File CRISPRseek/inst/extdata/featureVecorsWithNinPAM.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File CRISPRseek/inst/extdata/gRNAsCpf1.RDS: readRDS().. ok; updateObject(DNAStringSet, check=FALSE).. no match, no-op ==> 0
File CRISPRseek/inst/extdata/gRNAsSpCas9.RDS: readRDS().. ok; updateObject(DNAStringSet, check=FALSE).. no match, no-op ==> 0
File CRISPRseek/inst/extdata/seqs2.5prime.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File CRISPRseek/inst/extdata/seqs2.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File CRISPRseek/inst/extdata/seqs2CFD.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File CRISPRseek/inst/extdata/testSeqForDeepCpf1.RDS: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File CRISPRseek/inst/extdata/ForTestinguniqueREs.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CrispRVariants/data/gol_clutch1.rda: load().. ok [1 object(s)]; updateObject(CrisprSet, check=FALSE).. returned an error ==> -1
File CrispRVariants/inst/extdata/ptena_GRCHz10_ref.rda: load().. ok [1 object(s)]; updateObject(DNAString, check=FALSE).. no match, no-op; nothing to update ==> 0
File crlmm/data/cnSetExample.rda: load().. ok [1 object(s)]; updateObject(CNSet, check=FALSE).. returned an error ==> -1
File crlmm/data/cnSetExample2.rda: load().. ok [1 object(s)]; updateObject(CNSet, check=FALSE).. returned an error ==> -1
File crossmeta/data-raw/homologene/homologene.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File crossmeta/data-raw/KEGG/gs.names.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File crossmeta/data-raw/KEGG/gslist.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File crossmeta/data-raw/platforms/gpl_bioc.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File crossmeta/data-raw/sources/sources.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File crossmeta/data-raw/species/org_pkg.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File crossmeta/data-raw/species/org_taxid.rds: readRDS().. ok; updateObject(integer, check=FALSE).. no match, no-op ==> 0
File crossmeta/data/gs.names.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File crossmeta/data/gslist.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File crossmeta/inst/testdata/Apoa1.RData: load().. ok [1 object(s)]; updateObject(RGList, check=FALSE).. no match, no-op; nothing to update ==> 0
File crossmeta/R/sysdata.rda: load().. ok [9 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.table, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(Token2.0, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File CSAR/data/CSAR-dataset.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File csaw/inst/exdata/exrange.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File csdR/data/normal_expression.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File csdR/data/sick_expression.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File CSSP/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File CSSP/data/bin.data.RData: load().. ok [1 object(s)]; updateObject(BinData, check=FALSE).. no match, no-op; nothing to update ==> 0
File CSSP/data/bindata.chr1.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File CSSP/data/bindpos.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CSSP/data/peakpos.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CSSP/data/sampleFit.RData: load().. ok [1 object(s)]; updateObject(CSSPFit, check=FALSE).. no match, no-op; nothing to update ==> 0
File CSSP/data/tagdat_chip.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CSSP/data/tagdat_input.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File CTDquerier/inst/extdata/universe.RDS: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File CTDquerier/data/gala.rda: load().. ok [1 object(s)]; updateObject(CTDdata, check=FALSE).. no match, no-op; nothing to update ==> 0
File cTRAP/dev/diffExprStat.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File cTRAP/data/cmapMetadata.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File cTRAP/data/cmapPerturbationsCompounds.rda: load().. ok [1 object(s)]; updateObject(perturbationChanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File cTRAP/data/cmapPerturbationsKD.rda: load().. ok [1 object(s)]; updateObject(perturbationChanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File cTRAP/data/counts.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File cTRAP/data/diffExprStat.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File cTRAP/data/ENCODEmetadata.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File cTRAP/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File cummeRbund/data/sampleData.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File cummeRbund/data/sampleData.RData: load().. ok [3 object(s)]; updateObject(CuffGene, check=FALSE).. no match, no-op; updateObject(CuffGeneSet, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File customProDB/inst/extdata/refseq/cosmic.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File customProDB/inst/extdata/refseq/dbsnpinCoding.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File customProDB/inst/extdata/refseq/exon_anno.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File customProDB/inst/extdata/refseq/ids.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File customProDB/inst/extdata/refseq/procodingseq.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File customProDB/inst/extdata/refseq/proseq.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File customProDB/inst/extdata/refseq/splicemax.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File cyanoFilter/README_cache/gfm/logtrans_d85ff0d017699f164d0ca0f3891f43bb.RData: load().. ok [2 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File cyanoFilter/README_cache/gfm/marginEvents_c0ca93e70f12f438430c589c39acd2e4.RData: load().. ok [2 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File cyanoFilter/README_cache/gfm/reading_214cb1182d9ae10cb08e8440e5b26666.RData: load().. ok [2 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File cyanoFilter/setting.RData: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File CyTOFpower/inst/extdata/df_precomputed_datasets.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File cytoKernel/data/cytoHDBMW.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File cytomapper/tests/testthat/testthat-problems.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File cytomapper/data/pancreasImages.RData: load().. ok [1 object(s)]; updateObject(CytoImageList, check=FALSE).. no match, no-op; nothing to update ==> 0
File cytomapper/data/pancreasMasks.RData: load().. ok [1 object(s)]; updateObject(CytoImageList, check=FALSE).. no match, no-op; nothing to update ==> 0
File cytomapper/data/pancreasSCE.RData: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File CytoML/tests/testthat/expect_result/flowJoWorkspace_expect.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
Skip package CytoTree ==> -3
File dada2/data/errBalancedF.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File dada2/data/errBalancedR.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File dada2/data/tperr1.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File dagLogo/data/ecoli.proteome.rda: load().. ok [1 object(s)]; updateObject(Proteome, check=FALSE).. no match, no-op; nothing to update ==> 0
File dagLogo/data/proteome.example.rda: load().. ok [1 object(s)]; updateObject(Proteome, check=FALSE).. no match, no-op; nothing to update ==> 0
File dagLogo/data/seq.example.rda: load().. ok [1 object(s)]; updateObject(dagPeptides, check=FALSE).. no match, no-op; nothing to update ==> 0
File daMA/data/cinfo.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File daMA/data/cinfoB.AB.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File daMA/data/cmat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File daMA/data/cmatB.AB.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File daMA/data/data.3x2.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File daMA/data/designs.basic.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File daMA/data/designs.composite.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File daMA/data/id.3x2.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File DAMEfinder/data/extractbams_output.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DAMEfinder/data/readtuples_output.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DaMiRseq/data/data_min.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DaMiRseq/data/data_norm.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File DaMiRseq/data/data_reduced.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DaMiRseq/data/data_relief.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DaMiRseq/data/df.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DaMiRseq/data/SE.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File DaMiRseq/data/selected_features.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DaMiRseq/data/SEtest_norm.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File DaMiRseq/data/sv.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DART/data/dataDART.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File dasper/data/junctions_example.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File dcanr/data/sim102.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File dce/inst/scripts/synthetic_benchmark/resources/pathways.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File dce/data/df_pathway_statistics.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File dcGSA/data/dcGSAtest.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ddCt/tests/units/runit.ddCtExpression.RData: load().. ok [1 object(s)]; updateObject(ddCtExpression, check=FALSE).. no match, no-op; nothing to update ==> 0
File ddCt/tests/units/runit.SDMFrame.RData: load().. ok [1 object(s)]; updateObject(SDMFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File dearseq/data/baduel_5gs.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File dearseq/data/PBT_gmt.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File debCAM/data/ratMix3.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File debrowser/inst/extdata/demo/demodata.Rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File debrowser/inst/extdata/demo/demodata2.Rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/deltaGrules.RData: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/deltaHrules.RData: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/deltaHrulesRNA.RData: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/deltaSrules.RData: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/deltaSrulesRNA.RData: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/HEC_MI1.RData: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/HEC_MI2.RData: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/MIQS.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/NonCodingRNA_Archaea.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/NonCodingRNA_Bacteria.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/NonCodingRNA_Eukarya.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/PFASUM.RData: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/RESTRICTION_ENZYMES.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File DECIPHER/data/TrainingSet_16S.RData: load().. ok [1 object(s)]; updateObject(Taxa, check=FALSE).. no match, no-op; nothing to update ==> 0
File deco/data/ALCLdata.RData: load().. ok [3 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(deco, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEComplexDisease/data/ann.er.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEComplexDisease/data/cl.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEComplexDisease/data/cluster.mod.rda: load().. ok [1 object(s)]; updateObject(cluster.module, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEComplexDisease/data/deg.rda: load().. ok [1 object(s)]; updateObject(deg, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEComplexDisease/data/deg.spc.rda: load().. ok [1 object(s)]; updateObject(deg.specific, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEComplexDisease/data/exp.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEComplexDisease/data/res.mod1.rda: load().. ok [1 object(s)]; updateObject(cluster.module, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEComplexDisease/data/res.mod2.rda: load().. ok [1 object(s)]; updateObject(cluster.module, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEComplexDisease/data/seed.mod.rda: load().. ok [1 object(s)]; updateObject(seed.module, check=FALSE).. no match, no-op; nothing to update ==> 0
File decompTumor2Sig/inst/extdata/Alexandrov_PMID_23945592_435_tumors-pmsignature-15sig.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File decompTumor2Sig/inst/extdata/Nik-Zainal_PMID_22608084-genomes-Alexandrov_3bases.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File decompTumor2Sig/inst/extdata/Nik-Zainal_PMID_22608084-genomes-Shiraishi_5bases_trDir.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File decompTumor2Sig/inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-G.Rdata: load().. ok [1 object(s)]; updateObject(MutationFeatureData, check=FALSE).. returned an error ==> -1
File decompTumor2Sig/inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-Param.Rdata: load().. ok [2 object(s)]; updateObject(MutationFeatureData, check=FALSE).. returned an error ==> -1
File decompTumor2Sig/inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sigall.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeconRNASeq/data/liver_kidney_ascii.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeconRNASeq/data/liver_kidney.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeconRNASeq/data/multi_tissue.rda: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeconRNASeq/data/rat_liver_brain.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File decontam/inst/extdata/MUCconc.rds: readRDS().. ok; updateObject(integer, check=FALSE).. no match, no-op ==> 0
File decontam/inst/extdata/MUClite.rds: readRDS().. ok; updateObject(phyloseq, check=FALSE).. no match, no-op ==> 0
File decontam/inst/extdata/samdf.rds: readRDS().. ok; updateObject(sample_data, check=FALSE).. no match, no-op ==> 0
File decontam/inst/extdata/st.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File deconvR/data/HumanCellTypeMethAtlas.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File deconvR/data/IlluminaMethEpicB5ProbeIDs.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File deconvR/inst/extdata/WGBS_GRanges.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File decoupleR/inst/testdata/inputs/input-dorothea_genesets.rds: readRDS().. ok; updateObject(spec_tbl_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/inputs/input-expr_matrix.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/aucell/output-aucell_dorothea_default.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/decouple/output-decouple_dorothea_default.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/fgsea/output-fgsea_dorothea_default.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/gsva/output-gsva_dorothea_default.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/mdt/output-mdt_dorothea_default.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/mlm/output-mlm_dorothea_default.rds: readRDS().. ok; updateObject(grouped_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/ora/output-ora_dorothea_default.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/udt/output-udt_dorothea_default.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/ulm/output-ulm_dorothea_default.rds: readRDS().. ok; updateObject(grouped_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/viper/output-viper_dorothea_default.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/wmean/output-wmean_dorothea_default.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File decoupleR/inst/testdata/outputs/wsum/output-wsum_dorothea_default.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File DeepPINCS/data/antiviral_drug.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeepPINCS/data/example_bioassay.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeepPINCS/data/example_cci.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeepPINCS/data/example_chem.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeepPINCS/data/example_cpi.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeepPINCS/data/example_pd.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeepPINCS/data/example_ppi.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeepPINCS/data/example_prot.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeepPINCS/data/SARS_CoV2_3CL_Protease.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File deepSNV/data/counts.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File deepSNV/data/HIVmix.RData: load().. ok [1 object(s)]; updateObject(deepSNV, check=FALSE).. no match, no-op; nothing to update ==> 0
File deepSNV/data/phiX.RData: load().. ok [1 object(s)]; updateObject(deepSNV, check=FALSE).. no match, no-op; nothing to update ==> 0
File deepSNV/data/pi.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File deepSNV/data/RCC.RData: load().. ok [1 object(s)]; updateObject(deepSNV, check=FALSE).. no match, no-op; nothing to update ==> 0
File deepSNV/data/trueSNVs.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DegNorm/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File DegNorm/data/coverage_res_chr21.RData: load().. ok [1 object(s)]; updateObject(CoverageClass, check=FALSE).. no match, no-op; nothing to update ==> 0
File DegNorm/data/res_DegNorm_chr21.RData: load().. ok [1 object(s)]; updateObject(DegNormClass, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEGraph/data/Loi2008_DEGraphVignette.RData: load().. ok [4 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEGreport/data/geneInfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEGreport/data/humanGender.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File DelayedTensor/data/human_mid_brain.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DelayedTensor/data/mouse_mid_brain.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/bigBinSize.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/binnedDeltaPlot.rda: load().. ok [1 object(s)]; updateObject(gg, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/binnedDeltaSE.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/binnedSummarizedExperiment.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/deltaSE.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/miniDeltaSE.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/miniSE.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/miniSEDF.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/numPermutations.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/plotTitle.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/pValue.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/regionOfInterest.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/significanceType.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/significantRegions.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/significantRegionsPlot.rda: load().. ok [1 object(s)]; updateObject(gg, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/smallBins.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/smallBinSize.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/smallerDeltaSE.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/smallSetOfSmallBins.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/viewpointRegion.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/weightsExampleBins.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaCaptureC/data/weightsExampleGr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File deltaGseg/data/deltaGseg.rda: load().. ok [8 object(s)]; updateObject(pvclust, check=FALSE).. no match, no-op; updateObject(Trajectories, check=FALSE).. no match, no-op; updateObject(TransTrajectories, check=FALSE).. no match, no-op; updateObject(TransTrajectories, check=FALSE).. no match, no-op; updateObject(Trajectories, check=FALSE).. no match, no-op; updateObject(SegTrajectories, check=FALSE).. no match, no-op; updateObject(SegSeriesTrajectories, check=FALSE).. no match, no-op; updateObject(TransTrajectories, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeMAND/data/inputExample.rda: load().. ok [5 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeMixT/vignettes/Res_3comp/res.S1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File DeMixT/data/test.data.2comp.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeMixT/data/test.data.3comp.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeMixT/vignettes/Res_2comp/res.GS.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeMixT/vignettes/Res_2comp/res.GS.SP.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeMixT/vignettes/Res_2comp/res.S1.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeMixT/vignettes/Res_2comp/res.S1.SP.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeMixT/vignettes/Res_2comp/res.S2.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeMixT/vignettes/Res_3comp/res.S1.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DeMixT/vignettes/res.PRAD.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEP/data/DiUbi_ExpDesign.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEP/data/DiUbi.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEP/data/UbiLength_ExpDesign.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEP/data/UbiLength.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEP/R/sysdata.rda: load().. ok [9 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File DepecheR/data/testData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DepecheR/data/testDataDepeche.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DepecheR/data/testDataSNE.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/data/genomeData.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/data/genomeDataRaw.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/data/genomeFstats.RData: load().. ok [1 object(s)]; updateObject(Rle, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/data/genomeInfo.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/data/genomeRegions.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/data/genomicState.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/inst/extdata/chr21/annotation.Rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/inst/extdata/chr21/coveragePrep.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/inst/extdata/chr21/fstats.Rdata: load().. ok [1 object(s)]; updateObject(Rle, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/inst/extdata/chr21/optionsStats.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/inst/extdata/chr21/regions.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File derfinder/inst/extdata/chr21/timeinfo.Rdata: load().. ok [1 object(s)]; updateObject(POSIXct, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEScan2/inst/extdata/peaks/RData/peaksGRL_all_files.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File DEScan2/inst/extdata/regions/regions.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File DEScan2/inst/extdata/tests/counts/finalRegionsSE.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File DEScan2/inst/extdata/tests/inputdata/FCGRL.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File DEScan2/inst/extdata/tests/peaks/FC1_GRL.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File DEScan2/inst/extdata/tests/peaks/peaks_all_samples.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File DEScan2/inst/extdata/tests/z/z_matrix.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File DEsingle/data/TestData.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/data.RData: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/Disease_GAD.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/Disease_OMIM.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/Drug_DrugBank.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/edgeLists.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/GO_bp.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/GO_cc.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/GO_mf.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/KEGG.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/libraryEntrezToExternalNomenclature.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/libraryEntrezToHGNC.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/miRNA.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEsubs/inst/extdata/Data/TF.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEWSeq/data/SLBP_K562_w50s20.rda: load().. ok [1 object(s)]; updateObject(DESeqDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEWSeq/data/slbpDds.rda: load().. ok [1 object(s)]; updateObject(DESeqDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEWSeq/data/slbpRegions.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEWSeq/data/slbpVst.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DEWSeq/data/slbpWindows.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DFP/data/rmadataset.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File DIAlignR/data/alignObj_DIAlignR.rda: load().. ok [1 object(s)]; updateObject(AffineAlignObj, check=FALSE).. returned an error ==> -1
File DIAlignR/data/masterXICs_DIAlignR.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DIAlignR/data/multipeptide_DIAlignR.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DIAlignR/data/oswFiles_DIAlignR.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DIAlignR/data/XIC_QFNNTDIVLLEDFQK_3_DIAlignR.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DiffBind/data/tamoxifen_analysis.rda: load().. ok [1 object(s)]; updateObject(DBA, check=FALSE).. no match, no-op; nothing to update ==> 0
File DiffBind/data/tamoxifen_counts.rda: load().. ok [1 object(s)]; updateObject(DBA, check=FALSE).. no match, no-op; nothing to update ==> 0
File DiffBind/data/tamoxifen_greylist.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DiffBind/data/tamoxifen_peaks.rda: load().. ok [1 object(s)]; updateObject(DBA, check=FALSE).. no match, no-op; nothing to update ==> 0
File DiffBind/inst/extra/ktypes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DiffBind/inst/extra/parallelFactor.rda: load().. ok [4 object(s)]; updateObject(DBA, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File DiffBind/inst/extra/spikes.rda: load().. ok [3 object(s)]; updateObject(DBA, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File diffcoexp/data/gse4158part.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File diffGeneAnalysis/data/rawdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File diffHic/inst/exdata/cuts.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File diffloop/inst/rda/geneinfo.h.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File diffloop/inst/rda/geneinfo.m.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File diffloop/inst/rda/human.genes.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File diffloop/inst/rda/loops.small.rda: load().. ok [1 object(s)]; updateObject(loops, check=FALSE).. no match, no-op; nothing to update ==> 0
File diffuStats/data/graph_toy.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File diffUTR/data/example_bin_se.RData: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File diffUTR/data/example_gene_annotation.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File diffUTR/data/rn6_PAS.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File Dino/data/multimodalDat.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Dino/data/pbmcSmall.RData: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Dino/data/unimodalDat.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Director/data/ovca.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DirichletMultinomial/data/bestgrp.rda: load().. ok [1 object(s)]; updateObject(DMNGroup, check=FALSE).. no match, no-op; nothing to update ==> 0
File DirichletMultinomial/data/fit.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DirichletMultinomial/data/xval.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File discordant/data/TCGA_Breast_miRNASeq_voom.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File discordant/data/TCGA_Breast_miRNASeq.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File discordant/data/TCGA_Breast_RNASeq_voom.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File discordant/data/TCGA_Breast_RNASeq.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File discordant/data/TCGA_GBM_miRNA_microarray.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File discordant/data/TCGA_GBM_transcript_microarray.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File DiscoRhythm/data/discoODAexclusionMatrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DiscoRhythm/data/discoODAid2name.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File distinct/data/Kang_subset.RData: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File distinct/data/res.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File dittoSeq/data/demuxletExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File divergence/data/breastTCGA_ER.RData: load().. ok [1 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File divergence/data/breastTCGA_Group.RData: load().. ok [1 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File divergence/data/breastTCGA_Mat.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File divergence/data/msigdb_Hallmarks.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File dks/data/dksdata.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DMRcaller/data/DMRsNoiseFilterCG.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File DMRcaller/data/GEs.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File DMRcaller/data/methylationDataList.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File DMRcaller/data/syntheticDataReplicates.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File DMRforPairs/data/DMRforPairs_data.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DMRScan/data/DMRScan.methylationData.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DMRScan/data/DMRScan.phenotypes.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File dmrseq/data/annot.chr21.rda: load().. ok [1 object(s)]; updateObject(SimpleGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File dmrseq/data/BS.chr21.rda: load().. ok [1 object(s)]; updateObject(BSseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File dmrseq/data/dmrs.ex.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File DNABarcodeCompatibility/data/IlluminaIndexes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DNABarcodeCompatibility/data/IlluminaIndexesRaw.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DNABarcodes/data/mutatedReads.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File DNABarcodes/data/supplierSet.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File DNAcopy/data/coriell.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DominoEffect/data/DominoData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DominoEffect/data/SnpData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DominoEffect/data/TestData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Doscheda/data/doschedaData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Doscheda/data/processedExample.rda: load().. ok [1 object(s)]; updateObject(ChemoProtSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/DGN_EXTID2PATHID.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/DGN_PATHID2EXTID.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/DGN_PATHID2NAME.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/DO2ALLEG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/DO2EG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/DOIC.rda: load().. ok [1 object(s)]; updateObject(GOSemSimDATA, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/DOLite2EG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/DOLiteTerm.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/dotbl.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/EG2ALLDO.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/EG2DO.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/EG2DOLite.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/geneList.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/NCG_EXTID2PATHID.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/NCG_PATHID2EXTID.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/NCG_PATHID2NAME.rda: load().. ok [1 object(s)]; updateObject(NULL, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/VDGN_EXTID2PATHID.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/VDGN_PATHID2EXTID.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DOSE/data/VDGN_PATHID2NAME.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File doseR/data/hmel.data.doser.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File doseR/data/hmel.se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File dpeak/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File dpeak/data/exampleData.RData: load().. ok [1 object(s)]; updateObject(DpeakData, check=FALSE).. no match, no-op; nothing to update ==> 0
File drawProteins/data/five_rel_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File drawProteins/data/five_rel_list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File drawProteins/data/protein_json.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File drawProteins/data/rel_A_features.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File drawProteins/data/rel_json.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File drawProteins/data/tnfs_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DriverNet/data/sampleDriversList.rda: load().. ok [1 object(s)]; updateObject(DriverNetResult, check=FALSE).. no match, no-op; nothing to update ==> 0
File DriverNet/data/sampleGeneNames.rda: load().. ok [1 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File DriverNet/data/sampleInfluenceGraph.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DriverNet/data/samplePatientExpressionMatrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DriverNet/data/samplePatientMutationMatrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DriverNet/data/samplePatientOutlierMatrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DriverNet/data/sampleRandomDriversResult.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File drugTargetInteractions/inst/extdata/paralogs1_res_list.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File drugTargetInteractions/inst/extdata/paralogs2_res_list.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File drugTargetInteractions/inst/extdata/res_list90_ens.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File drugTargetInteractions/inst/extdata/res_list90.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File drugTargetInteractions/inst/extdata/results/cmp_ids.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File drugTargetInteractions/inst/scripts/paralogs1_res_list.rds: readRDS().. failed! ==> -2
File drugTargetInteractions/inst/scripts/paralogs2_res_list.rds: readRDS().. failed! ==> -2
File drugTargetInteractions/inst/scripts/res_list90_ens.rds: readRDS().. failed! ==> -2
File drugTargetInteractions/inst/scripts/res_list90.rds: readRDS().. failed! ==> -2
File DrugVsDisease/data/customClust.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DrugVsDisease/data/customDB.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File DrugVsDisease/data/customedge.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DrugVsDisease/data/customsif.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File DrugVsDisease/data/profiles.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DrugVsDisease/data/selprofile.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DSS/data/RRBS.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File DSS/data/seqData.rda: load().. ok [1 object(s)]; updateObject(SeqCountSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File dStruct/data/lai2019.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File dStruct/data/wan2014.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Dm.tnumber.RData: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Doelken2008.RData: load().. ok [10 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Hs.tnumber.RData: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Miller2011.RData: load().. ok [4 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Miller2011dynamic.RData: load().. ok [4 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Mm.tnumber.RData: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Sc.ribig.ensg.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Sc.rpg.ensg.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Sc.stress.ensg.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Sc.tf.ensg.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Sc.tnumber.RData: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Sp.tnumber.RData: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File DTA/data/Sun2011.RData: load().. ok [7 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Dune/data/clusMat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Dune/data/nuclei.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File dupRadar/data/dupRadar_examples.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File easyreporting/inst/shiny_examples/volcano_app/degs.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File EBarrays/data/gould.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EBcoexpress/data/fiftyGenes.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EBSEA/data/exonCounts.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EBSeq/data/GeneMat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EBSeq/data/IsoList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EBSeq/data/IsoMultiList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EBSeq/data/MultiGeneMat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EBSeqHMM/data/GeneExampleData.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EBSeqHMM/data/IsoExampleList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoli.genome.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoli.m52.genome.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenome.operon.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeBNUM.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeBNUM2ENZYME.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeBNUM2GENBANK.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeBNUM2GENEPRODUCT.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeBNUM2MULTIFUN.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeBNUM2STRAND.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeBNUM2SYMBOL.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeCHRLOC.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeMULTIFUN2GO.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeSTRAND.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeSYMBOL.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeSYMBOL2AFFY.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/ecoligenomeSYMBOL2BNUM.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ecolitk/data/multiFun.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File EDASeq/data/yeastGC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File EDASeq/data/yeastLength.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File edge/data/endotoxin.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File edge/data/gibson.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File edge/data/kidney.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/cate.gene.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/cate.ratio.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/diffgene.genes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/expr.filter.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/goenrich.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/human.gene.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/human.grn.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/human.tf.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/markers.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/mouse.gene.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/mouse.grn.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/mouse.tf.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/SandlerFPKM.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/tissueGenes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eegc/data/tissueGroup.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/attr.human.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/attr.mouse.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/biogrid.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/example_annotations.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/example_binary_network.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/example_coexpression.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/example_neighbor_voting.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/GO.human.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/GO.mouse.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/GO.voc.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/ortho.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGAD/data/pheno.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EGSEA/data/arraydata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File eiR/data/example_compounds.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File eisaR/inst/extdata/Fig3abc_GSE33252_rawcounts_exonic.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File eisaR/inst/extdata/Fig3abc_GSE33252_rawcounts_intronic.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File EmpiricalBrownsMethod/data/ebmTestData.RData: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File enhancerHomologSearch/inst/extdata/al.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File enhancerHomologSearch/inst/extdata/aln_hs.rds: readRDS().. ok; updateObject(Enhancers, check=FALSE).. returned an error ==> -1
File enhancerHomologSearch/inst/extdata/aln_mm.rds: readRDS().. ok; updateObject(Enhancers, check=FALSE).. returned an error ==> -1
File enhancerHomologSearch/data/motifs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EnMCB/data/demo_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EnMCB/data/demo_MCBinformation.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EnMCB/data/demo_survival_data.rda: load().. ok [1 object(s)]; updateObject(Surv, check=FALSE).. no match, no-op; nothing to update ==> 0
File ENmix/inst/mage_ref.RData: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ENmix/inst/oxBS.MLE.RData: load().. ok [4 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ENmix/inst/unitTests/testDigests.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EnrichedHeatmap/inst/extdata/chr21_chromatin_states.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File EnrichedHeatmap/inst/extdata/chr21_test_data.RData: load().. ok [5 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File EnrichedHeatmap/inst/extdata/H3K4me1_corr_normalize_to_tss.RData: load().. ok [1 object(s)]; updateObject(normalizedMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EnrichedHeatmap/inst/extdata/neg_cr_order_by_dist_closeness.RData: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File EnrichedHeatmap/inst/extdata/neg_cr.RData: load().. ok [3 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File ensembldb/inst/YGRanges.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File EpiDISH/data/centBloodSub.m.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EpiDISH/data/centDHSbloodDMC.m.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EpiDISH/data/centEpiFibFatIC.m.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EpiDISH/data/centEpiFibIC.m.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EpiDISH/data/DummyBeta.m.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EpiDISH/data/LiuDataSub.m.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File epigenomix/data/eSet.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File epigenomix/data/fpkm.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epigenomix/data/mappedReads.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File epigenomix/data/transToTSS.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epigraHMM/data/helas3.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File epihet/data/background.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epihet/data/datTraits.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epihet/data/DEG.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epihet/data/DEH.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epihet/data/diffhetmatrix.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epihet/data/moduledm.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epihet/data/modulesil.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epihet/data/myValues.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File epihet/data/promoter.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File epihet/data/sharedmatrix.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epiNEM/data/sameith_GO.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File epiNEM/data/sameith_string.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File epiNEM/data/samscreen.rda: load().. ok [1 object(s)]; updateObject(epiScreen, check=FALSE).. no match, no-op; nothing to update ==> 0
File epiNEM/data/sim.rda: load().. ok [1 object(s)]; updateObject(epiSim, check=FALSE).. no match, no-op; nothing to update ==> 0
File epiNEM/data/wageningen_GO.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File epiNEM/data/wageningen_string.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File epiNEM/data/wagscreen.rda: load().. ok [1 object(s)]; updateObject(epiScreen, check=FALSE).. no match, no-op; nothing to update ==> 0
File epistack/data/stackepi_gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File epistack/data/stackepi.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File EpiTxDb/data/rmbase_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File epivizr/data/tcga_colon_blocks.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File epivizr/data/tcga_colon_curves.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File epivizr/data/tcga_colon_expression.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File epivizrChart/data/bcode_eset.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File epivizrChart/data/cgi_gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File epivizrChart/data/sumexp.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File epivizrChart/data/tcga_colon_blocks.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File epivizrChart/data/tcga_colon_curves.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File epivizrChart/data/tcga_colon_expression.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File erccdashboard/data/ERCC.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File erccdashboard/data/SEQC.Example.RData: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File erma/data/abbCIcols.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File erma/data/abbCIstates.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File erma/data/farhSE.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File erma/data/short_celltype.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File erma/data/states_25.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ERSSA/data/combinations.partial.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ERSSA/data/condition_table.full.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ERSSA/data/condition_table.partial.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ERSSA/data/count_table.filtered.partial.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ERSSA/data/count_table.full.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ERSSA/data/count_table.partial.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ERSSA/data/deg.partial.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File esATAC/inst/extdata/MotifPFM.rds: readRDS().. ok; updateObject(PFMatrixList, check=FALSE).. no match, no-op ==> 0
File eudysbiome/data/diffGenera.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File eudysbiome/data/harmGenera.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File eudysbiome/data/microCount.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File eudysbiome/data/microDiff.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File evaluomeR/data/bioMetrics.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File evaluomeR/data/ontMetrics.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File evaluomeR/data/rnaMetrics.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/AllEvents_RNASeq_MP.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/AllEvents_RNASeq.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/ArrayDatamultipath.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/ArraysData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/EventXtrans.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/Fit.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/MyPrimers_taqman.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/MyPrimers.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/PSIss.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/SG_RNASeq.rda: load().. ok [1 object(s)]; updateObject(SGFeatureCounts, check=FALSE).. no match, no-op; nothing to update ==> 0
File EventPointer/data/TxD.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File EWCE/inst/extdata/bootstrap_results.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File EWCE/inst/extdata/tt_results.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ExiMiR/data/galenv.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ExiMiR/data/GSE19183.rda: load().. ok [1 object(s)]; updateObject(AffyBatch, check=FALSE).. no match, no-op; nothing to update ==> 0
File ExiMiR/data/GSE20122.rda: load().. ok [1 object(s)]; updateObject(AffyBatch, check=FALSE).. no match, no-op; nothing to update ==> 0
File exomeCopy/data/exomecounts.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File exomePeak2/inst/extdata/mod_annot.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File exomePeak2/inst/extdata/sep_ex_dm.rds: readRDS().. ok; updateObject(SummarizedExomePeak, check=FALSE).. no match, no-op ==> 0
File exomePeak2/inst/extdata/sep_ex_mod.rds: readRDS().. ok; updateObject(SummarizedExomePeak, check=FALSE).. no match, no-op ==> 0
File ExpressionAtlas/data/allExps.rda: load().. ok [1 object(s)]; updateObject(SimpleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File ExpressionAtlas/data/atlasRes.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ExpressionAtlas/data/rnaseqExps.rda: load().. ok [1 object(s)]; updateObject(SimpleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File factDesign/data/estrogen.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File famat/data/compl_data_result.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File famat/data/genes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File famat/data/interactions_result.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File famat/data/listk.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File famat/data/listr.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File famat/data/listw.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File famat/data/meta.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File famat/R/sysdata.rda: load().. ok [10 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File farms/data/testAffyBatch.rda: load().. ok [2 object(s)]; updateObject(AffyBatch, check=FALSE).. no match, no-op; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File fastLiquidAssociation/data/testmat.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File fastseg/data/coriell.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File fastseg/data/fastsegData.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File FCBF/data/scDengue.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File fCI/data/fci.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File fCI/data/multi.dimensional.fci.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File fcoex/data/fc.rda: load().. ok [1 object(s)]; updateObject(fcoex, check=FALSE).. returned an error ==> -1
File fcoex/data/mini_pbmc3k.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File fdrame/data/design.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File fdrame/data/exp.arr.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File FEAST/data/Yan.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File fedup/data/geneDouble.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File fedup/data/geneMulti.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File fedup/data/geneSingle.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File fedup/data/pathwaysGMT.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File fedup/data/pathwaysTXT.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File fedup/data/pathwaysXLSX.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File FELLA/data/FELLA.sample.RData: load().. ok [1 object(s)]; updateObject(FELLA.DATA, check=FALSE).. no match, no-op; nothing to update ==> 0
File FELLA/data/input.sample.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File fgga/data/CfData.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File FGNet/data/FEA_tools.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File FGNet/data/GOEvidenceCodes.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File FGNet/data/groupTypes.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File FGNet/data/organisms.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File fgsea/data/examplePathways.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File fgsea/data/exampleRanks.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File FindIT2/data/ATAC_normCount.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File FindIT2/data/RNA_normCount.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File FindIT2/data/RNADiff_LEC2_GR.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File FindIT2/data/test_featureSet.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File FindIT2/data/test_geneSet.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File FindIT2/data/TF_target_database.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowAI/data/Bcells.rda: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowBeads/data/beads1.rda: load().. ok [1 object(s)]; updateObject(BeadFlowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowBeads/data/beads2.rda: load().. ok [1 object(s)]; updateObject(BeadFlowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowBin/data/amlsample.rda: load().. ok [1 object(s)]; updateObject(FlowSample, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowcatchR/data/candidate.platelets.RData: load().. ok [1 object(s)]; updateObject(ParticleSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowcatchR/data/MesenteriumSubset.RData: load().. ok [1 object(s)]; updateObject(Frames, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowCL/data/flowCL_archive.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowClean/data/synPerturbed.rda: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowClust/data/rituximab.RData: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowCore/tests/testthat/expectRes.new.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowCore/tests/testthat/expectResults.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowCore/tests/testthat/ref_flowframes.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowCore/data/GvHD.rda: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowCut/data/flowCutData.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowDensity/inst/extdata/sampleFCS_1.Rdata: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowDensity/inst/extdata/sampleFCS_2.Rdata: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowDensity/inst/extdata/sampleFCS_3_FMO.Rdata: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowDensity/inst/extdata/sampleFCS_3.Rdata: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowFP/data/fs1.rda: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowFP/data/fs2.rda: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowFP/data/plate.rda: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowGraph/data/fg_data_fca.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowGraph/data/fg_data_pos2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowGraph/data/fg_data_pos30.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowMeans/data/x.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowMerge/data/RituximabFlowClustFit.RData: load().. ok [1 object(s)]; updateObject(flowClustList, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowPeaks/data/barcode.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowPeaks/data/concave.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowPlots/data/adultsNeonates.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowPlots/data/marginalDF.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowPlots/data/markerMatrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowPlots/data/pfdDF.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowPlots/data/pfdPartsList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowPlots/data/profileDF.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowSpecs/data/fullPanel.rda: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowSpecs/data/specMat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowSpecs/data/unmixCtrls.rda: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowStats/data/BackGating.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowStats/data/ITN.rda: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowTime/data/dipdoubletGate.rda: load().. ok [1 object(s)]; updateObject(polygonGate, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowTime/data/dipsingletGate.rda: load().. ok [1 object(s)]; updateObject(polygonGate, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowTime/data/hapdoubletGate.rda: load().. ok [1 object(s)]; updateObject(polygonGate, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowTime/data/hapsingletGate.rda: load().. ok [1 object(s)]; updateObject(polygonGate, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowTime/data/yeastGate.rda: load().. ok [1 object(s)]; updateObject(polygonGate, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowTime/inst/extdata/C6Gates.RData: load().. ok [5 object(s)]; updateObject(polygonGate, check=FALSE).. no match, no-op; updateObject(polygonGate, check=FALSE).. no match, no-op; updateObject(polygonGate, check=FALSE).. no match, no-op; updateObject(polygonGate, check=FALSE).. no match, no-op; updateObject(polygonGate, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowTime/inst/extdata/SORPGates.RData: load().. ok [5 object(s)]; updateObject(polygonGate, check=FALSE).. no match, no-op; updateObject(polygonGate, check=FALSE).. no match, no-op; updateObject(polygonGate, check=FALSE).. no match, no-op; updateObject(polygonGate, check=FALSE).. no match, no-op; updateObject(polygonGate, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowVS/data/HD.RData: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File flowWorkspace/Meta/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/cv_gh.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/empty_pop.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getAllDescendants_cd3_gh.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getAllDescendants_cd4_gh.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getAllDescendants_cd8_gh.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getAxisLabels_gh.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getCompensationMatrices_gh.rds: readRDS().. ok; updateObject(compensation, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getData_COMPASS_gs.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getGate_gs_ellipse.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getGate_gs_polygon.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getGate_gs.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getGraph_gh.rds: readRDS().. ok; updateObject(graphNEL, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getIndice_singlet_gh.rds: readRDS().. ok; updateObject(logical, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getIndiceMat_gh.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getIndices_gs.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getNodes_gh.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/getTransformations_gh.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/kw_gh.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/kw_gs.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File flowWorkspace/tests/testthat/expect_result/layoutGraph_gh.rds: readRDS().. ok; updateObject(graphNEL, check=FALSE).. no match, no-op ==> 0
File fmcsR/data/fmcstest.rda: load().. ok [1 object(s)]; updateObject(SDFset, check=FALSE).. no match, no-op; nothing to update ==> 0
File fobitools/data/fobi_terms.rda: load().. ok [1 object(s)]; updateObject(ontology_index, check=FALSE).. no match, no-op; nothing to update ==> 0
File fobitools/data/fobi.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File fobitools/data/foods.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File fobitools/data/idmap.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File fobitools/vignettes/data/sample_ffq.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File fobitools/vignettes/data/ST000629_MetaboAnalyst_MapNames.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File FoldGO/data/bggenes_hum.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File FoldGO/data/bggenes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File FoldGO/data/degenes_hum.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File FoldGO/data/degenes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File FoldGO/data/down_annotobj.rda: load().. ok [1 object(s)]; updateObject(FuncAnnotGroupsTopGO, check=FALSE).. no match, no-op; nothing to update ==> 0
File FoldGO/data/down_groups.rda: load().. ok [1 object(s)]; updateObject(GeneGroups, check=FALSE).. no match, no-op; nothing to update ==> 0
File FoldGO/data/rna_seq_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File FoldGO/data/up_annotobj.rda: load().. ok [1 object(s)]; updateObject(FuncAnnotGroupsTopGO, check=FALSE).. no match, no-op; nothing to update ==> 0
File FoldGO/data/up_groups.rda: load().. ok [1 object(s)]; updateObject(GeneGroups, check=FALSE).. no match, no-op; nothing to update ==> 0
File FunChIP/data/GR100.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File FunChIP/data/peaks.rda: load().. ok [8 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File funtooNorm/R/sysdata.rda: load().. ok [4 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File GA4GHclient/inst/extdata/vignette.rda: load().. ok [6 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(CollapsedVCF, check=FALSE).. no match, no-op; updateObject(DFrame, check=FALSE).. no match, no-op; updateObject(CollapsedVCF, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gage/data/bods.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File gage/data/carta.gs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gage/data/egSymb.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File gage/data/go.gs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gage/data/gse16873.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File gage/data/kegg.gs.dise.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gage/data/kegg.gs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gage/data/khier.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File gage/data/korg.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File gaia/data/crc_markers.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gaia/data/crc.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gaia/data/synthCNV_Matrix.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gaia/data/synthMarkers_Matrix.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GAPGOM/data/expset.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GAPGOM/data/id_translation_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GAPGOM/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GAprediction/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(cv.glmnet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GARS/data/GARS_classes.rda: load().. ok [1 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File GARS/data/GARS_data_norm.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GARS/data/GARS_fit_list.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File GARS/data/GARS_Fitness_score.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File GARS/data/GARS_pop_list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GARS/data/GARS_popul.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GARS/data/GARS_res_GA.rda: load().. ok [1 object(s)]; updateObject(GarsSelectedFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File GateFinder/data/LPSData.rda: load().. ok [3 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gcatest/data/sim_geno.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File gcatest/data/sim_trait.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File gCrisprTools/data/aln.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File gCrisprTools/data/ann.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gCrisprTools/data/es.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File gCrisprTools/data/essential.genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File gCrisprTools/data/fit.RData: load().. ok [1 object(s)]; updateObject(MArrayLM, check=FALSE).. no match, no-op; nothing to update ==> 0
File gCrisprTools/data/resultsDF.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gcrma/data/affinity.spline.coefs.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File GDCRNATools/data/DEGAll.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GDCRNATools/data/enrichOutput.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GDCRNATools/data/lncTarget.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GDCRNATools/data/mirCounts.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GDCRNATools/data/pcTarget.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GDCRNATools/data/rnaCounts.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GDCRNATools/R/sysdata.rda: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gdsfmt/inst/unitTests/valid/standard.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gemini/data/counts.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File gemini/data/guide.annotation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gemini/data/Input.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gemini/data/Model.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gemini/data/sample.replicate.annotation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genArise/data/Simon.rda: load().. ok [1 object(s)]; updateObject(Spot, check=FALSE).. no match, no-op; nothing to update ==> 0
File genArise/data/WT.dataset.rda: load().. ok [1 object(s)]; updateObject(DataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneAccord/data/all_genes_tbl.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneAccord/data/avg_rates_m.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneAccord/data/clone_tbl_all_pats_all_trees.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneAccord/data/ecdf_list.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneAccord/data/ensg_reactome_path_map.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneAccord/data/ensmusg_reactome_path_map.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneAccord/data/list_of_clon_excl_all_pats.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneAccord/data/list_of_num_trees_all_pats.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneBreak/data/copynumber.data.chr18.rda: load().. ok [1 object(s)]; updateObject(cghCall, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneBreak/data/copynumber.data.chr20.rda: load().. ok [1 object(s)]; updateObject(cghCall, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneBreak/data/copynumber.data.chr21.rda: load().. ok [1 object(s)]; updateObject(cghCall, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneBreak/data/ens.gene.ann.hg18.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneBreak/data/ens.gene.ann.hg19.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneBreak/data/ens.gene.ann.hg38.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File geneClassifiers/data/exampleMAS5.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File geneClassifiers/R/sysdata.rda: load().. ok [9 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneExpressionSignature/data/exampleSet.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/claudinLowData.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/expos.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/mod1.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/mod2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/modelOvcAngiogenic.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/nkis.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/pam50.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/pam50.robust.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/pam50.scale.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/scmgene.robust.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/scmod1.robust.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/scmod2.robust.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sig.endoPredict.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sig.gene70.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sig.gene76.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sig.genius.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sig.ggi.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sig.oncotypedx.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sig.pik3cags.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sig.tamr13.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sigOvcAngiogenic.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sigOvcCrijns.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sigOvcSpentzos.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sigOvcTCGA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/sigOvcYoshihara.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/ssp2003.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/ssp2003.robust.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/ssp2003.scale.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/ssp2006.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/ssp2006.robust.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/ssp2006.scale.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genefu/data/vdxs.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneGA/data/wSet.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneGeneInteR/data/data.SNP.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneGeneInteR/data/gene.pair.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneGeneInteR/inst/extdata/dataImported.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneGeneInteR/inst/extdata/dataImputed.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneGeneInteR/inst/extdata/dataScour.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneGeneInteR/inst/extdata/GGIRes.Rdata: load().. ok [1 object(s)]; updateObject(GGInetwork, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneMeta/data/Nevins.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneNetworkBuilder/data/ce.IDsMap.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneNetworkBuilder/data/ce.interactionmap.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneNetworkBuilder/data/ce.mapIDs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneNetworkBuilder/data/ce.miRNA.map.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneNetworkBuilder/data/example.data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneNetworkBuilder/data/hs.IDsMap.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneNetworkBuilder/data/hs.interactionmap.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneNetworkBuilder/data/hs.mapIDs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneNetworkBuilder/data/hs.miRNA.map.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneOverlap/data/GeneOverlap.RData: load().. ok [3 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File geneplast/data/gpdata.gs.RData: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(phylo, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File geneplast/data/ppi.gs.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File geneplotter/data/expressionSet133a.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneRegionScan/data/exampleProbeLevelSet.rdata: load().. ok [3 object(s)]; updateObject(ProbeLevelSet, check=FALSE).. no match, no-op; updateObject(DNAStringSet, check=FALSE).. no match, no-op; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GENESIS/tests/testthat/testdata/old_nullmod_glm.rds: readRDS().. ok; updateObject(GENESIS.nullModel, check=FALSE).. no match, no-op ==> 0
File GENESIS/tests/testthat/testdata/old_nullmod_glmm.rds: readRDS().. ok; updateObject(GENESIS.nullMixedModel, check=FALSE).. no match, no-op ==> 0
File GENESIS/tests/testthat/testdata/old_nullmod_lm.rds: readRDS().. ok; updateObject(GENESIS.nullModel, check=FALSE).. no match, no-op ==> 0
File GENESIS/tests/testthat/testdata/old_nullmod_lmm.rds: readRDS().. ok; updateObject(GENESIS.nullMixedModel, check=FALSE).. no match, no-op ==> 0
File GENESIS/tests/testthat/testdata/old_nullmod_wls.rds: readRDS().. ok; updateObject(GENESIS.nullModel, check=FALSE).. no match, no-op ==> 0
File GENESIS/data/HapMap_ASW_MXL_KINGmat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GENESIS/data/sample_annotation_1KG.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File geNetClassifier/data/geneSymbols.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File geNetClassifier/data/leukemiasClassifier.RData: load().. ok [1 object(s)]; updateObject(GeNetClassifierReturn, check=FALSE).. returned an error ==> -1
File GeneticsPed/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File GeneTonic/data/enrichr_output_macrophage.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneTonic/data/fgseaRes.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneTonic/data/gostres_macrophage.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneTonic/data/res_de_macrophage.RData: load().. ok [1 object(s)]; updateObject(DESeqResults, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeneTonic/data/res_enrich_macrophage.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File geneXtendeR/data/rat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File geneXtendeR/data/samplepeaksinput.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File genoCN/data/init.Para.CNA.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genoCN/data/init.Para.CNV.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File genoCN/data/snpData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genoCN/data/snpInfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genomation/data/cage.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File genomation/data/cpgi.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File genomation/data/genes.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File genomation/data/promoters.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomeInfoDb/inst/extdata/assembly_accessions.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File genomeIntervals/data/gen_ints.rda: load().. ok [3 object(s)]; updateObject(Genome_intervals_stranded, check=FALSE).. no match, no-op; updateObject(Genome_intervals_stranded, check=FALSE).. no match, no-op; updateObject(Genome_intervals_stranded, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicAlignments/vignettes/precomputed_results/exbytx.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicAlignments/vignettes/precomputed_results/U1.sbcompHITSa.rda: load().. ok [1 object(s)]; updateObject(SortedByQueryHits, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicAlignments/vignettes/precomputed_results/U1.sbcompHITSb.rda: load().. ok [1 object(s)]; updateObject(SortedByQueryHits, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicDataCommons/R/sysdata.rda: load().. ok [4 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicDistributions/data/cellTypeMetadata.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicDistributions/data/chromSizes_hg19.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicDistributions/data/exampleOpenSignalMatrix_hg19.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicDistributions/data/geneModels_hg19.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicDistributions/data/setB_100.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicDistributions/data/TSS_hg19.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicDistributions/data/vistaEnhancers.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicFeatures/inst/extdata/sample_ranges.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File GenomicFeatures/inst/extdata/cD.exByEdge-SG-Vig.Rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicFeatures/inst/extdata/cD.exsByGenes-SG-Vig.Rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicFeatures/inst/extdata/events.Rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicFiles/inst/extdata/seqinfo.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File genomicInstability/data/hg38.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File genomicInstability/data/mm10.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicInteractions/data/hg19.refseq.transcripts.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicInteractions/data/hic_example_data.rda: load().. ok [1 object(s)]; updateObject(GenomicInteractions, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicInteractions/data/mm9_refseq_promoters.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicInteractions/data/thymus_enhancers.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicScores/inst/extdata/avgs.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File GenomicScores/inst/extdata/avgsbmi.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File GenomicScores/inst/extdata/cadd.v1.3.hg19.chr22.rds: readRDS().. ok; updateObject(Rle, check=FALSE).. no match, no-op ==> 0
File GenomicScores/inst/extdata/eyersids.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File GenomicScores/inst/extdata/mcap.v1.0.hg19.chr22.rds: readRDS().. ok; updateObject(Rle, check=FALSE).. no match, no-op ==> 0
File GenomicScores/inst/extdata/origphastCons100wayhg193UTR.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File GenomicScores/inst/extdata/origphastCons100wayhg19CDS.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File GenomicSuperSignature/tests/testthat/microTCGA.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File GenomicSuperSignature/data/droplist.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicSuperSignature/data/miniAllZ.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicSuperSignature/data/miniRAVmodel.RData: load().. ok [1 object(s)]; updateObject(PCAGenomicSignatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicSuperSignature/data/miniTCGA.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenomicSuperSignature/data/res_hcut.rda: load().. ok [1 object(s)]; updateObject(hclust, check=FALSE).. no match, no-op; nothing to update ==> 0
File genphen/data/dichotomous.phenotype.saap.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File genphen/data/genotype.saap.msa.RData: load().. ok [1 object(s)]; updateObject(AAMultipleAlignment, check=FALSE).. no match, no-op; nothing to update ==> 0
File genphen/data/genotype.saap.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File genphen/data/genotype.snp.msa.RData: load().. ok [1 object(s)]; updateObject(DNAMultipleAlignment, check=FALSE).. no match, no-op; nothing to update ==> 0
File genphen/data/genotype.snp.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File genphen/data/phenotype.saap.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File genphen/data/phenotype.snp.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenVisR/data/brcaMAF.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenVisR/data/cytoGeno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenVisR/data/HCC1395_Germline.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenVisR/data/HCC1395_N.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenVisR/data/HCC1395_T.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenVisR/data/hg19chr.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenVisR/data/LucCNseg.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenVisR/data/PIK3CA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GenVisR/data/SNPloci.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeoDiff/data/demoData.rda: load().. ok [1 object(s)]; updateObject(NanoStringGeoMxSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeoDiff/data/kidney.rda: load().. ok [1 object(s)]; updateObject(NanoStringGeoMxSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeoDiff/data/NBthDEmod2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeoDiff/data/NBthmDEmod2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeoDiff/data/NBthmDEmod2slope.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GeomxTools/inst/extdata/DSP_NGS_Example_Data/demoData.rds: readRDS().. ok; updateObject(NanoStringGeoMxSet, check=FALSE).. no match, no-op ==> 0
File gep2pep/inst/extdata/testgep.RDS: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File gep2pep/inst/extdata/testgmd.RDS: readRDS().. ok; updateObject(GeneSetCollection, check=FALSE).. no match, no-op ==> 0
File gespeR/inst/extdata/TR_screen_A.rds: readRDS().. ok; updateObject(dgCMatrix, check=FALSE).. no match, no-op ==> 0
File gespeR/inst/extdata/TR_screen_B.rds: readRDS().. ok; updateObject(dgCMatrix, check=FALSE).. no match, no-op ==> 0
File gespeR/inst/extdata/TR_screen_C.rds: readRDS().. ok; updateObject(dgCMatrix, check=FALSE).. no match, no-op ==> 0
File gespeR/inst/extdata/TR_screen_D.rds: readRDS().. ok; updateObject(dgCMatrix, check=FALSE).. no match, no-op ==> 0
File gespeR/vignettes/workflow/gespeR_fits.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File gespeR/vignettes/workflow/gespeR_GSPs.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File gespeR/data/stabilityfits.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ggmsa/R/sysdata.rda: load().. ok [5 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(glyph_polygon, check=FALSE).. no match, no-op; nothing to update ==> 0
File GGPA/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File GGPA/data/simulation.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GIGSEA/data/heart.metaXcan.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GIGSEA/data/MSigDB.KEGG.Pathway.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GIGSEA/data/MSigDB.miRNA.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GIGSEA/data/MSigDB.TF.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GIGSEA/data/TargetScan.miRNA.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File girafe/inst/extdata/mgi_gi.RData: load().. ok [1 object(s)]; updateObject(Genome_intervals_stranded, check=FALSE).. no match, no-op; nothing to update ==> 0
File GISPA/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File GISPA/data/data.rda: load().. ok [3 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GISPA/vignettes/data.rda: load().. ok [3 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GLAD/data/arrayCGH.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GLAD/data/cytoband.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GLAD/data/snijders.RData: load().. ok [15 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GLAD/data/veltman.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GladiaTOX/inst/extdata/data_for_vignette.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File Glimma/inst/RNAseq123/contr.matrix.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File Glimma/inst/RNAseq123/design.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File Glimma/inst/RNAseq123/dge.rds: readRDS().. ok; updateObject(DGEList, check=FALSE).. no match, no-op ==> 0
File Glimma/tests/testthat/test-v1_data_DESeqDataSet.RData: load().. ok [7 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(DESeqDataSet, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; nothing to update ==> 0
File Glimma/tests/testthat/test-v1_data_DGEExact.RData: load().. ok [6 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(DGEExact, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File Glimma/tests/testthat/test-v1_data_DGELRT.RData: load().. ok [6 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(DGELRT, check=FALSE).. no match, no-op; nothing to update ==> 0
File Glimma/tests/testthat/test-v1_data_invalid_names_glMDPlot.RData: load().. ok [2 object(s)]; updateObject(MArrayLM, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Glimma/tests/testthat/test-v1_data_little_mait_DGELRT.RData: load().. ok [1 object(s)]; updateObject(DGELRT, check=FALSE).. no match, no-op; nothing to update ==> 0
File Glimma/tests/testthat/test-v1_data_MDS_DESeq.RData: load().. ok [1 object(s)]; updateObject(DESeqDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Glimma/tests/testthat/test-v1_data_MDS_DGEList.RData: load().. ok [1 object(s)]; updateObject(DGEList, check=FALSE).. no match, no-op; nothing to update ==> 0
File Glimma/tests/testthat/test-v1_data_pasilla.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Glimma/tests/testthat/test-v1_data_volcano_glXYPlot.RData: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Glimma/tests/testthat/test-v1_data_voom.RData: load().. ok [6 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(MArrayLM, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File glmSparseNet/data/string.network.700.cache.RData: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GlobalAncova/data/bindata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GlobalAncova/data/colon.normal.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GlobalAncova/data/colon.pheno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GlobalAncova/data/colon.tumour.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GlobalAncova/data/pathways.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GlobalAncova/data/phenodata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GlobalAncova/data/vantVeer.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File globalSeq/data/toydata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GmicR/inst/extdata/GMIC_Builder_disc.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GmicR/inst/extdata/GMIC_Builder.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GmicR/inst/extdata/GMIC_Final.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GmicR/inst/extdata/GMIC_net.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GmicR/inst/extdata/sample_dat.Rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gmoviz/data/bright_colours_opaque.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File gmoviz/data/bright_colours_transparent.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File gmoviz/data/nice_colours.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File gmoviz/data/pastel_colours.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File gmoviz/data/rich_colours.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File GMRP/data/beta.data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GMRP/data/cad.data.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File GMRP/data/lpd.data.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File GMRP/data/SNP358.data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GMRP/data/SNP368annot.data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOexpress/data/AlvMac_allgenes.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOexpress/data/AlvMac_allGO.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOexpress/data/AlvMac_GOgenes.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOexpress/data/AlvMac_results.pVal.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOexpress/data/AlvMac_results.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOexpress/data/AlvMac.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOexpress/data/microarray2dataset.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOexpress/data/prefix2dataset.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOfuncR/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOpro/data/exrtcga.RData: load().. ok [1 object(s)]; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File goProfiles/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File goProfiles/data/CD4Ids.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File goProfiles/data/clustKidneyMF2.rda: load().. ok [1 object(s)]; updateObject(equivClust, check=FALSE).. no match, no-op; nothing to update ==> 0
File goProfiles/data/drosophila.rda: load().. ok [3 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File goProfiles/data/hugoIds.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File goProfiles/data/kidneyGeneLists.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File goProfiles/data/omimIds.rda: load().. ok [8 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File goProfiles/data/prostateIds.rda: load().. ok [4 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOSemSim/data/gotbl.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File goseq/data/genes.RData: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOSim/data/ICsBPhumanall.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOSim/data/ICsCChumanall.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOSim/data/ICsMFhumanall.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File goSTAG/data/goSTAG_example_gene_lists.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File goSTAG/data/goSTAG_go_genes_human.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File goSTAG/data/goSTAG_go_genes_mouse.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File goSTAG/data/goSTAG_go_genes_rat.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File goSTAG/data/rat_cancer_therapeutics_gene_lists.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOstats/data/Bdists.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOstats/data/Ndists.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOstats/inst/UnitTests/ghgans10.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOsummaries/data/gs_kmeans.rda: load().. ok [1 object(s)]; updateObject(gosummaries, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOsummaries/data/gs_limma_exp.rda: load().. ok [1 object(s)]; updateObject(gosummaries, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOsummaries/data/gs_limma.rda: load().. ok [1 object(s)]; updateObject(gosummaries, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOsummaries/data/gs_pca.rda: load().. ok [1 object(s)]; updateObject(gosummaries, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOsummaries/data/metabolomic_example.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOsummaries/data/metagenomic_example.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOsummaries/data/tissue_example.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GOTHiC/data/lymphoid_chr20_paired_filtered.rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File goTools/data/probeID.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GPA/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File gpart/data/geneinfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gpart/data/geno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gpart/data/SNPinfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gprege/data/DGdat_p63.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gprege/data/FragmentDellaGattaData.RData: load().. ok [5 object(s)]; updateObject(logical, check=FALSE).. no match, no-op; updateObject(logical, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gprege/data/FullDellaGattaData.RData: load().. ok [5 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(logical, check=FALSE).. no match, no-op; updateObject(logical, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File granulator/data/bulkRNAseq_ABIS.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File granulator/data/groundTruth_ABIS.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File granulator/data/sigMatrix_ABIS_S0.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File granulator/data/sigMatrix_ABIS_S1.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File granulator/data/sigMatrix_ABIS_S2.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File granulator/data/sigMatrix_ABIS_S3.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File graph/data/apopGraph.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File graph/data/biocRepos.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File graph/data/defunctGraph.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File graph/data/esetsFemale.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File graph/data/esetsMale.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File graph/data/graphExamples.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File graph/data/integrinMediatedCellAdhesion.rda: load().. ok [2 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File graph/data/MAPKsig.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File graph/data/pancrCaIni.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File GraphAT/data/causton.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GraphAT/data/ccCM.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GraphAT/data/depthmatBP.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GraphAT/data/depthmatCC.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GraphAT/data/depthmatMF.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GraphAT/data/giaever.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GraphAT/data/mRNAclusters.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GraphAT/data/nNamescc.rda: load().. ok [1 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File GraphAT/data/Phenoclusters.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GreyListChIP/data/ce10.blacklist.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GreyListChIP/data/ce11.blacklist.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GreyListChIP/data/dm3.blacklist.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GreyListChIP/data/dm6.blacklist.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GreyListChIP/data/grch37.blacklist.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GreyListChIP/data/grch38.blacklist.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GreyListChIP/data/greyList.RData: load().. ok [1 object(s)]; updateObject(GreyList, check=FALSE).. returned an error ==> -1
File GreyListChIP/data/hg19.blacklist.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GreyListChIP/data/hg38.blacklist.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GreyListChIP/data/mm10.blacklist.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GreyListChIP/data/mm9.blacklist.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GRmetrics/data/inputCaseA.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File GRmetrics/data/inputCaseC.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File groHMM/inst/extdata/Vignette.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GRridge/data/dataFarkas.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File GRridge/data/dataSimlin.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GRridge/data/dataVerlaat.rda: load().. ok [5 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File GRridge/data/dataWurdinger.rda: load().. ok [4 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSALightning/data/expression.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSALightning/data/sampleInfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSALightning/data/targetGenes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSAR/data/p53DataSet.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSCA/data/geneIDdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSCA/data/Oct4ESC_TG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSCA/data/STAT1_TG.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSCA/inst/extdata/allreffile.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gscreend/inst/extdata/gscreend_analysed_experiment.RData: load().. failed! ==> -2
File GSEABenchmarkeR/inst/extdata/malacards/GO_BP.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File GSEABenchmarkeR/inst/extdata/malacards/GO_MF.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File GSEABenchmarkeR/inst/extdata/malacards/KEGG.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File GSEABenchmarkeR/inst/extdata/myEData/GSE42057x.rds: readRDS().. ok; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File GSEABenchmarkeR/inst/extdata/myEData/GSE7305x.rds: readRDS().. ok; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File GSEAmining/data/genesets_sel.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gsean/data/GO_dme.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gsean/data/KEGG_hsa.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSgalgoR/inst/extdata/results/final_1.rda: load().. ok [1 object(s)]; updateObject(galgo.Obj, check=FALSE).. returned an error ==> -1
File GSgalgoR/inst/extdata/results/final_2.rda: load().. ok [1 object(s)]; updateObject(galgo.Obj, check=FALSE).. returned an error ==> -1
File GSReg/data/juncExprsSimulated.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSReg/vignettes/DIRACAn.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GSVA/inst/extdata/cache4vignette_leukemia_es.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File gtrellis/inst/extdata/df_control.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File gtrellis/inst/extdata/df_tumor.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File gtrellis/inst/extdata/gencode_v19_protein_coding_genes.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File gtrellis/inst/extdata/gwasCatalog.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GUIDEseq/data/peaks.gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GUIDEseq/data/uniqueCleavageEvents.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File GUIDEseq/inst/extdata/testbothRunSum.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File GUIDEseq/inst/extdata/testPeaks.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/alTrackGenes.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/biomTrack.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/biomTrack2.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/bmTrack.rda: load().. ok [1 object(s)]; updateObject(BiomartGeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/collapseTrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/cpgIslands.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/cyp2b10.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/denseAnnTrack.rda: load().. ok [1 object(s)]; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/dtHoriz.rda: load().. ok [1 object(s)]; updateObject(DataTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/geneDetails.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/geneModels.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/idTrack.rda: load().. ok [1 object(s)]; updateObject(IdeogramTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/itrack.rda: load().. ok [1 object(s)]; updateObject(IdeogramTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/twoGroups.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File Gviz/data/ucscItems.rda: load().. ok [11 object(s)]; updateObject(GenomeAxisTrack, check=FALSE).. no match, no-op; updateObject(DataTrack, check=FALSE).. no match, no-op; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(DataTrack, check=FALSE).. no match, no-op; updateObject(IdeogramTrack, check=FALSE).. no match, no-op; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; updateObject(AnnotationTrack, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWAS.BAYES/data/RealDataInfo.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWAS.BAYES/data/RealDataKinship.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWAS.BAYES/data/RealDataSNPs_Y.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWAS.BAYES/data/vignette_kinship_dat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWAS.BAYES/data/vignette_lm_dat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
Skip package gwascat ==> -3
File GWASTools/data/centromeres.hg18.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/centromeres.hg19.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/centromeres.hg38.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/HLA.hg18.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/HLA.hg19.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/HLA.hg38.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/pcaSnpFilters.hg18.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/pcaSnpFilters.hg19.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/pcaSnpFilters.hg38.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/pseudoautosomal.hg18.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/pseudoautosomal.hg19.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/pseudoautosomal.hg38.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWASTools/data/relationsMeanVar.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File gwasurvivr/inst/extdata/gds_example.scan.rdata: load().. ok [1 object(s)]; updateObject(ScanAnnotationDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File gwasurvivr/inst/extdata/gds_example.snp.rdata: load().. ok [1 object(s)]; updateObject(SnpAnnotationDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWENA/data/gtex_expr.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWENA/data/gtex_traits.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWENA/data/kuehne_expr.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File GWENA/data/kuehne_traits.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File h5vc/data/bases.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File hapFabia/data/chr1ASW1000G.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File hapFabia/data/hapRes.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File hapFabia/data/mergedIBDsegmentList.RData: load().. ok [1 object(s)]; updateObject(IBDsegmentList, check=FALSE).. no match, no-op; nothing to update ==> 0
File hapFabia/data/res.RData: load().. ok [1 object(s)]; updateObject(Factorization, check=FALSE).. no match, no-op; nothing to update ==> 0
File hapFabia/data/simu.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Harshlight/data/sim.int.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Harshlight/data/sim.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File HDTD/data/VEGFmouse.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File heatmaps/inst/extdata/H3K4me3_30p_neg.rds: readRDS().. ok; updateObject(SimpleRleList, check=FALSE).. no match, no-op ==> 0
File heatmaps/inst/extdata/H3K4me3_30p_pos.rds: readRDS().. ok; updateObject(SimpleRleList, check=FALSE).. no match, no-op ==> 0
File heatmaps/data/HeatmapExamples.RData: load().. ok [7 object(s)]; updateObject(Heatmap, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(CompressedRleList, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(Heatmap, check=FALSE).. no match, no-op; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File HELP/data/base.stacking.thermodynamics.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File HEM/data/mubcp.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HEM/data/pbrain.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hermes/tests/unit_testing_results.rds: readRDS().. ok; updateObject(testthat_results, check=FALSE).. no match, no-op ==> 0
File hermes/data/expression_set.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File hermes/data/hermes_data.rda: load().. ok [1 object(s)]; updateObject(HermesData, check=FALSE).. no match, no-op; nothing to update ==> 0
File hermes/data/multi_assay_experiment.rda: load().. ok [1 object(s)]; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File hermes/data/summarized_experiment.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File Herper/inst/extdata/Bioc_Pkg_Details.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File HGC/data/Pollen.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File hiAnnotator/data/genes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hiAnnotator/data/sites.ctrl.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hiAnnotator/data/sites.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HIBAG/data/HapMap_CEU_Geno.rdata: load().. ok [1 object(s)]; updateObject(hlaSNPGenoClass, check=FALSE).. no match, no-op; nothing to update ==> 0
File HIBAG/data/HLA_Type_Table.rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HIBAG/inst/extdata/ModelList.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File HIBAG/inst/extdata/OutOfBag.RData: load().. ok [1 object(s)]; updateObject(hlaAttrBagObj, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/brain_table.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/centromere_locations.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/cooler.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/hg19_blacklist.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/hg38_blacklist.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/HMEC.chr10.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/HMEC.chr22.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/hmec.IS.rda: load().. ok [1 object(s)]; updateObject(GInteractions, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/NHEK.chr10.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/NHEK.chr22.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiCcompare/data/nhek.IS.rda: load().. ok [1 object(s)]; updateObject(GInteractions, check=FALSE).. no match, no-op; nothing to update ==> 0
File hierGWAS/data/simGWAS.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hierinf/data/simGWAS.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File HilbertCurve/inst/extdata/chinese_dynasty.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HilbertCurve/inst/extdata/cidr_list.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File HilbertCurve/inst/extdata/mouse_net.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File HilbertCurve/inst/extdata/refseq_chr1.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File HilbertCurve/inst/extdata/zebrafish_net.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiLDA/inst/extdata/hildaLocal.rdata: load().. failed! ==> -2
File HiLDA/inst/extdata/sample.rdata: load().. ok [1 object(s)]; updateObject(MutationFeatureData, check=FALSE).. no match, no-op; nothing to update ==> 0
File hipathia/data/brca_data.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File hipathia/data/brca_design.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hipathia/data/brca.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File hipathia/data/comp.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hipathia/data/exp_data.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File hipathia/data/go_vals.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File hipathia/data/path_vals.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File hipathia/data/results.rda: load().. ok [1 object(s)]; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File HIPPO/data/ensg_hgnc.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HIPPO/data/toydata.RData: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File hiReadsProcessor/data/FLX_seqProps.RData: load().. ok [1 object(s)]; updateObject(SimpleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File hiReadsProcessor/data/psl.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HiTC/data/Nora_5C.RData: load().. ok [2 object(s)]; updateObject(HTClist, check=FALSE).. no match, no-op; updateObject(HTClist, check=FALSE).. no match, no-op; nothing to update ==> 0
File hmdbQuery/data/hmdb_disease.rda: load().. ok [1 object(s)]; updateObject(DataFrame, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File hmdbQuery/data/hmdb_gene.rda: load().. ok [1 object(s)]; updateObject(DataFrame, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File hmdbQuery/data/hmdb_omim.rda: load().. ok [1 object(s)]; updateObject(DataFrame, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File hmdbQuery/data/hmdb_protein.rda: load().. ok [1 object(s)]; updateObject(DataFrame, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File hmdbQuery/data/hmdb1.rda: load().. ok [1 object(s)]; updateObject(HmdbEntry, check=FALSE).. returned an error ==> -1
File HMMcopy/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File HMMcopy/data/tumour.rda: load().. ok [5 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; updateObject(data.table, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.table, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File hopach/data/golub.RData: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPAanalyze/data/hpa_histology_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPAanalyze/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/hpaCancer.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/hpaCancer16.1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/hpaNormalTissue.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/hpaNormalTissue16.1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/hpaSecretome.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/hpaSubcellularLoc.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/hpaSubcellularLoc14.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/hpaSubcellularLoc16.1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/rnaGeneCellLine.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/rnaGeneCellLine16.1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/data/rnaGeneTissue.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hpar/inst/extdata/hpaRelease.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPiP/data/enrich.df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPiP/data/example_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPiP/data/Gold_ReferenceSet.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPiP/data/host_se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPiP/data/predicted_PPIs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPiP/data/unlabel_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPiP/data/UP000464024_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPiP/data/viral_se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File HPiP/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; updateObject(data.table, check=FALSE).. no match, no-op; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File HTqPCR/data/qPCRpros.RData: load().. ok [1 object(s)]; updateObject(qPCRset, check=FALSE).. no match, no-op; nothing to update ==> 0
File HTqPCR/data/qPCRraw.RData: load().. ok [1 object(s)]; updateObject(qPCRset, check=FALSE).. no match, no-op; nothing to update ==> 0
File HTSeqGenie/inst/test-data/tp53_dbsnp.Rdata: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File HTSFilter/data/sultan.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File HumanTranscriptomeCompendium/data/HumanTranscriptomeCompendium.colnames.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File HumanTranscriptomeCompendium/data/uniqueAcc_120518.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File hummingbird/data/exampleHummingbird.RData: load().. ok [7 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File HybridMTest/data/correlation.data.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File HybridMTest/data/GroupComp.data.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File hypeR/inst/extdata/genesets.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File hypeR/inst/extdata/testdat.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File hypeR/data/limma.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File hypeR/data/wgcna.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File iASeq/data/sampleASE.RData: load().. ok [4 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File iasva/inst/extdata/iasva_anns_test.Rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File iasva/inst/extdata/iasva_counts_test.Rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File iBMQ/data/gene.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File iBMQ/data/genepos.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iBMQ/data/genotype.liver.rda: load().. ok [1 object(s)]; updateObject(SnpSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File iBMQ/data/map.liver.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iBMQ/data/phenotype.liver.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File iBMQ/data/PPA.liver.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File iBMQ/data/probe.liver.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iBMQ/data/snp.rda: load().. ok [1 object(s)]; updateObject(SnpSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File iBMQ/data/snppos.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iCARE/data/bc_data.rda: load().. ok [14 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(formula, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(icare, check=FALSE).. no match, no-op; nothing to update ==> 0
File icetea/inst/extdata/testTSS_grl.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File icetea/docs/reference/testTSS.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File iChip/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File iChip/data/oct4.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iChip/data/p53.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iClusterPlus/data/breast.chr17.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File iClusterPlus/data/coord.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iClusterPlus/data/gbm.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iClusterPlus/data/glp.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File iClusterPlus/data/simuResult.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File iClusterPlus/data/variation.hg18.v10.nov.2010.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iCNV/data/icnv_res0.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File iCNV/data/icnv.demo.array_lrrbaf_22.rda: load().. ok [4 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File iCNV/data/icnv.demo.bambaf_22.rda: load().. ok [6 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File iCNV/data/icnv.demo.plrObj_22_2.rda: load().. ok [3 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File iCNV/data/icnv.demo.plrObj_22.rda: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File iCOBRA/data/cobradata_example_sval.rda: load().. ok [1 object(s)]; updateObject(COBRAData, check=FALSE).. no match, no-op; nothing to update ==> 0
File iCOBRA/data/cobradata_example.rda: load().. ok [1 object(s)]; updateObject(COBRAData, check=FALSE).. no match, no-op; nothing to update ==> 0
File iCOBRA/inst/extdata/cobradata_example_simres.Rdata: load().. ok [1 object(s)]; updateObject(SimResults, check=FALSE).. returned an error ==> -1
File IdeoViz/data/binned_fullGenome.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File IdeoViz/data/binned_multiSeries.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File IdeoViz/data/binned_singleSeries.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File IdeoViz/data/examples.rda: load().. ok [3 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File IdeoViz/data/wins_discrete.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File IdeoViz/data/wins_entiregenome.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File IdeoViz/data/wins.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File idiogram/data/Cf.cytoband.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File idiogram/data/Hs.cytoband.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File idiogram/data/idiogramExample.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(chromLocation, check=FALSE).. no match, no-op; updateObject(chromLocation, check=FALSE).. no match, no-op; nothing to update ==> 0
File idiogram/data/Mm.cytoband.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File idiogram/data/Rn.cytoband.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/Disorder40.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/Disorder60.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/Disorder85.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/DUNMat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/EDSSMat50.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/EDSSMat60.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/EDSSMat62.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/EDSSMat70.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/EDSSMat75.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/EDSSMat80.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/EDSSMat90.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/GorillaTP53.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/KDNorm.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/pKaData.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/data/TP53Sequences.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File idpr/R/sysdata.rda: load().. ok [6 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File idr2d/data/chiapet.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File idr2d/data/chipseq.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File idr2d/data/hic.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File iGC/data/hg19DBNM.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File IgGeneUsage/data/CDR3_Epitopes.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IgGeneUsage/data/Ig_SE.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File IgGeneUsage/data/Ig.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IgGeneUsage/data/IGHV_HCV.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File igvR/inst/extdata/tbl.mef2cGWAS.variants.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File igvR/inst/extdata/tbl.with.MotifDbNames.Rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ILoReg/data/pbmc3k_500.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File imageHTS/inst/submorph/data/classifier.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMAS/data/bamfilestest.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMAS/data/sampleclinical.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMAS/data/sampleGroups.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMAS/data/samplemethyl.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMAS/data/samplemethyllocus.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMAS/data/samplesnp.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMAS/data/samplesnplocus.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMMAN/data/Celegance.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMMAN/data/FruitFly.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMMAN/data/H.sapiens.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IMMAN/data/R.norvegicus.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ImmuneSpaceR/inst/extdata/saved_con.rds: readRDS().. Registered S3 methods overwritten by 'dendextend':
  method       from   
  rev.hclust   vegan  
  text.pvclust pvclust
Registered S3 method overwritten by 'seriation':
  method         from 
  reorder.hclust vegan
ok; updateObject(ImmuneSpaceConnection, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY180_fcs_control_files.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY180_fcs_sample_files.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY180_mbaa.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY180_neut_ab_titer.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY269_demographics.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY269_elisa.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY269_elispot.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY269_fcs_analyzed_result.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY269_gene_expression_files.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY269_hai.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY269_pcr.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File ImmuneSpaceR/tests/testthat/datasets/SDY28_hla_typing.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File immunoClust/data/dat.exp.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File immunoClust/data/dat.fcs.RData: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File immunoClust/data/dat.meta.RData: load().. ok [1 object(s)]; updateObject(immunoMeta, check=FALSE).. no match, no-op; nothing to update ==> 0
File immunotation/inst/extdata/AFND_valid_alleles.RData: load().. failed! ==> -2
File impute/data/khanmiss.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File INDEED/data/Met_Group_GU.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File INDEED/data/Met_GU.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File INDEED/data/Met_name_GU.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File INDEED/data/pvalue_M_GU.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File infercnv/data/HMM_states.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File infercnv/data/infercnv_annots_example.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File infercnv/data/infercnv_data_example.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File infercnv/data/infercnv_genes_example.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File infercnv/data/infercnv_object_example.rda: load().. ok [1 object(s)]; updateObject(infercnv, check=FALSE).. no match, no-op; nothing to update ==> 0
File infercnv/data/mcmc_obj.rda: load().. ok [1 object(s)]; updateObject(MCMC_inferCNV, check=FALSE).. no match, no-op; nothing to update ==> 0
File infinityFlow/data/steady_state_lung_annotation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File infinityFlow/data/steady_state_lung_backbone_specification.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File infinityFlow/data/steady_state_lung.rda: load().. ok [1 object(s)]; updateObject(flowSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Informeasure/inst/extdata/tcga.brca.testdata.Rdata: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File InPAS/data/utr3.mm10.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File InPAS/inst/extdata/eset.MAQC.rda: load().. ok [1 object(s)]; updateObject(UTR3eSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File InPAS/inst/extdata/polyA.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File INPower/inst/sampleData/data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File INSPEcT/inst/INSPEcT_GUI_sample_dataset.rds: readRDS().. ok; updateObject(INSPEcT, check=FALSE).. no match, no-op ==> 0
File INSPEcT/inst/nascentInspObj.rds: readRDS().. ok; updateObject(INSPEcT, check=FALSE).. no match, no-op ==> 0
File INSPEcT/inst/nascentInspObj10.rds: readRDS().. ok; updateObject(INSPEcT, check=FALSE).. no match, no-op ==> 0
File INSPEcT/data/allcounts.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File INSPEcT/data/featureWidths.RData: load().. ok [2 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File INSPEcT/data/libsizes.RData: load().. ok [2 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File INSPEcT/data/matureSim2replicates.RData: load().. ok [1 object(s)]; updateObject(INSPEcT, check=FALSE).. no match, no-op; nothing to update ==> 0
File INSPEcT/data/matureSim3replicates.RData: load().. ok [1 object(s)]; updateObject(INSPEcT, check=FALSE).. no match, no-op; nothing to update ==> 0
File INSPEcT/data/nascentSim2replicates.RData: load().. ok [1 object(s)]; updateObject(INSPEcT, check=FALSE).. no match, no-op; nothing to update ==> 0
File INSPEcT/data/nascentSim3replicates.RData: load().. ok [1 object(s)]; updateObject(INSPEcT, check=FALSE).. no match, no-op; nothing to update ==> 0
File InTAD/data/enhSelCoords.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File InTAD/data/loops_imr90.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File InTAD/data/mbAnnData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File InTAD/data/mbSamplesRPKM.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File InTAD/data/mbSelEnhSignals.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File InTAD/data/tad_hg19.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File InTAD/data/txsSel.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/arcExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/bubbleExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/chord.pExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/chordExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/cnvExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/geneExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/heatmapExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/hg19_ideogram.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/histogramExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/lineExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/linkExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/lollipopExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/scatterExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/snpExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File interacCircos/data/wigExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File InteractiveComplexHeatmap/inst/extdata/2d_density_xy.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File InteractiveComplexHeatmap/data/rand_mat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File interactiveDisplay/data/expr.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File interactiveDisplay/data/mmgr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File interactiveDisplay/data/mmgrl.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File interactiveDisplay/data/se.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File InterCellar/data/input.data.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File InterCellar/R/sysdata.rda: load().. ok [6 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntEREst/data/mdsChr22ExObj.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntEREst/data/mdsChr22IntSpObj.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntEREst/data/mdsChr22Obj.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntEREst/data/pwmU12db.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntEREst/data/u12.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File InterMineR/data/PL_DiabetesGenes.rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File InterMineR/data/PL_FlyTF_site_specific_TFs.rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntramiRExploreR/data/Affy1_Distance_Final.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntramiRExploreR/data/Affy1_Pearson_Final.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntramiRExploreR/data/Affy2_Distance_Final.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntramiRExploreR/data/Affy2_Pearson_Final.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntramiRExploreR/data/miRNA_ID_to_Function.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IntramiRExploreR/data/miRNA_summary_DB.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File inveRsion/data/ac.RData: load().. ok [1 object(s)]; updateObject(accuracy, check=FALSE).. no match, no-op; nothing to update ==> 0
File inveRsion/data/gDat.RData: load().. ok [1 object(s)]; updateObject(GenoDat, check=FALSE).. -Set up object of class: GenoDat- 
no match, no-op; nothing to update ==> 0
File inveRsion/data/hapCode.RData: load().. ok [1 object(s)]; updateObject(HaploCode, check=FALSE).. no match, no-op; nothing to update ==> 0
File inveRsion/data/invList.RData: load().. ok [1 object(s)]; updateObject(inversionList, check=FALSE).. no match, no-op; nothing to update ==> 0
File inveRsion/data/scanRes.RData: load().. ok [1 object(s)]; updateObject(scan, check=FALSE).. no match, no-op; nothing to update ==> 0
File iPAC/data/KRAS.Mutations.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File iPAC/data/PIK3CA.Mutations.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File iPath/data/GSDB_example.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File iPath/data/PRAD_data.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File IRISFGM/data/example_object.rda: load().. ok [1 object(s)]; updateObject(IRISFGM, check=FALSE).. no match, no-op; nothing to update ==> 0
File ISAnalytics/inst/testdata/test_population_expected.Rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File ISAnalytics/inst/testdata/test_population_iss.Rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File ISAnalytics/inst/testdata/test_population_meta.Rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File ISAnalytics/data/association_file.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File ISAnalytics/data/integration_matrices.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File ISAnalytics/data/proto_oncogenes.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ISAnalytics/data/refGenes_hg19.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ISAnalytics/data/refGenes_mm9.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ISAnalytics/data/tumor_suppressors.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File iSeq/data/nrsf.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
Skip package isobar ==> -3
File IsoCorrectoR/data/IsoCorrectoR.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File IsoformSwitchAnalyzeR/data/exampleSwitchList.RData: load().. ok [1 object(s)]; updateObject(switchAnalyzeRlist, check=FALSE).. no match, no-op; nothing to update ==> 0
File IsoformSwitchAnalyzeR/data/exampleSwitchListAnalyzed.RData: load().. ok [1 object(s)]; updateObject(switchAnalyzeRlist, check=FALSE).. no match, no-op; nothing to update ==> 0
File IsoformSwitchAnalyzeR/data/exampleSwitchListIntermediary.RData: load().. ok [1 object(s)]; updateObject(switchAnalyzeRlist, check=FALSE).. no match, no-op; nothing to update ==> 0
File IsoGeneGUI/inst/doc/exampleData/dopamine2.rda: load().. ok [4 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(logical, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File ISoLDE/data/filteredASRcounts.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ISoLDE/data/normASRcounts.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ISoLDE/data/rawASRcounts.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ISoLDE/data/target.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File isomiRs/data/dat286.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File isomiRs/data/isoExample.rda: load().. ok [4 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File isomiRs/data/mirData.rda: load().. ok [1 object(s)]; updateObject(IsomirDataSeq, check=FALSE).. no match, no-op; nothing to update ==> 0
File isomiRs/data/mirTritation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iterativeBMA/data/testClass.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File iterativeBMA/data/testData.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File iterativeBMA/data/trainClass.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File iterativeBMA/data/trainData.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File iterativeBMAsurv/data/testCens.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File iterativeBMAsurv/data/testData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iterativeBMAsurv/data/testSurv.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File iterativeBMAsurv/data/trainCens.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File iterativeBMAsurv/data/trainData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iterativeBMAsurv/data/trainSurv.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File iteremoval/data/SummarizedData.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File iteremoval/data/SWRG0.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File iteremoval/data/SWRG1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IVAS/data/sampleexp.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IVAS/data/samplesnp.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File IVAS/data/samplesnplocus.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ivygapSE/data/ivySE.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File IWTomics/data/ETn_example.RData: load().. ok [1 object(s)]; updateObject(IWTomicsData, check=FALSE).. no match, no-op; nothing to update ==> 0
File IWTomics/data/features_example.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File IWTomics/data/regions_example.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File IWTomics/data/regionsFeatures_center.RData: load().. ok [1 object(s)]; updateObject(IWTomicsData, check=FALSE).. no match, no-op; nothing to update ==> 0
File IWTomics/data/regionsFeatures_scale.RData: load().. ok [1 object(s)]; updateObject(IWTomicsData, check=FALSE).. no match, no-op; nothing to update ==> 0
File karyoploteR/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/Meta/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File KBoost/data/D4_multi_1.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/D4_multi_2.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/D4_multi_3.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/D4_multi_4.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/D4_multi_5.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/G_D4_multi_1.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/G_D4_multi_2.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/G_D4_multi_3.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/G_D4_multi_4.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/G_D4_multi_5.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/Gerstein_Prior_ENET_2.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/Human_TFs.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/IRMA_Gold.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/irma_off.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KBoost/data/irma_on.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KCsmart/data/hsMirrorLocs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File KCsmart/data/hsSampleData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File KCsmart/data/mmMirrorLocs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File kebabs/data/CCoil.RData: load().. ok [4 object(s)]; updateObject(AAStringSet, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File kebabs/data/TFBS.RData: load().. ok [4 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File KEGGgraph/data/KEGGPATHID2NAME.RData: load().. ok [1 object(s)]; updateObject(AnnDbBimap, check=FALSE).. no match, no-op; nothing to update ==> 0
File KEGGgraph/inst/extdata/colorectalcancerSPIA.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File keggorthology/data/keggOrthDF.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File keggorthology/data/KOgraph.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File KinSwingR/data/example_phosphoproteome.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File KinSwingR/data/phosphositeplus_human.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File KnowSeq/inst/extdata/expressionExample.RData: load().. ok [7 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File LACE/data/inference.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File LACE/data/longitudinal_sc_variants.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File LBE/data/golub.pval.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File LBE/data/hedenfalk.pval.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File ldblock/data/EUR_singletons.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ldblock/data/sampinf_1kg.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LEA/data/tutorial.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File LedPred/data/crm.features.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LedPred/data/feature.ranking.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LedPred/tests/testthat/data_iris2/feature.ranking.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LedPred/tests/testthat/data_iris2/iris2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LedPred/tests/testthat/data_iris2/x.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LedPred/tests/testthat/data_iris2/y.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File lefser/data/zeller14.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File les/data/spikeInData.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File les/data/spikeInStat.RData: load().. ok [2 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File lfa/data/hgdp_subset.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File LinkHD/data/Ruminotypes.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File LinkHD/data/Taraoceans.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Linnorm/data/Islam2011.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Linnorm/data/LIHC.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Linnorm/data/SEQC.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File lionessR/data/OSdata.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File lipidr/data/data_normalized.rda: load().. ok [1 object(s)]; updateObject(LipidomicsExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File lipidr/data/lipidDefaults.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File lipidr/data/lipidnames_pattern.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File LOBSTAHS/data/default.acylRanges.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LOBSTAHS/data/default.adductHierarchies.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LOBSTAHS/data/default.componentCompTable.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LOBSTAHS/data/default.LOBdbase.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File LOBSTAHS/data/default.oxyRanges.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LOBSTAHS/data/default.rt.windows.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File loci2path/data/loci2path.demo.rda: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(geneSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File logicFS/data/data.logicfs.RData: load().. ok [2 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File LOLA/data/sample_input.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File LOLA/data/sample_universe.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File LowMACA/data/BLOSUM62.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File LowMACA/data/lmObj.RData: load().. ok [1 object(s)]; updateObject(LowMACA, check=FALSE).. no match, no-op; nothing to update ==> 0
File LowMACA/data/LowMACA_AML.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LPE/data/Ley.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File lpNet/data/SahinRNAi2008.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File LRcell/data/example_gene_pvals.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File LRcell/data/example_LRcell_res.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File LRcell/data/mouse_celltypes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File LRcell/data/mouse_FC_marker_genes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File lumi/data/example.lumi.rda: load().. ok [1 object(s)]; updateObject(LumiBatch, check=FALSE).. no match, no-op; nothing to update ==> 0
File lumi/data/example.lumiMethy.rda: load().. ok [1 object(s)]; updateObject(MethyLumiM, check=FALSE).. no match, no-op; nothing to update ==> 0
File lumi/data/example.methyTitration.rda: load().. ok [1 object(s)]; updateObject(MethyLumiM, check=FALSE).. no match, no-op; nothing to update ==> 0
File M3C/data/desx.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File M3C/data/mydata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File m6Aboost/inst/extdata/test.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File maanova/data/abf1.RData: load().. ok [1 object(s)]; updateObject(madata, check=FALSE).. no match, no-op; nothing to update ==> 0
File maanova/data/kidney.RData: load().. ok [1 object(s)]; updateObject(madata, check=FALSE).. no match, no-op; nothing to update ==> 0
File macat/data/stjd.RData: load().. ok [1 object(s)]; updateObject(MACATData, check=FALSE).. no match, no-op; nothing to update ==> 0
File maCorrPlot/data/oligodata.rda: load().. ok [6 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MACPET/inst/extdata/MACPET_GenomeMapData.rda: load().. ok [1 object(s)]; updateObject(GenomeMap, check=FALSE).. no match, no-op; nothing to update ==> 0
File MACPET/inst/extdata/MACPET_pinterData.rda: load().. ok [1 object(s)]; updateObject(PInter, check=FALSE).. no match, no-op; nothing to update ==> 0
File MACPET/inst/extdata/MACPET_pintraData.rda: load().. ok [1 object(s)]; updateObject(PIntra, check=FALSE).. no match, no-op; nothing to update ==> 0
File MACPET/inst/extdata/MACPET_pselfData.rda: load().. ok [1 object(s)]; updateObject(PSelf, check=FALSE).. no match, no-op; nothing to update ==> 0
File MACPET/inst/extdata/MACPET_psfitData.rda: load().. ok [1 object(s)]; updateObject(PSFit, check=FALSE).. no match, no-op; nothing to update ==> 0
File MACPET/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MACSQuantifyR/inst/extdata/drugs.RDS: readRDS().. ok; updateObject(MACSQuant, check=FALSE).. no match, no-op ==> 0
File MACSQuantifyR/inst/extdata/drugs.Rdata: load().. ok [4 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(MACSQuant, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File made4/data/khan.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File made4/data/NCI60.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MADSEQ/inst/AQP7/hg19_AQP7_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MADSEQ/inst/AQP7/hg38_AQP7_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MADSEQ/inst/AQP7/hs37d5_AQP7_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MADSEQ/inst/gap/hg19_gap_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MADSEQ/inst/gap/hg38_gap_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MADSEQ/inst/gap/hs37d5_gap_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MADSEQ/inst/HLA/hg19_HLA_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MADSEQ/inst/HLA/hg38_HLA_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MADSEQ/inst/HLA/hs37d5_HLA_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MADSEQ/data/aneuploidy_chr18.RData: load().. ok [1 object(s)]; updateObject(MadSeq, check=FALSE).. no match, no-op; nothing to update ==> 0
File maftools/inst/extdata/legacy_signatures.RDs: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File maftools/inst/extdata/protein_domains.RDs: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File maftools/inst/extdata/SBS_signatures.RDs: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MAGAR/inst/extdata/MethQTLResult_chr18/anno_geno.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGAR/inst/extdata/MethQTLResult_chr18/anno_meth.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGAR/inst/extdata/MethQTLResult_chr18/correlation_blocks.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MAGAR/inst/extdata/MethQTLResult_chr18/result_frame.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGAR/inst/extdata/reduced_methQTL/anno_geno.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGAR/inst/extdata/reduced_methQTL/anno_meth.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGAR/inst/extdata/reduced_methQTL/pheno_data.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGAR/inst/extdata/MethQTLResult_chr18/MethQTLResult.RData: load().. ok [1 object(s)]; updateObject(MethQTLResult, check=FALSE).. no match, no-op; nothing to update ==> 0
File MAGAR/inst/extdata/reduced_methQTL/MethQTLInput.RData: load().. ok [1 object(s)]; updateObject(MethQTLInput, check=FALSE).. no match, no-op; nothing to update ==> 0
File MAGeCKFlute/inst/extdata/corum.all.entrez.hsa.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/corum.all.entrez.mmu.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/GeneID_Annotation_hsa_mmu.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/GeneID_Annotation_hsa.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/GeneID_Annotation_mmu_hsa.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/GeneID_Annotation_mmu.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/go.all.entrez.hsa.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/go.all.entrez.mmu.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/HOM_GeneID_Annotation_mmu_hsa.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/kegg.all.entrez.hsa.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/kegg.all.entrez.mmu.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/ProteinID_Annotation_hsa.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/ProteinID_Annotation_mmu.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/reactome.all.entrez.hsa.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/reactome.all.entrez.mmu.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAGeCKFlute/inst/extdata/Zuber_Essential.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MAI/data/untargeted_LCMS_data.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File maigesPack/data/gastro.RData: load().. ok [5 object(s)]; updateObject(maigesPreRaw, check=FALSE).. no match, no-op; updateObject(maiges, check=FALSE).. no match, no-op; updateObject(maigesRaw, check=FALSE).. no match, no-op; updateObject(maigesRaw, check=FALSE).. no match, no-op; updateObject(maiges, check=FALSE).. no match, no-op; nothing to update ==> 0
File MAIT/data/MAIT_sample.RData: load().. ok [1 object(s)]; updateObject(MAIT, check=FALSE).. no match, no-op; nothing to update ==> 0
File MAIT/data/MAITtables.RData: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MAIT/vignettes/MAIT_objectAnn.RData: load().. ok [1 object(s)]; updateObject(MAIT, check=FALSE).. no match, no-op; nothing to update ==> 0
File MANOR/data/flags.RData: load().. ok [19 object(s)]; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; updateObject(flag, check=FALSE).. no match, no-op; nothing to update ==> 0
File MANOR/data/qscores.RData: load().. ok [10 object(s)]; updateObject(qscore, check=FALSE).. no match, no-op; updateObject(qscore, check=FALSE).. no match, no-op; updateObject(qscore, check=FALSE).. no match, no-op; updateObject(qscore, check=FALSE).. no match, no-op; updateObject(qscore, check=FALSE).. no match, no-op; updateObject(qscore, check=FALSE).. no match, no-op; updateObject(qscore, check=FALSE).. no match, no-op; updateObject(qscore, check=FALSE).. no match, no-op; updateObject(qscore, check=FALSE).. no match, no-op; updateObject(qscore, check=FALSE).. no match, no-op; nothing to update ==> 0
File MANOR/data/spatial.RData: load().. ok [4 object(s)]; updateObject(arrayCGH, check=FALSE).. no match, no-op; updateObject(arrayCGH, check=FALSE).. no match, no-op; updateObject(arrayCGH, check=FALSE).. no match, no-op; updateObject(arrayCGH, check=FALSE).. no match, no-op; nothing to update ==> 0
File MantelCorr/data/GolubTrain.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File marr/data/msprepCOPD.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File marray/data/swirl.RData: load().. ok [1 object(s)]; updateObject(marrayRaw, check=FALSE).. no match, no-op; nothing to update ==> 0
File martini/data/minigwas.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File martini/data/minippi.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File martini/data/minisnpMapping.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File martini/tests/testthat/examplegwas.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File maser/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File maSigPro/data/data.abiotic.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File maSigPro/data/edesign.abiotic.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File maSigPro/data/edesignCT.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File maSigPro/data/edesignDR.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File maSigPro/data/ISOdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File maSigPro/data/ISOdesign.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File maSigPro/data/NBdata.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File maSigPro/data/NBdesign.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File maskBAD/data/AffyBatch.rda: load().. ok [2 object(s)]; updateObject(AffyBatch, check=FALSE).. no match, no-op; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File maskBAD/data/exmask.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MassArray/data/MassArray.example.data.RData: load().. ok [1 object(s)]; updateObject(MassArrayData, check=FALSE).. returned an error ==> -1
File massiR/data/massi.eset.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File massiR/data/massi.test.dataset.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File massiR/data/massi.test.probes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File massiR/data/y.probes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MassSpecWavelet/data/exampleMS.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MAST/data/maits.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MAST/data/predicted_sig.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MAST/data/vbeta.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MAST/data/vbetaFA.RData: load().. ok [1 object(s)]; updateObject(FluidigmAssay, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File MAST/tests/testthat/SingleCellAssay-Object-MASTClassic.RData: load().. failed! ==> -2
File matchBox/data/matchBoxExpression.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File matter/data/matter_ex.rda: load().. ok [2 object(s)]; updateObject(bigglm, check=FALSE).. no match, no-op; updateObject(prcomp, check=FALSE).. no match, no-op; nothing to update ==> 0
File matter/data/matter_msi.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File matter/data/matter_sim.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MBCB/data/MBCBExpressionData.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MBQN/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MBttest/data/dat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MBttest/data/jkttcell.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MBttest/data/skjt.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MCbiclust/tests/testthat/ccle_bic.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MCbiclust/tests/testthat/ccle_cv.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File MCbiclust/tests/testthat/ccle_fork.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File MCbiclust/tests/testthat/ccle_pc1.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File MCbiclust/tests/testthat/ccle_ps.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File MCbiclust/tests/testthat/ccle_seed.rds: readRDS().. ok; updateObject(integer, check=FALSE).. no match, no-op ==> 0
File MCbiclust/tests/testthat/ccle_sort.rds: readRDS().. ok; updateObject(integer, check=FALSE).. no match, no-op ==> 0
File MCbiclust/data/CCLE_samples.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MCbiclust/data/CCLE_small.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MCbiclust/data/Mitochondrial_genes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File MCbiclust/R/sysdata.rda: load().. ok [7 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mCSEA/data/exprTest.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File mCSEA/data/precomputedmCSEA.rda: load().. ok [2 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mdp/data/example_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mdp/data/example_pheno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mdp/data/sample_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mdqc/data/allQC.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MDTS/inst/extdata/bins.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File MDTS/inst/extdata/counts.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MDTS/inst/extdata/pD.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEAT/data/CpGs_in_MEAT.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEAT/data/CpGs_in_MEAT2.0.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEAT/data/elasticnet_model_MEAT.rda: load().. ok [1 object(s)]; updateObject(elnet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEAT/data/elasticnet_model_MEAT2.0.rda: load().. ok [1 object(s)]; updateObject(elnet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEAT/data/gold.mean.MEAT.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEAT/data/gold.mean.MEAT2.0.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEAT/data/GSE121961_pheno.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEAT/data/GSE121961.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEB/data/real_data_dsp.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEB/data/real_data_sp.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEB/data/sim_data_dsp.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEB/data/sim_data_sp.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEDME/data/testMEDMEset.rda: load().. ok [1 object(s)]; updateObject(MEDMEset, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEIGOR/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MEIGOR/data/bayesFitExample.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEIGOR/data/CellNOptR_example.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEIGOR/data/CNORodeExample.RData: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(CNOlist, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MEIGOR/data/simpleExample.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Melissa/inst/extdata/encode-coef.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File Melissa/data/melissa_encode_dt.rda: load().. ok [1 object(s)]; updateObject(melissa_data_obj, check=FALSE).. no match, no-op; nothing to update ==> 0
File Melissa/data/melissa_synth_dt.rda: load().. ok [1 object(s)]; updateObject(melissa_data_obj, check=FALSE).. no match, no-op; nothing to update ==> 0
File memes/data/example_ame_large.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File memes/data/example_ame.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File memes/data/example_chip_summits.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File memes/data/example_dreme_by_binding.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File memes/data/example_dreme_tomtom.rda: load().. ok [1 object(s)]; updateObject(universalmotif_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File memes/data/example_dreme.rda: load().. ok [1 object(s)]; updateObject(universalmotif_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File memes/data/example_fimo.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File memes/data/example_peaks.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File memes/data/example_rnaseq.rda: load().. ok [1 object(s)]; updateObject(grouped_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File memes/data/example_tomtom.rda: load().. ok [1 object(s)]; updateObject(universalmotif_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File Mergeomics/data/job_kda_analyze.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File meshes/data/hsamd.rda: load().. ok [1 object(s)]; updateObject(GOSemSimDATA, check=FALSE).. no match, no-op; nothing to update ==> 0
File meshes/data/meshtbl.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MesKit/inst/extdata/signatures.cosmic.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MesKit/inst/extdata/signatures.etiology.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MesKit/inst/extdata/signatures.exome.cosmic.v3.may2019.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MesKit/inst/extdata/signatures.nature2013.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File messina/data/tcga_kirc_example.rda: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(Surv, check=FALSE).. no match, no-op; nothing to update ==> 0
File Metab/data/exampleAMDISReport.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Metab/data/exampleBiomass.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Metab/data/exampleHtest.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Metab/data/exampleIonLib.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Metab/data/exampleMetReport.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Metab/data/exampleMSLfile.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metabCombiner/data/metabBatches.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metabCombiner/data/plasma20.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metabCombiner/data/plasma30.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metabolomicsWorkbenchR/R/sysdata.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metabomxtr/data/euMetabCData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metabomxtr/data/euMetabData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metabomxtr/data/metabdata.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaboSignal/data/directionality_reactions.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaboSignal/data/hpaNormalTissue.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaboSignal/data/kegg_pathways.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaboSignal/data/keggNet_example.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaboSignal/data/mergedNet_example.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaboSignal/data/MetaboSignal_table.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaboSignal/data/ppiNet_example.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaboSignal/data/regulatory_interactions.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaCCA/data/testDataMetaCCA.rda: load().. ok [8 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene/data/promoters_hg18.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene/data/promoters_hg19.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene/data/promoters_mm10.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene/data/promoters_mm9.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(Bam_Handler, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene2/inst/extdata/fake_align1.sam.coverage_rpm.RData: load().. ok [1 object(s)]; updateObject(CompressedRleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene2/inst/extdata/fake_align1.sam.coverage.RData: load().. ok [1 object(s)]; updateObject(SimpleRleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene2/inst/extdata/fake_align1.sam.regions.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene2/inst/extdata/fake_align2.sam.coverage_rpm.RData: load().. ok [1 object(s)]; updateObject(CompressedRleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene2/inst/extdata/fake_align2.sam.coverage.RData: load().. ok [1 object(s)]; updateObject(SimpleRleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene2/inst/extdata/fake_align2.sam.regions.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene2/inst/extdata/fake_align3.sam.coverage_rpm.RData: load().. ok [1 object(s)]; updateObject(CompressedRleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene2/inst/extdata/fake_align3.sam.coverage.RData: load().. ok [1 object(s)]; updateObject(SimpleRleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagene2/inst/extdata/fake_align3.sam.regions.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagenomeSeq/inst/extdata/lungfit.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File metagenomeSeq/data/lungData.rda: load().. ok [1 object(s)]; updateObject(MRexperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File metagenomeSeq/data/mouseData.rda: load().. ok [1 object(s)]; updateObject(MRexperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File metahdep/data/gloss.rda: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File metahdep/data/HGU.DifExp.list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metahdep/data/HGU.newnames.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metahdep/data/HGU.prep.list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaMS/data/errf.RData: load().. ok [1 object(s)]; updateObject(lm, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaMS/data/exptable.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaMS/data/FEMsettings.RData: load().. ok [4 object(s)]; updateObject(metaMSsettings, check=FALSE).. no match, no-op; updateObject(metaMSsettings, check=FALSE).. no match, no-op; updateObject(metaMSsettings, check=FALSE).. no match, no-op; updateObject(metaMSsettings, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaMS/data/GCresults.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaMS/data/LCDBtest.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaMS/data/LCresults.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaMS/data/threeStdsDB.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaMS/data/threeStdsInfo.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaMS/data/threeStdsNIST.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaNeighbor/data/GOhuman.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaNeighbor/data/GOmouse.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaNeighbor/data/mn_data.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File metapone/data/hmdbCompMZ.metapone.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metapone/data/hmdbCompMZ.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metapone/data/neg.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File metapone/data/pa.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metapone/data/pos.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaSeq/data/BreastCancer.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaSeq/data/pvals.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaSeq/data/Result.Meta.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaSeq/data/StudyA.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaSeq/data/text.busca_unix.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaSeq/data/text.busca_win.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaSeq/data/text.n.menor_unix.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaSeq/data/text.n.menor_win.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaseqR2/data/hg19pvalues.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaseqR2/data/mm9GeneData.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metaseqR2/inst/extra/scvBiasCorrectionFits.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File metavizr/inst/extdata/loman.RData: load().. ok [1 object(s)]; updateObject(SimpleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File metavizr/inst/extdata/ZellerG_2014.RData: load().. ok [1 object(s)]; updateObject(SimpleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetaVolcanoR/data/diffexplist.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetCirc/data/convertExampleDF.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetCirc/data/convertMsp2Spectra.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetCirc/data/idMSMStissueproject.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetCirc/data/sd01_outputXCMS.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetCirc/data/sd02_deconvoluted.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetCirc/data/similarityMat.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetCirc/data/spectra.RData: load().. ok [1 object(s)]; updateObject(MSpectra, check=FALSE).. no match, no-op; nothing to update ==> 0
File methimpute/data/arabidopsis_chromosomes.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File methimpute/data/arabidopsis_genes.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File methimpute/data/arabidopsis_TEs.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File methimpute/data/arabidopsis_toydata.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File methInheritSim/vignettes/demo_runSim/meth_S1_1_3_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/meth_S1_1_3_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/meth_S1_1_6_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/meth_S1_1_6_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methDiff_S1_1_3_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methDiff_S1_1_3_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methDiff_S1_1_6_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methDiff_S1_1_6_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methylGR_S1_1_3_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methylGR_S1_1_3_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methylGR_S1_1_6_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methylGR_S1_1_6_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methylObj_S1_1_3_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methylObj_S1_1_3_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methylObj_S1_1_6_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/methylObj_S1_1_6_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/simData_S1_1_3_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/simData_S1_1_3_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/simData_S1_1_6_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/simData_S1_1_6_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/stateDiff_S1_1_3_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/stateDiff_S1_1_3_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/stateDiff_S1_1_6_0.9_0.8_0.5_1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/stateDiff_S1_1_6_0.9_0.8_0.5_2.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/syntheticChr_S1_1.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/treatment_S1_1_3.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File methInheritSim/vignettes/demo_runSim/treatment_S1_1_6.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File methInheritSim/data/dataSimExample.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File methInheritSim/data/samplesForChrSynthetic.RData: load().. ok [1 object(s)]; updateObject(methylBase, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethPed/data/MethPed_900probes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethPed/data/MethPed_sample.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethPed/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethReg/data/clinical.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethReg/data/dna.met.chr21.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethReg/data/gene.exp.chr21.log2.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethReg/R/sysdata.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File methrix/data/methrix_data.rda: load().. ok [1 object(s)]; updateObject(methrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethylAid/data/exampleData.RData: load().. ok [1 object(s)]; updateObject(summarizedData, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylCC/data/FlowSorted.Blood.450k.sub.RData: load().. ok [1 object(s)]; updateObject(RGChannelSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylCC/data/offMethRegions.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylCC/data/onMethRegions.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylclock/data/progress_data.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylclock/data/progress_vars.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylGSA/data/CpG2Genetoy.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylGSA/data/cpgtoy.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylGSA/data/GSlisttoy.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylInheritance/inst/extdata/methylObj_001.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/permutationResultsForSites.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/resultsForTransgenerationalAnalysis.RDS: readRDS().. ok; updateObject(methylInheritanceAllResults, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/observations/SITES/SITES_observed_results.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/permutations/SITES/SITES_permutation_1.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/permutations/SITES/SITES_permutation_10.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/permutations/SITES/SITES_permutation_2.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/permutations/SITES/SITES_permutation_3.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/permutations/SITES/SITES_permutation_4.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/permutations/SITES/SITES_permutation_5.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/permutations/SITES/SITES_permutation_6.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/permutations/SITES/SITES_permutation_7.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/permutations/SITES/SITES_permutation_8.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST_01/permutations/SITES/SITES_permutation_9.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST/SITES/SITES_observed_results.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST/SITES/SITES_permutation_1.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST/SITES/SITES_permutation_2.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST/SITES/SITES_permutation_3.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST/TILES/TILES_observed_results.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST/TILES/TILES_permutation_1.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST/TILES/TILES_permutation_2.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/inst/extdata/TEST/TILES/TILES_permutation_3.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/vignettes/demo_01/SITES/SITES_observed_results.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/vignettes/demo_02/SITES/SITES_permutation_1.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/vignettes/demo_02/SITES/SITES_permutation_2.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/vignettes/test_restart/TILES/TILES_observed_results.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/vignettes/test_restart/TILES/TILES_permutation_1.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/vignettes/test_restart/TILES/TILES_permutation_2.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylInheritance/data/demoForTransgenerationalAnalysis.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylInheritance/data/methylInheritanceResults.RData: load().. ok [1 object(s)]; updateObject(methylInheritanceAllResults, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylInheritance/data/samplesForTransgenerationalAnalysis.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylKit/data/methylKit.RData: load().. ok [3 object(s)]; updateObject(methylRawList, check=FALSE).. no match, no-op; updateObject(methylBase, check=FALSE).. no match, no-op; updateObject(methylDiff, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethylMix/data/BatchData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethylMix/data/GEcancer.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethylMix/data/METcancer.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethylMix/data/METnormal.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethylMix/data/ProbeAnnotation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MethylMix/data/SNPprobes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylPipe/inst/extdata/DMRs.Rdata: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylPipe/inst/extdata/gec.H1.Rdata: load().. ok [1 object(s)]; updateObject(GEcollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylPipe/inst/extdata/gec.IMR90.Rdata: load().. ok [1 object(s)]; updateObject(GEcollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylPipe/inst/extdata/GR_chr20.Rdata: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylPipe/inst/extdata/uncov_GR.Rdata: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylscaper/inst/extdata/singlecell_subset.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylscaper/inst/extdata/singlemolecule_example.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File methylscaper/data/human_bm.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylscaper/data/mouse_bm.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylscaper/data/reads_sm.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylscaper/data/ref_seq.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylscaper/data/singlecell_subset.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylscaper/data/singlemolecule_example.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylSig/data/bsseq_destranded.rda: load().. ok [1 object(s)]; updateObject(BSseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylSig/data/bsseq_multichrom.rda: load().. ok [1 object(s)]; updateObject(BSseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylSig/data/bsseq_stranded.rda: load().. ok [1 object(s)]; updateObject(BSseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylSig/data/promoters_gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylSig/R/sysdata.rda: load().. ok [25 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(BSseq, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylumi/data/CpGs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File methylumi/data/mldat.rda: load().. ok [1 object(s)]; updateObject(MethyLumiSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetID/data/demo1.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetID/data/demo2.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetID/data/InchiKey.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetID/data/kegg_network.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetNet/data/mat_test.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetNet/data/peaklist_example.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetNet/data/x_annotation.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MetNet/data/x_test.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Mfuzz/data/yeast.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MGFM/data/ds2.mat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MGFR/data/ref.mat.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File mgsa/data/example.rda: load().. ok [2 object(s)]; updateObject(MgsaSets, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File mia/data/dmn_se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File mia/data/enterotype.rda: load().. ok [1 object(s)]; updateObject(TreeSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File mia/data/esophagus.rda: load().. ok [1 object(s)]; updateObject(TreeSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File mia/data/GlobalPatterns.rda: load().. ok [1 object(s)]; updateObject(TreeSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File mia/data/soilrep.rda: load().. ok [1 object(s)]; updateObject(TreeSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File miaViz/data/col_graph.rda: load().. ok [1 object(s)]; updateObject(tbl_graph, check=FALSE).. no match, no-op; nothing to update ==> 0
File miaViz/data/row_graph_order.rda: load().. ok [1 object(s)]; updateObject(tbl_graph, check=FALSE).. no match, no-op; nothing to update ==> 0
File miaViz/data/row_graph.rda: load().. ok [1 object(s)]; updateObject(tbl_graph, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiome/data/atlas1006.rda: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiome/data/dietswap.rda: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiome/data/hitchip.taxonomy.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiome/data/peerj32.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiomeMarker/inst/extdata/dada2_seqtab.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File microbiomeMarker/inst/extdata/dada2_taxtab.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File microbiomeMarker/tests/testthat/data/data_tax_duplicate.rds: readRDS().. ok; updateObject(phyloseq, check=FALSE).. no match, no-op ==> 0
File microbiomeMarker/tests/testthat/data/generate_cladogram_annotation.rds: readRDS().. ok; updateObject(marker_table, check=FALSE).. no match, no-op ==> 0
File microbiomeMarker/data/caporaso.rda: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiomeMarker/data/cid_ying.rda: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiomeMarker/data/ecam.rda: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiomeMarker/data/enterotypes_arumugam.rda: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiomeMarker/data/kostic_crc.rda: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiomeMarker/data/oxygen.rda: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiomeMarker/data/pediatric_ibd.rda: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiomeMarker/data/spontaneous_colitis.rda: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File microbiomeMarker/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File MicrobiomeProfiler/data/microbiota_taxlist.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File MicrobiomeProfiler/data/Psoriasis_data.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File MicrobiomeProfiler/data/Rat_data.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File MicrobiomeProfiler/R/sysdata.rda: load().. ok [11 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File MicrobiotaProcess/inst/extdata/seqtab.nochim.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MicrobiotaProcess/inst/extdata/taxa_tab.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MicrobiotaProcess/data/hmp_aerobiosis_small.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MicrobiotaProcess/data/kostic2012crc.rda: load().. ok [1 object(s)]; updateObject(MPSE, check=FALSE).. no match, no-op; nothing to update ==> 0
File MicrobiotaProcess/data/mouse.time.mpse.rda: load().. ok [1 object(s)]; updateObject(MPSE, check=FALSE).. no match, no-op; nothing to update ==> 0
File MicrobiotaProcess/data/test_otu_data.rda: load().. ok [1 object(s)]; updateObject(MPSE, check=FALSE).. no match, no-op; nothing to update ==> 0
File microRNA/data/hsSeqs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File microRNA/data/hsTargets.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File microRNA/data/mmSeqs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File microRNA/data/mmTargets.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File microRNA/data/s3utr.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/data/allele_frequencies.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/data/dict_dist_grantham.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/data/kir_frequencies.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/data/MiDAS_tut_HLA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/data/MiDAS_tut_KIR.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/data/MiDAS_tut_object.rda: load().. ok [1 object(s)]; updateObject(MiDAS, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/data/MiDAS_tut_pheno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/inst/extdata/A_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/B_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/C_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DMA_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DMB_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DOA_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DOB_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DPA1_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DPB1_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DQA1_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DQB1_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DRA_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DRB1_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DRB3_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DRB4_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/DRB5_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/E_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/F_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/G_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/HFE_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/MICA_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/MICB_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/TAP1_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/TAP2_prot.Rdata: load().. failed! ==> -2
File midasHLA/inst/extdata/test_aa_variation.Rdata: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/inst/extdata/test_hla_analyze.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/inst/extdata/test_hla_calls_res.Rdata: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/inst/extdata/test_hla_calls.Rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File midasHLA/inst/extdata/test_hla_kir_interactions.Rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIGSA/data/bcMigsaRes.RData: load().. ok [1 object(s)]; updateObject(MIGSAres, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIGSA/data/migsaRes.RData: load().. ok [1 object(s)]; updateObject(MIGSAres, check=FALSE).. no match, no-op; nothing to update ==> 0
File miloR/data/sim_discrete.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File miloR/data/sim_trajectory.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIMOSA/data/ICS.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mina/data/hmp_des.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mina/data/hmp_otu.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File mina/data/maize_asv.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File mina/data/maize_asv2.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File mina/data/maize_des.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mina/data/maize_des2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mina/data/maize.rda: load().. ok [1 object(s)]; updateObject(mina, check=FALSE).. no match, no-op; nothing to update ==> 0
File MineICA/data/icaSetCarbayo.rda: load().. ok [1 object(s)]; updateObject(IcaSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File minet/data/syn.data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File minet/data/syn.net.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File minfi/inst/unitTests/digest_compartments.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File minfi/inst/unitTests/digest_preprocessFunnorm.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File minfi/inst/unitTests/digest_preprocessIllumina.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File minfi/inst/unitTests/digest_preprocessNoob.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File minfi/inst/unitTests/digest_preprocessQuantile.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File minfi/inst/unitTests/digest_preprocessRaw.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File minfi/inst/unitTests/digest_preprocessSWAN.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MinimumDistance/inst/extdata/md_granges.rds: readRDS().. ok; updateObject(MinDistGRanges, check=FALSE).. returned an error ==> -1
File MinimumDistance/inst/extdata/mdgr.rds: readRDS().. ok; updateObject(MinDistGRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File MinimumDistance/data/md_exp.rda: load().. ok [1 object(s)]; updateObject(MinDistExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File MinimumDistance/data/md_gr.rda: load().. ok [1 object(s)]; updateObject(MinDistGRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File MinimumDistance/data/trioSetListExample.rda: load().. ok [1 object(s)]; updateObject(TrioSetList, check=FALSE).. no match, no-op; nothing to update ==> 0
File MinimumDistance/inst/extdata/baf.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MinimumDistance/inst/extdata/logRratio.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MinimumDistance/inst/extdata/pedigreeInfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MinimumDistance/inst/extdata/pennCNV_MendelianProb.rda: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File MinimumDistance/inst/extdata/sample.sheet.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MinimumDistance/inst/extdata/trioSet12023chr12.rda: load().. ok [1 object(s)]; updateObject(TrioSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MinimumDistance/inst/scripts/logR.baf.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MiPP/data/colon.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MiPP/data/leukemia.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File miQC/data/hgsoc_metrics.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIRA/data/bigBinDT1.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIRA/data/bigBinDT2.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIRA/data/exampleAnnoDT1.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIRA/data/exampleAnnoDT2.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIRA/data/exampleBins.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIRA/data/exampleBSDT.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIRA/data/exampleBSseqObj.RData: load().. ok [1 object(s)]; updateObject(BSseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File MIRA/data/exampleRegionSet.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File MiRaGE/data/gene_exp.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRBaseConverter/data/miRNATest.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRBaseConverter/R/sysdata.rda: load().. ok [10 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRcomp/data/lifetech.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRcomp/data/qpcRb4.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRcomp/data/qpcRb5.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRcomp/data/qpcRdefault.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRcomp/data/qpcRl5.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRcomp/data/qpcRlinexp.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
Skip package mirIntegrator ==> -3
File miRLAB/inst/extdata/database.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRmine/data/miRmine.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRNAmeConverter/data/example-miRNAs.rdata: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRNApath/data/mirnaobj.rda: load().. ok [1 object(s)]; updateObject(mirnapath, check=FALSE).. no match, no-op; nothing to update ==> 0
File miRSM/data/BRCASampleData.rda: load().. ok [5 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. MATCH, object updated; updateObject(SummarizedExperiment, check=FALSE).. MATCH, object updated; updateObject(SummarizedExperiment, check=FALSE).. MATCH, object updated; updateObject(SummarizedExperiment, check=FALSE).. MATCH, object updated; updateObject(SummarizedExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File mirTarRnaSeq/data/Combine.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/corr_0.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/final_results.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/geneVariant.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/inter0.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/miRanda.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/miRandaM.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/miRNA_fc.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/miRNA_fc2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/miRNA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/miRNA0_2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/miRNA0_5.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/miRNA2_5.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/mRNA_fc.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/mRNA_fc2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/mRNA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/mRNA0_2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/mRNA0_5.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/mRNA2_5.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/outs.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/outs2.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/results.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/sig_corrs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/sig_InterR.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mirTarRnaSeq/data/some_model.rda: load().. ok [1 object(s)]; updateObject(glm, check=FALSE).. no match, no-op; nothing to update ==> 0
File missRows/data/NCI60.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File mistyR/data/synthetic.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitch/data/genesetsExample.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitch/data/k36a.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitch/data/k9a.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitch/data/myImportedData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitch/data/myList.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitch/data/resExample.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitch/data/rna.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitoClone2/inst/extdata/sample_example1.RDS: readRDS().. ok; updateObject(mutationCalls, check=FALSE).. no match, no-op ==> 0
File mitoClone2/data/M_P1.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitoClone2/data/M_P2.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitoClone2/data/N_P1.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitoClone2/data/N_P2.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitoClone2/inst/extdata/example_counts.Rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitoClone2/inst/extdata/LudwigFig7.Rda: load().. ok [1 object(s)]; updateObject(mutationCalls, check=FALSE).. no match, no-op; nothing to update ==> 0
File mitoClone2/R/sysdata.rda: load().. ok [10 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/breast.TCGA.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/breast.tumors.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/diverse.16S.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/Koren.16S.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/linnerud.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/liver.toxicity.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/multidrug.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/nutrimouse.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/srbct.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/stemcells.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/vac18.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/vac18.simulated.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/data/yeast.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mixOmics/inst/testdata/predict.mint.splsda.rda: load().. failed! ==> -2
File MLP/inst/exampleFiles/exampleGeneSet.rda: load().. ok [1 object(s)]; updateObject(geneSetMLP, check=FALSE).. no match, no-op; nothing to update ==> 0
File MLP/inst/exampleFiles/exampleMLPResult.rda: load().. ok [1 object(s)]; updateObject(MLP, check=FALSE).. no match, no-op; nothing to update ==> 0
File MLP/inst/exampleFiles/examplePValues.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File MLP/inst/exampleFiles/expressionSetGcrma.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MLSeq/data/cervical.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MLSeq/inst/extdata/availableModels.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File MLSeq/inst/extdata/modelDescriptions.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File MMAPPR2/tests/testthat/test_data/objects/post_calcdist_dummy_md.RDS: readRDS().. ok; updateObject(MmapprData, check=FALSE).. no match, no-op ==> 0
File MMAPPR2/tests/testthat/test_data/objects/post_loess_dummy_md.RDS: readRDS().. ok; updateObject(MmapprData, check=FALSE).. no match, no-op ==> 0
File MMAPPR2/tests/testthat/test_data/objects/post_peakref_dummy_md.RDS: readRDS().. ok; updateObject(MmapprData, check=FALSE).. no match, no-op ==> 0
File MMAPPR2/tests/testthat/test_data/objects/post_prepeak_dummy_md.RDS: readRDS().. ok; updateObject(MmapprData, check=FALSE).. no match, no-op ==> 0
File MMAPPR2/tests/testthat/test_data/objects/vep_flags.RDS: readRDS().. ok; updateObject(VEPFlags, check=FALSE).. no match, no-op ==> 0
File MMDiff2/data/Cfp1-Peaks.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File MMDiff2/data/mm9-Genes.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File MMDiff2/data/MMD.RData: load().. ok [1 object(s)]; updateObject(DBAmmd, check=FALSE).. no match, no-op; nothing to update ==> 0
File MMUPHin/data/CRC_abd.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MMUPHin/data/CRC_meta.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MMUPHin/data/vaginal_abd.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MMUPHin/data/vaginal_meta.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mnem/data/app.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File moanin/data/exampleData.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MODA/data/synthetic.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ModCon/data/cds.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ModCon/data/Codons.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ModCon/data/hbg.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ModCon/data/hex.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ModCon/R/sysdata.rda: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File Modstrings/data/MOD_RNA_DICT_MODOMICS.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Modstrings/data/MOD_RNA_DICT_TRNADB.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Modstrings/data/modsDNA.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Modstrings/data/modsRNA.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MOFA2/inst/extdata/test_data.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File mogsa/data/NCI60_4array_supdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File mogsa/data/NCI60_4arrays.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MOMA/data/example.gbm.mae.rda: load().. ok [1 object(s)]; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File MOMA/data/gbm.pathways.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MOMA/data/gene.map.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MOMA/data/mutSig.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File MOMA/R/sysdata.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File monaLisa/inst/extdata/atac_liver_vs_lung.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File monaLisa/inst/extdata/LMRsESNPmerged.gr.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File monaLisa/inst/extdata/results.binned_6mer_enrichment_LMRs.rds: readRDS().. ok; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File monaLisa/inst/extdata/results.binned_motif_enrichment_LMRs.rds: readRDS().. ok; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File monocle/data/spike_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File monocle/inst/extdata/lung_exprs_data.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File monocle/inst/extdata/lung_feature_data.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File monocle/inst/extdata/lung_phenotype_data.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/dataFilt.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/dataGRN.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/dataURA.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/DEGsmatrix.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/DiseaseList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/EAGenes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/GDCprojects.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/geneInfo.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/GEO_TCGAtab.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/knownDriverGenes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/listMoonlight.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MoonlightR/data/tabGrowBlock.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mosaics/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MOSim/data/sampleData.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/data/encodemotif.rda: load().. ok [1 object(s)]; updateObject(MotifList, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/data/example.pvalue.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/data/example.results.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/data/factorbook.rda: load().. ok [1 object(s)]; updateObject(MotifList, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/data/hocomoco.rda: load().. ok [1 object(s)]; updateObject(MotifList, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/data/homer.rda: load().. ok [1 object(s)]; updateObject(MotifList, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/data/motifbreakR_motif.rda: load().. ok [1 object(s)]; updateObject(MotifList, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/inst/example.pvalue.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/inst/extdata/example.pvalue.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/inst/extdata/example.snpfrombed.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifbreakR/inst/extdata/pca.enhancer.snps.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/cisbp.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/flyFactorSurvey.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/hocomoco10.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/hocomoco11.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/homer.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/hPDI.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/jaspar.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/jaspar2014.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/jaspar2016.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/jaspar2018.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/jolma2013.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/ScerTF.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/stamlab.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/SwissRegulon.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/tfs/tfs-1683-lambert.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/extdata/uniprobe.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/scripts/import/fbgns.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/scripts/import/jaspar2018/metaData.Rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/unitTests/single_matrices/cisbp_matrix.Rdata: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MotifDb/inst/unitTests/single_matrices/uniprobe_matrix.Rdata: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File motifmatchr/data/example_motifs.rda: load().. ok [1 object(s)]; updateObject(PFMatrixList, check=FALSE).. no match, no-op; nothing to update ==> 0
File MPFE/data/patternsExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File mpra/data/mpraSetAggExample.rda: load().. ok [1 object(s)]; updateObject(MPRASet, check=FALSE).. no match, no-op; nothing to update ==> 0
File mpra/data/mpraSetAllelicExample.rda: load().. ok [1 object(s)]; updateObject(MPRASet, check=FALSE).. no match, no-op; nothing to update ==> 0
File mpra/data/mpraSetExample.rda: load().. ok [1 object(s)]; updateObject(MPRASet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MPRAnalyze/data/ChrEpi.rda: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(logical, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MsFeatures/data/se.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File MsFeatures/inst/extdata/cors.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File msgbsR/data/cuts.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File msgbsR/data/ratdata.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File msgbsR/data/ratdata2.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File msImpute/data/pxd007959.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File msImpute/data/pxd010943.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File msImpute/data/pxd014777.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File msmsEDA/data/msms.dataset.rda: load().. ok [1 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File msmsEDA/data/pnms.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File msmsTests/data/msms.spk.rda: load().. ok [1 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/iTRAQ4.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/iTRAQ5.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/iTRAQ8.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/iTRAQ9.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/itraqdata.RData: load().. ok [1 object(s)]; updateObject(MSnExp, check=FALSE).. returned an error ==> -1
File MSnbase/data/msnset.rda: load().. ok [1 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/msnset2.rda: load().. ok [1 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/naset.rda: load().. ok [1 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT10.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT10ETD.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT10HCD.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT11.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT11HCD.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT16.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT16HCD.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT6.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT6b.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT7.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/data/TMT7b.RData: load().. ok [1 object(s)]; updateObject(ReporterIons, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/inst/extdata/ipqfres.rda: load().. ok [5 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; updateObject(MSnSet, check=FALSE).. no match, no-op; updateObject(MSnSet, check=FALSE).. no match, no-op; updateObject(MSnSet, check=FALSE).. no match, no-op; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/inst/extdata/M.rda: load().. ok [1 object(s)]; updateObject(MSmap, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/inst/extdata/M2.rda: load().. ok [1 object(s)]; updateObject(MSmap, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSnbase/inst/extdata/msx.rda: load().. ok [1 object(s)]; updateObject(MSnExp, check=FALSE).. returned an error ==> -1
File MSnbase/inst/extdata/msx0.rda: load().. ok [1 object(s)]; updateObject(MSnExp, check=FALSE).. returned an error ==> -1
File MSnID/data/c_elegans.RData: load().. ok [1 object(s)]; updateObject(MSnID, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSPrep/data/COPD_131.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSPrep/data/msquant.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File msPurity/inst/extdata/iwqe5.rds: readRDS().. ok; updateObject(lm, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/1_purityA_pa_OLD.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/1_purityA_pa.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/10_input_filterflagremove.rds: readRDS().. ok; updateObject(XCMSnExp, check=FALSE).. returned an error ==> -1
File msPurity/inst/extdata/tests/purityA/2_frag4feature_pa_OLD.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/2_frag4feature_pa.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/3_filterFragSpectra_pa_OLD.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/3_filterFragSpectra_pa.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/4_averageIntraFragSpectra_no_filter_pa_OLD.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/4_averageIntraFragSpectra_no_filter_pa.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/5_averageInterFragSpectra_no_filter_pa_OLD.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/5_averageInterFragSpectra_no_filter_pa.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/6_averageAllFragSpectra_no_filter_pa_OLD.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/6_averageAllFragSpectra_no_filter_pa.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/7_averageIntraFragSpectra_with_filter_pa_OLD.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/7_averageIntraFragSpectra_with_filter_pa.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/8_averageInterFragSpectra_with_filter_pa_OLD.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/8_averageInterFragSpectra_with_filter_pa.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/9_averageAllFragSpectra_with_filter_pa_OLD.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityA/9_averageAllFragSpectra_with_filter_pa.rds: readRDS().. ok; updateObject(purityA, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityX/1_purityX_grouped_px.rds: readRDS().. ok; updateObject(purityX, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/purityX/1_purityX_single_px.rds: readRDS().. ok; updateObject(purityX, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/xcms/ms_only_xcmsnexp.rds: readRDS().. ok; updateObject(XCMSnExp, check=FALSE).. returned an error ==> -1
File msPurity/inst/extdata/tests/xcms/ms_only_xset_OLD.rds: readRDS().. ok; updateObject(xcmsSet, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/xcms/msms_only_xcmsnexp.rds: readRDS().. ok; updateObject(XCMSnExp, check=FALSE).. returned an error ==> -1
File msPurity/inst/extdata/tests/xcms/msms_only_xset_OLD.rds: readRDS().. ok; updateObject(xcmsSet, check=FALSE).. no match, no-op ==> 0
File msPurity/inst/extdata/tests/xcms/msms_only_xset.rds: readRDS().. ok; updateObject(xcmsSet, check=FALSE).. no match, no-op ==> 0
File msqrob2/data/pe.RData: load().. ok [1 object(s)]; updateObject(QFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstats/data/DDARawData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstats/data/DDARawData.Skyline.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstats/data/DIARawData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstats/data/SRMRawData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsLiP/data/LiPRawData.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsLiP/data/model_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsLiP/data/MSstatsLiP_formatted_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsLiP/data/SkylineTest.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsLiP/data/summarized_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsLiP/data/TrPRawData.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsLOBD/data/raw_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsLOBD/data/spikeindata.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsPTM/data/raw.input.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsPTM/data/raw.input.tmt.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsPTM/data/summary.data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsPTM/data/summary.data.tmt.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsQC/data/QCloudDDA.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsQC/data/QCloudSRM.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsQC/data/QuiCDIA.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsQC/data/S9Site54.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsQCgui/data/S9Site54.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsSampleSize/data/classification_results.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsSampleSize/data/OV_SRM_train_annotation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsSampleSize/data/OV_SRM_train.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsSampleSize/data/simulated_datasets.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsSampleSize/data/variance_estimation.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/annotation.mine.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/annotation.mq.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/annotation.pd.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/evidence.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/input.pd.rda: load().. ok [1 object(s)]; updateObject(MSstatsValidated, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/proteinGroups.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/quant.pd.msstats.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/raw.mine.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/raw.om.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/raw.pd.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File MSstatsTMT/data/test.pairwise.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Mulcom/data/benchVign.rda: load().. ok [2 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Mulcom/data/others.rda: load().. ok [5 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File MultiAssayExperiment/data/miniACC.RData: load().. ok [1 object(s)]; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File MultiBaC/Meta/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MultiBaC/data/multiyeast.rda: load().. ok [6 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MultiDataSet/data/rset.rda: load().. ok [1 object(s)]; updateObject(ResultSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiGSEA/data/metabolome.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiGSEA/data/proteome.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiGSEA/data/transcriptome.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiHiCcompare/data/HCT116_r1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiHiCcompare/data/HCT116_r2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiHiCcompare/data/HCT116_r3.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiHiCcompare/data/HCT116_r4.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiHiCcompare/data/HCT116_r5.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiHiCcompare/data/HCT116_r6.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiHiCcompare/data/hg19_cyto.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File multiHiCcompare/data/hg38_cyto.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File multiHiCcompare/data/hicexp_diff.rda: load().. ok [1 object(s)]; updateObject(Hicexp, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiHiCcompare/data/hicexp2.rda: load().. ok [1 object(s)]; updateObject(Hicexp, check=FALSE).. returned an error ==> -1
File MultiMed/data/NavyAdenoma.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiMiR/inst/extdata/counts_table.Rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File multiMiR/inst/extdata/strains_factor.Rds: readRDS().. ok; updateObject(factor, check=FALSE).. no match, no-op ==> 0
File multiSight/data/biosignerRes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiSight/data/deseqRes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiSight/data/diabloRes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiSight/data/enrichResList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiSight/data/omic2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiSight/data/runMultiEnrichment_result.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File multiSight/R/sysdata.rda: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(block.splsda, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File multtest/data/golub.RData: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MungeSumstats/data/sumstatsColHeaders.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File MungeSumstats/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File muscat/data/example_sce.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File muscle/data/umax.rda: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File musicatk/data/cosmic_v2_sigs.rda: load().. ok [1 object(s)]; updateObject(musica_result, check=FALSE).. no match, no-op; nothing to update ==> 0
File musicatk/data/cosmic_v3_dbs_sigs.rda: load().. ok [1 object(s)]; updateObject(musica_result, check=FALSE).. returned an error ==> -1
File musicatk/data/cosmic_v3_indel_sigs.rda: load().. ok [1 object(s)]; updateObject(musica_result, check=FALSE).. returned an error ==> -1
File musicatk/data/cosmic_v3_sbs_sigs_exome.rda: load().. ok [1 object(s)]; updateObject(musica_result, check=FALSE).. returned an error ==> -1
File musicatk/data/cosmic_v3_sbs_sigs.rda: load().. ok [1 object(s)]; updateObject(musica_result, check=FALSE).. returned an error ==> -1
File musicatk/data/dbs_musica.rda: load().. ok [1 object(s)]; updateObject(musica, check=FALSE).. no match, no-op; nothing to update ==> 0
File musicatk/data/indel_musica.rda: load().. ok [1 object(s)]; updateObject(musica, check=FALSE).. no match, no-op; nothing to update ==> 0
File musicatk/data/musica_annot.rda: load().. ok [1 object(s)]; updateObject(musica, check=FALSE).. no match, no-op; nothing to update ==> 0
File musicatk/data/musica_sbs96_tiny.rda: load().. ok [1 object(s)]; updateObject(musica, check=FALSE).. no match, no-op; nothing to update ==> 0
File musicatk/data/musica_sbs96.rda: load().. ok [1 object(s)]; updateObject(musica, check=FALSE).. no match, no-op; nothing to update ==> 0
File musicatk/data/musica.rda: load().. ok [1 object(s)]; updateObject(musica, check=FALSE).. no match, no-op; nothing to update ==> 0
File musicatk/data/rep_range.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File musicatk/data/res_annot.rda: load().. ok [1 object(s)]; updateObject(musica_result, check=FALSE).. returned an error ==> -1
File musicatk/data/res.rda: load().. ok [1 object(s)]; updateObject(musica_result, check=FALSE).. returned an error ==> -1
File MutationalPatterns/inst/states/blood_dbs_counts.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/blood_grl_dbs_context.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/blood_grl_dbs.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/blood_grl_indel_context.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/blood_grl_indel.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/blood_grl_mbs.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/blood_grl.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File MutationalPatterns/inst/states/blood_indel_counts.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/blood_indels_counts_split_region.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/blood_indels_longmatrix_split_region.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/blood_mbs_counts.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/blosum62.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/bootstrapped_snv_refit.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/context_mismatches.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/CTCF_g_data.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/dbs_refit.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/distr_data.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/grl_split_region.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/indel_refit.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/lesion_segregation.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/mut_mat_data_extended.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/mut_mat_data.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/mut_mat_longregions.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/mut_mat_repli.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/mut_mat_s_data.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/mut_mat_splitregions.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/nmf_res_data.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/nmf_res_strand_data.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/promoter_flanking_g_data.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/promoter_g_data.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/read_vcfs_as_granges_output.rds: readRDS().. ok; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/regional_sims.rds: readRDS().. ok; updateObject(region_cossim, check=FALSE).. returned an error ==> -1
File MutationalPatterns/inst/states/regulatory_data.rds: readRDS().. ok; updateObject(Mart, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/repli_strand.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/snv_refit.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/strict_best_snv_refit.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MutationalPatterns/inst/states/strict_snv_refit.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File MWASTools/data/KEGG_metabolic_paths.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File MWASTools/data/metabo_SE.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File MWASTools/data/MS_data.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File MWASTools/data/targetMetabo_SE.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File mygene/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File NADfinder/inst/extdata/ideo.mm10.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File NADfinder/data/single.count.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File NADfinder/data/triplicate.count.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File NanoStringDiff/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File NanoStringDiff/data/NanoStringData.rda: load().. ok [1 object(s)]; updateObject(NanoStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File NanoStringQCPro/data/example_rccSet.rdata: load().. ok [1 object(s)]; updateObject(RccSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File NanoTube/data/ExamplePathways.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File NanoTube/data/ExampleResults.rda: load().. ok [1 object(s)]; updateObject(MArrayLM, check=FALSE).. no match, no-op; nothing to update ==> 0
File NBSplice/data/designMatrix.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NBSplice/data/geneIso.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NBSplice/data/isoCounts.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NBSplice/data/myDSResults.rda: load().. ok [1 object(s)]; updateObject(NBSpliceRes, check=FALSE).. no match, no-op; nothing to update ==> 0
File NBSplice/data/myIsoDataSet.rda: load().. ok [1 object(s)]; updateObject(IsoDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File ncGTW/data/xcmsExamples.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File NCIgraph/data/NCIgraphVignette.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ndexr/Meta/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File nearBynding/inst/extdata/transcript_list.Rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File NeighborNet/inst/extdata/dataColorectal21510.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NeighborNet/inst/extdata/dataColorectal32323.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NeighborNet/inst/extdata/dataColorectal4183.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NeighborNet/inst/extdata/dataColorectal8671.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NeighborNet/inst/extdata/dataColorectal9348.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NeighborNet/inst/extdata/listofgenes.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netbiov/data/artificial1.graph.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File netbiov/data/artificial2.graph.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File netbiov/data/color_list.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netbiov/data/gnet_bcell.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File netbiov/data/modules_bcell.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netbiov/data/modules_PPI_Athalina.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netbiov/data/PPI_Athalina.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File netboost/data/tcga_aml_meth_rna_chr18.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netboxr/data/netbox2010.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netboxr/data/pathway_commons_v8_reactome.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/cnv_GR.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/cnv_netPass.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/cnv_netScores.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/cnv_patientNetCount.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/cnv_pheno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/cnv_TTstatus.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/confmat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/featScores.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/genes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/MB.pheno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/modelres.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/npheno.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/pathway_GR.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/pathwayList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/pheno_full.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/pheno.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/predRes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/silh.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/toymodel.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netDx/data/xpr.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File netOmics/data/hmp_T2D.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File NetPathMiner/data/ex_biopax.rda: load().. ok [1 object(s)]; updateObject(biopax, check=FALSE).. no match, no-op; nothing to update ==> 0
File NetPathMiner/data/ex_kgml_sig.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File NetPathMiner/data/ex_microarray.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File NetPathMiner/data/ex_sbml.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File NetPathMiner/inst/extdata/env_data.RData: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netprioR/data/simulation.rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netresponse/data/dna.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netresponse/data/osmo.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netresponse/data/toydata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File NetSAM/data/NetSAMOutput_Example.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File netSmooth/data/human.ppi.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File netSmooth/data/mouse.ppi.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File netSmooth/data/smallPPI.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File netSmooth/data/smallscRNAseq.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File networkBMA/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File networkBMA/data/dream4.rda: load().. ok [6 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File networkBMA/data/vignette.rda: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netZooR/data/exon.size.RData: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File netZooR/data/genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File netZooR/data/monsterRes.RData: load().. ok [1 object(s)]; updateObject(monsterAnalysis, check=FALSE).. no match, no-op; nothing to update ==> 0
File netZooR/data/mut.ucec.RData: load().. ok [1 object(s)]; updateObject(table, check=FALSE).. no match, no-op; nothing to update ==> 0
File netZooR/data/small1976.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File netZooR/data/yeast.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File NeuCA/data/Baron_scRNA.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File NeuCA/data/Seg_scRNA.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ngsReports/data/gcTheoretical.RData: load().. ok [1 object(s)]; updateObject(TheoreticalGC, check=FALSE).. no match, no-op; nothing to update ==> 0
File NOISeq/data/Marioni.RData: load().. ok [6 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File NOISeq/data/myCounts.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File NOISeq/data/noiseq.RData: load().. ok [1 object(s)]; updateObject(Output, check=FALSE).. no match, no-op; nothing to update ==> 0
File nondetects/data/nature2008.rda: load().. ok [1 object(s)]; updateObject(qPCRset, check=FALSE).. no match, no-op; nothing to update ==> 0
File nondetects/data/oncogene2013.rda: load().. ok [1 object(s)]; updateObject(qPCRset, check=FALSE).. no match, no-op; nothing to update ==> 0
File nondetects/data/sagmb2011.rda: load().. ok [1 object(s)]; updateObject(qPCRset, check=FALSE).. no match, no-op; nothing to update ==> 0
File NoRCE/data/brain_disorder_ncRNA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NoRCE/data/brain_mirna.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NoRCE/data/breastmRNA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NoRCE/data/mirna.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File NoRCE/data/mrna.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NoRCE/data/ncRegion.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NoRCE/data/tad_dmel.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File NoRCE/data/tad_hg19.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File NoRCE/data/tad_hg38.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File NoRCE/data/tad_mm10.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File normalize450K/R/sysdata.rda: load().. ok [5 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_data_only_values_small.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_data_only_values.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_data_small.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_data.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_design_small.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_design.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_stat_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_stat_summarized_experiment.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_summarized_experiment.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_wide_data.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormalyzerDE/data/example_wide_design.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormqPCR/data/Bladder.RData: load().. ok [1 object(s)]; updateObject(qPCRBatch, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormqPCR/data/BladderRepro.RData: load().. ok [1 object(s)]; updateObject(qPCRBatch, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormqPCR/data/Colon.RData: load().. ok [1 object(s)]; updateObject(qPCRBatch, check=FALSE).. no match, no-op; nothing to update ==> 0
File NormqPCR/data/geNorm.RData: load().. ok [1 object(s)]; updateObject(qPCRBatch, check=FALSE).. no match, no-op; nothing to update ==> 0
File normr/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File NPARC/data/stauro_TPP_data_tidy.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File NTW/data/sos.data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File nucleR/data/nucleosome_htseq.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File nucleR/data/nucleosome_tiling.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File nuCpos/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File nuCpos/inst/extdata/INSEQ_DNAString.RData: load().. ok [1 object(s)]; updateObject(DNAString, check=FALSE).. no match, no-op; nothing to update ==> 0
File nuCpos/inst/extdata/inseq.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File nuCpos/R/sysdata.rda: load().. ok [60 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File NuPoP/R/sysdata.rda: load().. ok [47 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File NxtIRFcore/inst/extdata/example_NxtSE.Rds: readRDS().. ok; updateObject(NxtSE, check=FALSE).. no match, no-op ==> 0
File ODER/data/gtex_SRP012682_SRX222703_lung_auc_1.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File ODER/data/gtex_SRP012682_SRX222703_lung_coverage_1.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ODER/data/gtex_SRP012682_SRX222703_lung_erdelta_1.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ODER/data/gtex_SRP012682_SRX222703_lung_ers_1.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ODER/data/lung_junc_21_22.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ODER/data/pseudogene.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ODER/data/tissue_options.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File odseq/data/seqs.RData: load().. ok [1 object(s)]; updateObject(AAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File OGRE/inst/extdata/query/genes.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File OGRE/inst/extdata/subject/CGI.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File OGRE/inst/extdata/subject/TFBS.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File oligo/inst/unitTests/fids_ref0.rda: load().. ok [6 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File oligo/inst/unitTests/i0.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File oligo/inst/unitTests/rma_ref0.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File oligoClasses/inst/extdata/genomeAnnotatedDataFrameExample.rds: readRDS().. ok; updateObject(GenomeAnnotatedDataFrame, check=FALSE).. no match, no-op ==> 0
File oligoClasses/data/efsExample.rda: load().. ok [1 object(s)]; updateObject(ExpressionFeatureSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File oligoClasses/data/locusLevelData.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File oligoClasses/data/oligoSetExample.rda: load().. ok [1 object(s)]; updateObject(oligoSnpSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File oligoClasses/data/scqsExample.rda: load().. ok [1 object(s)]; updateObject(SnpCnvQSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File oligoClasses/data/sfsExample.rda: load().. ok [1 object(s)]; updateObject(SnpFeatureSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File oligoClasses/data/sqsExample.rda: load().. ok [1 object(s)]; updateObject(SnpQSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File oligoClasses/inst/extdata/gap_hg18.rda: load().. failed! ==> -2
File oligoClasses/inst/extdata/gap_hg19.rda: load().. failed! ==> -2
File oligoClasses/inst/extdata/seqlengths_hg18.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File oligoClasses/inst/extdata/seqlengths_hg19.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File OLIN/data/sw.olin.RData: load().. ok [1 object(s)]; updateObject(marrayNorm, check=FALSE).. no match, no-op; nothing to update ==> 0
File OLIN/data/sw.RData: load().. ok [1 object(s)]; updateObject(marrayRaw, check=FALSE).. no match, no-op; nothing to update ==> 0
File OLIN/data/sw.xy.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmaDB/data/group.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmaDB/data/hog.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmaDB/data/orthologs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmaDB/data/pairs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmaDB/data/protein.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmaDB/data/sequence_annotation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmaDB/data/sequence_map.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmaDB/data/taxonomy.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmaDB/data/xref.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File omicade4/data/NCI60_4arrays.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/TCGA.BC_Her2_cnv_exp.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/TCGA.BC.cnv.2k.60.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/TCGA.BC.fus.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/TCGA.BC.gene.exp.2k.60.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/TCGA.BC.sample60.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/TCGA.PAM50_genefu_hg18.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/UCSC.chr.colors.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/UCSC.hg18.chr.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/UCSC.hg18.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/UCSC.hg19.chr.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/UCSC.hg19.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/UCSC.mm10.chr.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/UCSC.mm10.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/UCSC.mm9.chr.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicCircos/data/UCSC.mm9.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File omicplotR/data/metadata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File omicplotR/data/otu_table.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File omicRexposome/data/asr.rda: load().. ok [1 object(s)]; updateObject(ResultSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File omicRexposome/data/crs.rda: load().. ok [1 object(s)]; updateObject(ResultSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File omicRexposome/data/mds.rda: load().. ok [1 object(s)]; updateObject(MultiDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmicsLonDA/data/omicslonda_data_example.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File omicsPrint/data/hg19.GoNLsnps.RData: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File omicsPrint/data/hm450.manifest.pop.GoNL.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File Omixer/vignettes/randomSeed.Rdata: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File Omixer/vignettes/sampleList.Rdata: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File OmnipathR/docs/reference/nichenet_results/networks.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File OmnipathR/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File Onassis/inst/extdata/list_of_annotations.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/Options_table.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/sample_granges.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/experiment_types.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/GEO_human_chip.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/GEOmethylation.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/h3k27ac_metadata.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/methylation_brenda_annot.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/organisms.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/pairwise_results.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/performances.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/samples_similarity.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/score_matrix.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File Onassis/inst/extdata/vignette_data/target_entities.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File oncomix/data/exprNmlIsof.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File oncomix/data/exprTumIsof.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File oncomix/data/queryRes.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoScore/data/genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoScore/data/query.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoScore/data/query.timepoints.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoScore/data/timepoints.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/data/benchmark_1_0.05.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/data/benchmark_1.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/data/benchmark_2.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/data/benchmark_3.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/data/ex_missing_drivers_b11.RData: load().. ok [1 object(s)]; updateObject(oncosimul, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/data/ex_missing_drivers_b12.RData: load().. ok [1 object(s)]; updateObject(oncosimul, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/data/examplePosets.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/data/examplesFitnessEffects.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/data/mcfLs.RData: load().. ok [1 object(s)]; updateObject(oncosimul, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/data/woAntibS.RData: load().. ok [1 object(s)]; updateObject(oncosimul, check=FALSE).. no match, no-op; nothing to update ==> 0
File OncoSimulR/inst/testdata_fee.RData: load().. ok [2 object(s)]; updateObject(fitnessEffects, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File oneSENSE/inst/extdata/myFFdatas.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File ontoProc/data/allGOterms.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ontoProc/data/humrna.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ontoProc/data/minicorpus.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ontoProc/data/packDesc2019.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ontoProc/data/PROSYM.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ontoProc/data/stopWords.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ontoProc/inst/app/extcl.rda: load().. ok [1 object(s)]; updateObject(ontology_index, check=FALSE).. no match, no-op; nothing to update ==> 0
File ontoProc/inst/ontoRda/cellOnto.rda: load().. ok [1 object(s)]; updateObject(ontology_index, check=FALSE).. no match, no-op; nothing to update ==> 0
File ontoProc/inst/ontoRda/co_0718.rda: load().. ok [1 object(s)]; updateObject(ontology_index, check=FALSE).. no match, no-op; nothing to update ==> 0
File openCyto/tests/testthat/expectResults.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File openCyto/tests/testthat/gatingResults.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File openPrimeR/data/Comparison.rda: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(DesignSettings, check=FALSE).. returned an error ==> -1
File openPrimeR/data/Ippolito.rda: load().. ok [3 object(s)]; updateObject(Primers, check=FALSE).. no match, no-op; updateObject(Templates, check=FALSE).. no match, no-op; updateObject(DesignSettings, check=FALSE).. returned an error ==> -1
File openPrimeR/data/RefCoverage.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File openPrimeR/data/Tiller.rda: load().. ok [3 object(s)]; updateObject(Primers, check=FALSE).. no match, no-op; updateObject(Templates, check=FALSE).. no match, no-op; updateObject(DesignSettings, check=FALSE).. returned an error ==> -1
File openPrimeR/R/sysdata.rda: load().. ok [6 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(glm, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
Skip package oposSOM ==> -3
File oppar/data/GSE46141.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File oppar/data/Maupin.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File oppar/data/tomlins.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File OrderedList/data/OL.data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OrderedList/data/OL.result.rda: load().. ok [1 object(s)]; updateObject(OrderedList, check=FALSE).. no match, no-op; nothing to update ==> 0
File ORFhunteR/inst/extdata/cl_model.rds: readRDS().. ok; updateObject(NULL, check=FALSE).. no match, no-op ==> 0
File ORFik/inst/extdata/Danio_rerio_sample/pshifted/shifting_table.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File ORFik/inst/extdata/Danio_rerio_sample/QC_STATS/countTable_mrna.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File ORFik/inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_cds.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File ORFik/inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_leaders.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File ORFik/inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_mrna.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File ORFik/inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_trailers.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File ORFik/inst/extdata/features.rdata: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File orthogene/data/exp_mouse_enst.rda: load().. ok [1 object(s)]; updateObject(dgeMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File orthogene/data/exp_mouse.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File orthogene/data/gprofiler_orgs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File orthogene/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File OSAT/data/example.setup.RData: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(gContainer, check=FALSE).. returned an error ==> -1
File OSAT/data/predefined.RData: load().. ok [7 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(BeadChip, check=FALSE).. no match, no-op; updateObject(BeadChip, check=FALSE).. no match, no-op; updateObject(BeadPlate, check=FALSE).. no match, no-op; updateObject(BeadPlate, check=FALSE).. no match, no-op; updateObject(BeadPlate, check=FALSE).. no match, no-op; updateObject(MSAroboticPlate, check=FALSE).. no match, no-op; nothing to update ==> 0
File Oscope/data/OscopeExampleData.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File OVESEG/data/countBT.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File OVESEG/data/RocheBT.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PAA/inst/extdata/Alzheimer.RData: load().. ok [1 object(s)]; updateObject(EListRaw, check=FALSE).. no match, no-op; nothing to update ==> 0
File PAA/inst/extdata/AlzheimerControls.RData: load().. ok [1 object(s)]; updateObject(EListRaw, check=FALSE).. no match, no-op; nothing to update ==> 0
File PAA/inst/extdata/BadData.RData: load().. ok [1 object(s)]; updateObject(EListRaw, check=FALSE).. no match, no-op; nothing to update ==> 0
File PAA/inst/extdata/DummyData.RData: load().. ok [1 object(s)]; updateObject(EListRaw, check=FALSE).. no match, no-op; nothing to update ==> 0
File PAA/inst/extdata/selectFeaturesResultsEns.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PAA/inst/extdata/selectFeaturesResultsFreq.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File packFinder/data/arabidopsisThalianaRefseq.rda: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File packFinder/data/packMatches.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File packFinder/tests/testthat/data-r/consensusSeqs.rda: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File padma/data/LUAD_subset.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File padma/data/mirtarbase.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File padma/data/msigdb.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File paircompviz/data/brokentrans.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pairkat/data/smokers.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File pandaR/data/pandaResult.rda: load().. ok [1 object(s)]; updateObject(panda, check=FALSE).. no match, no-op; nothing to update ==> 0
File pandaR/data/pandaResultPairs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pandaR/data/pandaToyData.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File panelcn.mops/data/panelcn.mops.rda: load().. ok [5 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File panp/data/gcrma.ExpressionSet.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File panp/data/NSMPnames.hgu133a.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File panp/data/NSMPnames.hgu133plus2.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File PANR/data/Bakal2007.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File PANR/data/Bakal2007Cluster.RData: load().. ok [2 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File PANR/data/bm.RData: load().. ok [1 object(s)]; updateObject(BetaMixture, check=FALSE).. no match, no-op; nothing to update ==> 0
File parody/data/bushfire.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File parody/data/tcost.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Path2PPI/data/ai.rda: load().. ok [6 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathifier/data/KEGG.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathifier/data/Sheffer.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PathoStat/data/asthma_pstat_data.rda: load().. ok [1 object(s)]; updateObject(PathoStat, check=FALSE).. no match, no-op; nothing to update ==> 0
File PathoStat/data/pstat_data_2_L1.rda: load().. ok [1 object(s)]; updateObject(PathoStat, check=FALSE).. no match, no-op; nothing to update ==> 0
File PathoStat/data/pstat_data_2_L2.rda: load().. ok [1 object(s)]; updateObject(PathoStat, check=FALSE).. no match, no-op; nothing to update ==> 0
File PathoStat/data/pstat_data.rda: load().. ok [1 object(s)]; updateObject(PathoStat, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathVar/data/bock.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathVar/data/pways.kegg.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathVar/data/pways.reactome.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/bods.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/cpd.accs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/cpd.names.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/cpd.simtypes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/demo.paths.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/gene.idtype.bods.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/gene.idtype.list.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/gse16873.d.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/kegg.met.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/KEGGEdgeSubtype.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/ko.ids.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/korg.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/paths.hsa.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/data/rn.list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathview/inst/extdata/kegg.sigmet.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathwayPCA/vignettes/circlePlotData.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File pathwayPCA/data/colon_pathwayCollection.rda: load().. ok [1 object(s)]; updateObject(pathwayCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathwayPCA/data/colonSurv_df.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathwayPCA/data/wikipwsHS_Entrez_pathwayCollection.rda: load().. ok [1 object(s)]; updateObject(pathwayCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File pathwayPCA/data/wikipwsHS_Symbol_pathwayCollection.rda: load().. ok [1 object(s)]; updateObject(pathwayCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File pcaMethods/data/helix.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File pcaMethods/data/metaboliteData.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File pcaMethods/data/metaboliteDataComplete.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/geneByHp.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/geneByTrait.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/geneDef.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/hp_ancestors.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/hp_class.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/hp_descendants.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/hpByTrait.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/hpDef.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/hqStrNw.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/hsEntrezByRPath.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/rPath.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PCAN/data/traitDef.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/cohortSubtypeDFs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/CSPC_MAE.rda: load().. ok [1 object(s)]; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/existingClassifierData.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/sampleClinicalModel.rda: load().. ok [1 object(s)]; updateObject(ClinicalModel, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/sampleCohortList.rda: load().. ok [1 object(s)]; updateObject(CohortList, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/sampleICGCmicro.rda: load().. ok [1 object(s)]; updateObject(SurvivalExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/samplePCOSPmodel.rda: load().. ok [1 object(s)]; updateObject(PCOSP, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/samplePCOSPpredList.rda: load().. ok [1 object(s)]; updateObject(CohortList, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/samplePCSIsurvExp.rda: load().. ok [1 object(s)]; updateObject(SurvivalExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/sampleRGAmodel.rda: load().. ok [1 object(s)]; updateObject(RGAModel, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/sampleRLSmodel.rda: load().. ok [1 object(s)]; updateObject(RLSModel, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/sampleTrainedPCOSPmodel.rda: load().. ok [1 object(s)]; updateObject(PCOSP, check=FALSE).. no match, no-op; nothing to update ==> 0
File PDATK/data/sampleValPCOSPmodel.rda: load().. ok [1 object(s)]; updateObject(PCOSP, check=FALSE).. no match, no-op; nothing to update ==> 0
File peco/data/cellcyclegenes_whitfield2002.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File peco/data/model_5genes_predict.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File peco/data/model_5genes_train.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File peco/data/sce_top101genes.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File peco/data/training_human.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pepStat/inst/shiny/pepStat.rda: load().. ok [10 object(s)]; updateObject(function, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(RangedData, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; nothing to update ==> 0
File PERFect/data/mock2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File periodicDNA/data/ce11_all_REs.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File periodicDNA/data/ce11_ATACseq.rda: load().. ok [1 object(s)]; updateObject(SimpleRleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File periodicDNA/data/ce11_proms_seqs.rda: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File periodicDNA/data/ce11_proms.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File periodicDNA/data/ce11_TSSs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File periodicDNA/data/ce11_WW_10bp.rda: load().. ok [1 object(s)]; updateObject(SimpleRleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File perturbatr/inst/extdata/graph_full.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File perturbatr/inst/extdata/graph_small.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File perturbatr/data/rnaiscreen.rda: load().. ok [1 object(s)]; updateObject(PerturbationData, check=FALSE).. no match, no-op; nothing to update ==> 0
Skip package PFP ==> -3
File pgca/tests/testthat/testdata/dict-file-output.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File pgca/tests/testthat/testdata/translated-df.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File pgca/data/BET1947_v339.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pgca/data/BET2007_v339.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pgca/data/BET2047_v339.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pgca/data/BET2067_v339.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File phantasus/data/es.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File phantasus/data/fgseaExample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File phantasus/inst/testdata/aa.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File phantasus/inst/testdata/GSE27112-GPL6103.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File phantasus/inst/testdata/wrapped_aa.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File phantasus/inst/testdata/wrapped_wrongFormat.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File phantasus/inst/testdata/wrongFormatFile.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File PharmacoGx/tests/testthat/cellInfo.GDSCsmall.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/cellNames.GDSCsmall.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/drug.perturbationSmall.rds: readRDS().. ok; updateObject(array, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/drug.sensitivity.discreteGDSCSmall.rds: readRDS().. ok; updateObject(array, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/drug.sensitivity.MANOVAGDSCSmall.rds: readRDS().. ok; updateObject(array, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/drug.sensitivityGDSCSmall.rds: readRDS().. ok; updateObject(array, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/drugInfo.GDSCsmall.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/drugNames.GDSCsmall.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/featureInfo.GDSCsmall.rds: readRDS().. ok; updateObject(DFrame, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/fNames.GDSCsmall.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/intersectedSmallData.rds: readRDS().. ok; updateObject(list, check=FALSE).. returned an error ==> -1
File PharmacoGx/tests/testthat/intersectedSmallDataStrict.rds: readRDS().. ok; updateObject(list, check=FALSE).. returned an error ==> -1
File PharmacoGx/tests/testthat/molecularProfiles.GDSCsmall.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/phenoInfo.GDSCsmall.rds: readRDS().. ok; updateObject(DFrame, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/sensitivityInfo.GDSCsmall.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/sensitivityMeasures.GDSCsmall.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/sensitivityProfiles.GDSCsmall.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File PharmacoGx/tests/testthat/subsetTo.CMAPsmaller.rds: readRDS().. ok; updateObject(PharmacoSet, check=FALSE).. returned an error ==> -1
File PharmacoGx/data/CCLEsmall.rda: load().. ok [1 object(s)]; updateObject(PharmacoSet, check=FALSE).. returned an error ==> -1
File PharmacoGx/data/CMAPsmall.rda: load().. ok [1 object(s)]; updateObject(PharmacoSet, check=FALSE).. returned an error ==> -1
File PharmacoGx/data/GDSCsmall.rda: load().. ok [1 object(s)]; updateObject(PharmacoSet, check=FALSE).. returned an error ==> -1
File PharmacoGx/data/HDAC_genes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File phemd/data/all_expn_data.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File phemd/data/all_genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File phemd/data/heatmap_genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File phemd/data/selected_genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File phemd/data/snames_data.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File phemd/vignettes/melanomaData.RData: load().. ok [5 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File phenoTest/data/epheno.RData: load().. ok [1 object(s)]; updateObject(epheno, check=FALSE).. no match, no-op; nothing to update ==> 0
File phenoTest/data/eset.genelevel.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File phenoTest/data/eset.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhenStat/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File PhenStat/inst/report/GeCoSy.Rdata: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhIPData/inst/libraries/virscan.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File PhIPData/inst/extdata/alias.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File phosphonormalizer/data/enriched.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File phosphonormalizer/data/non.enriched.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/KinaseFamily.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/KinaseMotifs.rda: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/phospho_L6_ratio_pe.rda: load().. ok [1 object(s)]; updateObject(PhosphoExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/phospho_L6_ratio.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/phospho_liverInsTC_RUV_sample.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/phospho.cells.Ins.pe.rda: load().. ok [1 object(s)]; updateObject(PhosphoExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/phospho.cells.Ins.sample.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/phospho.liver.Ins.TC.ratio.RUV.pe.RData: load().. ok [1 object(s)]; updateObject(PhosphoExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/PhosphoSitePlus.rda: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/SEGs.rda: load().. ok [2 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhosR/data/SPSs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/filteredProfile.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/finalProcessedProfile.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/fullProcessedProfile.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/idList.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/mainLongRaw.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/ppTaxonomyMatrix.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/ppTree.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/profileWithTaxonomy.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/rankList.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/superTaxonProfile.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/taxonNamesReduced.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PhyloProfile/data/taxonomyMatrix.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File phyloseq/data/enterotype.RData: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File phyloseq/data/esophagus.RData: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File phyloseq/data/GlobalPatterns.RData: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File phyloseq/data/soilrep.RData: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File phyloseq/inst/doc/Unweighted_UniFrac.RData: load().. ok [1 object(s)]; updateObject(dist, check=FALSE).. no match, no-op; nothing to update ==> 0
File piano/data/gsa_input.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File piano/data/gsa_results.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Pigengene/data/aml.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Pigengene/data/eigengenes33.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Pigengene/data/mds.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Pigengene/data/pigengene.RData: load().. ok [1 object(s)]; updateObject(pigengene, check=FALSE).. no match, no-op; nothing to update ==> 0
File pipeComp/data/clustMetricsCorr.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pipeComp/data/ctrlgenes.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pipeComp/data/exampleDEAresults.RData: load().. ok [1 object(s)]; updateObject(SimpleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File pipeComp/data/exampleResults.RData: load().. ok [1 object(s)]; updateObject(SimpleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File pipeComp/data/stableG.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pipeFrame/inst/extdata/pipeFrame.obj.rds: readRDS().. ok; updateObject(Renamer, check=FALSE).. returned an error ==> -1
File planet/data/ageCpGs.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File planet/data/ethnicityCpGs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File planet/data/plBetas.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File planet/data/plCellCpGsFirst.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File planet/data/plCellCpGsThird.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File planet/data/plColors.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File planet/data/plPhenoData.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File planet/R/sysdata.rda: load().. ok [6 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File plgem/data/LPSeset.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File PloGO2/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File plotgardener/R/sysdata.rda: load().. ok [32 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PLPE/data/plateletSet.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File pmm/data/kinome.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pmp/data/MTBLS79.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File pmp/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PoDCall/data/thrTable.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File podkat/data/b36Unmasked.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File podkat/data/b37Unmasked.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File podkat/data/hg18Unmasked.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File podkat/data/hg19Unmasked.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File podkat/data/hg38Unmasked.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File podkat/data/hgA.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File pogos/data/CCLE_drts.rda: load().. ok [1 object(s)]; updateObject(DRTraceSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File pogos/data/cell_lines_v1.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pogos/data/compounds_v1.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pogos/data/datasets_v1.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pogos/data/tissues_v1.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pogos/inst/mocks/iriCCLE.rda: load().. ok [1 object(s)]; updateObject(DRTraceSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/cdnaf.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/empirical_density.rda: load().. ok [1 object(s)]; updateObject(logspline, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/gtf_dataframe.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/ill100v4_mate1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/ill100v4_mate2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/ill100v4_single.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/ill100v5_mate1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/ill100v5_mate2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/ill100v5_single.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/loessfit1.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/loessfit2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/loessfit3.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/loessfit4.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/loessfit5.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/loessfit6.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/loessfit7.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File polyester/data/rnaf.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File POMA/data/st000284.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File POMA/data/st000336.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File powerTCR/data/repertoires.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File POWSC/data/es_mef_sce.RData: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File POWSC/data/GSE67835_AB_S7_sce.RData: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File ppcseq/data/counts.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File ppiStats/inst/extdata/intacty2hppMatrix.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pqsfinder/inst/extdata/gtrack_ahnak.RData: load().. ok [1 object(s)]; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File pqsfinder/tests/testthat/pqsfinder_1_4_4_patched.RData: load().. ok [5 object(s)]; updateObject(DNAString, check=FALSE).. no match, no-op; updateObject(PQSViews, check=FALSE).. no match, no-op; updateObject(difftime, check=FALSE).. no match, no-op; updateObject(PQSViews, check=FALSE).. no match, no-op; updateObject(difftime, check=FALSE).. no match, no-op; nothing to update ==> 0
File preciseTAD/data/arrowhead_gm12878_5kb.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File preciseTAD/data/tfbsList.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File PrecisionTrialDrawer/inst/extdata/TCGAtranslocation.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File PrecisionTrialDrawer/inst/extdata/TCGAtranslocationSamples.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File PrecisionTrialDrawer/data/cpDesign.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PrecisionTrialDrawer/data/cpObj.RData: load().. ok [1 object(s)]; updateObject(CancerPanel, check=FALSE).. no match, no-op; nothing to update ==> 0
File PrecisionTrialDrawer/data/cpObj2.RData: load().. ok [1 object(s)]; updateObject(CancerPanel, check=FALSE).. no match, no-op; nothing to update ==> 0
File PrecisionTrialDrawer/data/panelexample.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File primirTSS/R/sysdata.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File PrInCE/data/gold_standard.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PrInCE/data/kristensen_gaussians.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PrInCE/data/kristensen.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File PrInCE/data/scott_gaussians.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PrInCE/data/scott.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File proActiv/data/promoterAnnotation.gencode.v34.subset.rda: load().. ok [1 object(s)]; updateObject(PromoterAnnotation, check=FALSE).. no match, no-op; nothing to update ==> 0
File proBAMr/inst/extdata/GENCODE/exon_anno.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File proBAMr/inst/extdata/GENCODE/ids.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File proBAMr/inst/extdata/GENCODE/procodingseq.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File proBAMr/inst/extdata/GENCODE/proseq.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File proBAMr/inst/extdata/res/SAM.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File proBatch/data/example_peptide_annotation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File proBatch/data/example_proteome_matrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File proBatch/data/example_proteome.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File proBatch/data/example_sample_annotation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File procoil/data/PrOCoilModel.RData: load().. ok [1 object(s)]; updateObject(CCModel, check=FALSE).. no match, no-op; nothing to update ==> 0
File procoil/data/PrOCoilModelBA.RData: load().. ok [1 object(s)]; updateObject(CCModel, check=FALSE).. no match, no-op; nothing to update ==> 0
File profileplyr/data/gene_list_character.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File profileplyr/data/gene_list_dataframe.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File profileplyr/data/K27ac_GRlist_hind_liver_top5000.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File profileScoreDist/data/INR.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File progeny/data/model_human_full.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File progeny/data/model_mouse_full.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File progeny/data/vignette_data.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File projectR/data/AP.RNAseq6l3c3t.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File projectR/data/map.ESepiGen4c1l.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File projectR/data/map.RNAseq6l3c3t.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File projectR/data/p.ESepiGen4c1l.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File projectR/data/p.RNAseq6l3c3t.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File projectR/data/pd.ESepiGen4c1l.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File projectR/data/pd.RNAseq6l3c3t.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pRoloc/inst/extdata/marker_atha.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File pRoloc/inst/extdata/marker_dmel.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File pRoloc/inst/extdata/marker_ggal.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File pRoloc/inst/extdata/marker_hsap.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File pRoloc/inst/extdata/marker_mmus.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File pRoloc/inst/extdata/marker_scer_sgd.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File pRoloc/inst/extdata/marker_scer_uniprot.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File pRoloc/inst/extdata/mil.rds: readRDS().. ok; updateObject(MartInstanceList, check=FALSE).. no match, no-op ==> 0
File pRoloc/data/andy2011params.rda: load().. ok [1 object(s)]; updateObject(AnnotationParams, check=FALSE).. no match, no-op; nothing to update ==> 0
File pRoloc/data/dunkley2006params.rda: load().. ok [1 object(s)]; updateObject(AnnotationParams, check=FALSE).. no match, no-op; nothing to update ==> 0
File pRoloc/inst/extdata/dunkley2006pdunittest_20140408.rda: load().. ok [1 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File pRoloc/inst/extdata/dunkley2006pdunittest1.rda: load().. ok [1 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File pRoloc/inst/extdata/dunkley2006pdunittest2.rda: load().. ok [1 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File pRoloc/inst/extdata/params.rda: load().. ok [1 object(s)]; updateObject(GenRegRes, check=FALSE).. no match, no-op; nothing to update ==> 0
File pRoloc/inst/extdata/params2.rda: load().. ok [1 object(s)]; updateObject(GenRegRes, check=FALSE).. no match, no-op; nothing to update ==> 0
File pRoloc/inst/extdata/pdres.rda: load().. ok [1 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROMISE/data/phPatt.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROMISE/data/sampExprSet.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROMISE/data/sampGeneSet.rda: load().. ok [1 object(s)]; updateObject(GeneSetCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROPER/data/bottomly.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROPER/data/cheung.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROPER/data/GE.human.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROPER/data/gilad.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROPER/data/maqc.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROPER/data/pbmc.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROPS/data/example_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROPS/data/example_edges.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROPS/data/example_healthy.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PROPS/data/kegg_pathway_edges.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File proteinProfiles/data/ips_sample.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ProteoDisco/data/ProteoDiscographyExample.hg19.rda: load().. ok [1 object(s)]; updateObject(ProteoDiscography, check=FALSE).. returned an error ==> -1
File ProteomicsAnnotationHubData/inst/extdata/PXD000001Fasta.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ProteomicsAnnotationHubData/inst/extdata/PXD000001MSnSet.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ProteomicsAnnotationHubData/inst/extdata/PXD000001MzID.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ProteomicsAnnotationHubData/inst/extdata/PXD000001MzML.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ProteoMM/data/hs_peptides.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ProteoMM/data/mm_peptides.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PSEA/data/example.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File PSEA/data/expression_GSE19380.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File psichomics/inst/extdata/ex_gene_expression.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File psichomics/inst/extdata/ex_junctionQuant.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File psichomics/inst/extdata/ex_splicing_annotation.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File psichomics/inst/extdata/Sebestyen_et_al_2016.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File psichomics/inst/extdata/TCGAsampleType.RDS: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File psichomics/vignettes/BRCA_clinical.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File psichomics/vignettes/BRCA_geneExpr.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File psichomics/vignettes/BRCA_psi.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File PSICQUIC/inst/extdata/mycInteractions.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File psygenet2r/data/qr.rda: load().. ok [1 object(s)]; updateObject(DataGeNET.Psy, check=FALSE).. no match, no-op; nothing to update ==> 0
File psygenet2r/data/universe.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File psygenet2r/inst/extdata/disgenetCuratedUniverse.RData: load().. ok [1 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File psygenet2r/inst/extdata/topAnat.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PubScore/data/all_counts.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File PubScore/data/gene2pubmed_db.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File PubScore/data/hgcn_entrez_reference.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pulsedSilac/data/mefPE.rda: load().. ok [1 object(s)]; updateObject(SilacProteinExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File pulsedSilac/data/recycleLightLysine.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File pulsedSilac/data/wormsPE.rda: load().. ok [1 object(s)]; updateObject(SilacProteomicsExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File pulsedSilac/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File puma/data/Clust.exampleE.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File puma/data/Clust.exampleStd.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File puma/data/Clustii.exampleE.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File puma/data/Clustii.exampleStd.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File puma/data/eset_mmgmos.rda: load().. ok [1 object(s)]; updateObject(exprReslt, check=FALSE).. returned an error ==> -1
File puma/data/exampleE.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File puma/data/exampleStd.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File puma/data/hgu95aphis.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File PureCN/inst/extdata/issue184_2_mb.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File PureCN/data/centromeres.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PureCN/data/purecn.DNAcopy.bdry.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File PureCN/data/purecn.example.output.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File PWMEnrich/inst/extdata/bg.seq-test.RData: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File pwOmics/data/OmicsExampleData.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File pwOmics/inst/extdata/Genelists/Genelist_biocarta.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File pwOmics/inst/extdata/Genelists/Genelist_kegg.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File pwOmics/inst/extdata/Genelists/Genelist_nci.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File pwOmics/inst/extdata/Genelists/Genelist_reactome.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File pwrEWAS/vignettes/vignette_reduced.Rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File qcmetrics/data/n15psm.rda: load().. ok [1 object(s)]; updateObject(MSnSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File qcmetrics/inst/extdata/exp.rda: load().. ok [1 object(s)]; updateObject(MSnExp, check=FALSE).. returned an error ==> -1
File qcmetrics/inst/extdata/yqc.rda: load().. ok [1 object(s)]; updateObject(YAQCStats, check=FALSE).. returned an error ==> -1
File QDNAseq/data/LGG150.rda: load().. ok [1 object(s)]; updateObject(QDNAseqReadCounts, check=FALSE).. returned an error ==> -1
File QFeatures/data/feat1.rda: load().. ok [1 object(s)]; updateObject(QFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File QFeatures/data/feat2.rda: load().. ok [1 object(s)]; updateObject(QFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File QFeatures/data/feat3.rda: load().. ok [1 object(s)]; updateObject(QFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File QFeatures/data/ft_na.rda: load().. ok [1 object(s)]; updateObject(QFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File QFeatures/data/hlpsms.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File QFeatures/data/se_na2.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File qpcrNorm/data/qpcrBatch.object.rda: load().. ok [1 object(s)]; updateObject(qpcrBatch, check=FALSE).. no match, no-op; nothing to update ==> 0
File qpgraph/data/EcoliOxygen.RData: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File qPLEXanalyzer/tests/testthat/assignColours_rep.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/assignColours_sg.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/computeDiffStats.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/convertToMSnset_phospho_msnset.rds: readRDS().. ok; updateObject(MSnSet, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/getContrastResults.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/groupScaling.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/IRSnorm_exprs.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/IRSnorm_fdata.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/IRSnorm_pdata.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/mergePeptides_phos.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/mergePeptides.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/normalizeQuantiles.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/normalizeScaling_prot.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/normalizeScaling.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/regressIntensities.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/rowScaling.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/tests/testthat/summarizeIntensities.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File qPLEXanalyzer/data/ER_ARID1A_KO_MCF7.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File qPLEXanalyzer/data/exp2_Xlink.RData: load().. ok [3 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File qPLEXanalyzer/data/exp3_OHT_ESR1.RData: load().. ok [3 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File qPLEXanalyzer/data/human_anno.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File qPLEXanalyzer/data/mouse_anno.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File qsea/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File qsmooth/data/gc.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File quantiseqr/data/dataset_racle.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File quantiseqr/data/ti_quant_sim1700mixtures.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File quantro/data/flowSorted.RData: load().. ok [1 object(s)]; updateObject(MethylSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File quantsmooth/data/chr14.rda: load().. ok [6 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File quantsmooth/data/chrom.bands.hg18.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File quantsmooth/data/chrom.bands.hg19.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File quantsmooth/data/chrom.bands.hg38.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File quantsmooth/data/chrom.bands.mm10.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File quantsmooth/data/chrom.bands.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File qusage/data/fluExample.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File qusage/data/fluVaccine.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File qusage/data/GeneSets.RData: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File qvalue/data/hedenfalk.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File R3CPET/data/Biogrid.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File R3CPET/data/chromosoms.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File R3CPET/data/geneLocations.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File R3CPET/data/HPRD.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File R3CPET/data/RPKMS.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File R3CPET/inst/example/hlda.RData: load().. ok [1 object(s)]; updateObject(ChromMaintainers, check=FALSE).. no match, no-op; nothing to update ==> 0
File R3CPET/inst/example/nets.RData: load().. ok [1 object(s)]; updateObject(NetworkCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File r3Cseq/data/enzymeDb.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File r3Cseq/data/example.data.rda: load().. ok [1 object(s)]; updateObject(r3Cseq, check=FALSE).. returned an error ==> -1
File r3Cseq/data/hg18refGene.rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File r3Cseq/data/hg19refGene.rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File r3Cseq/data/mm10refGene.rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File r3Cseq/data/mm9refGene.rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File r3Cseq/data/Myb_prom_FB.rdata: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File r3Cseq/data/Myb_prom_FL.rdata: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File r3Cseq/data/rn5refGene.rdata: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File R453Plus1Toolbox/data/avaSetExample.RData: load().. ok [1 object(s)]; updateObject(AVASet, check=FALSE).. no match, no-op; nothing to update ==> 0
File R453Plus1Toolbox/data/avaSetFiltered_annot.RData: load().. ok [1 object(s)]; updateObject(AnnotatedVariants, check=FALSE).. no match, no-op; nothing to update ==> 0
File R453Plus1Toolbox/data/avaSetFiltered.RData: load().. ok [1 object(s)]; updateObject(AVASet, check=FALSE).. no match, no-op; nothing to update ==> 0
File R453Plus1Toolbox/data/breakpoints.RData: load().. ok [1 object(s)]; updateObject(Breakpoints, check=FALSE).. no match, no-op; nothing to update ==> 0
File R453Plus1Toolbox/data/captureArray.RData: load().. ok [1 object(s)]; updateObject(CompressedIRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File R453Plus1Toolbox/data/mapperSetExample.RData: load().. ok [1 object(s)]; updateObject(MapperSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File R453Plus1Toolbox/data/plotVariantsExample.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File R4RNA/data/helix.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File RadioGx/data/clevelandSmall.rda: load().. ok [1 object(s)]; updateObject(RadioSet, check=FALSE).. returned an error ==> -1
File rain/data/menetRNASeqMouseLiver.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ramr/data/ramr.rda: load().. ok [4 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File ramwas/inst/extdata/bigQC.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File ramwas/inst/extdata/cpgset.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File ramwas/inst/extdata/qc_sample.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File RandomWalkRestartMH/data/Disease_Network.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File RandomWalkRestartMH/data/GeneDiseaseRelations.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RandomWalkRestartMH/data/Pathway_Network.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File RandomWalkRestartMH/data/PPI_Network.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File randPack/data/alltabs.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File randPack/data/CT1.rda: load().. ok [1 object(s)]; updateObject(ClinicalTrial, check=FALSE).. no match, no-op; nothing to update ==> 0
File randPack/data/pD1.rda: load().. ok [1 object(s)]; updateObject(PatientData, check=FALSE).. no match, no-op; nothing to update ==> 0
File randPack/data/SampleData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File randPack/data/sco.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RankProd/data/Apples.rda: load().. ok [6 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(AsIs, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File RankProd/data/arab.rda: load().. ok [4 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File RankProd/data/golub.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File RankProd/data/lymphoma.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File RbcBook1/data/ALL.dist.rda: load().. ok [7 object(s)]; updateObject(dist, check=FALSE).. no match, no-op; updateObject(dist, check=FALSE).. no match, no-op; updateObject(dist, check=FALSE).. no match, no-op; updateObject(dist, check=FALSE).. no match, no-op; updateObject(dist, check=FALSE).. no match, no-op; updateObject(dist, check=FALSE).. no match, no-op; updateObject(dist, check=FALSE).. no match, no-op; nothing to update ==> 0
File RbcBook1/data/ALLperformance.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RbcBook1/data/kidpackperformance.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RbcBook1/data/Survperformance.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RBGL/data/FileDep.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File rBiopaxParser/data/biopaxexample.rda: load().. ok [1 object(s)]; updateObject(biopax, check=FALSE).. no match, no-op; nothing to update ==> 0
File rBiopaxParser/data/biopaxLevel3Example.RData: load().. ok [1 object(s)]; updateObject(biopax, check=FALSE).. no match, no-op; nothing to update ==> 0
File RBM/data/ovarian_cancer_methylation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rbsurv/data/gliomaSet.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcade/data/RcadeSTAT1.rda: load().. ok [1 object(s)]; updateObject(Rcade, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCAS/inst/extdata/hg19.sample.gtf.granges.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File RCAS/data/gff.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCAS/data/queryRegions.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCASPAR/data/Bergamaschi.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCASPAR/data/survData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rcellminer/data/Drug_MOA_Key.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rCGH/data/agilentDB_400K_GC.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rCGH/data/hg18.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rCGH/data/hg19.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rCGH/data/hg38.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RcisTarget/data/dbRegionsLoc_hg19.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File RcisTarget/data/motifAnnotations_dmel_v8.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File RcisTarget/data/motifAnnotations_dmel.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File RcisTarget/data/motifAnnotations_hgnc_v8.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File RcisTarget/data/motifAnnotations_hgnc.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File RcisTarget/data/motifAnnotations_mgi_v8.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File RcisTarget/data/motifAnnotations_mgi.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File RcisTarget/inst/examples/motifEnrichmentTable_wGenes.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File RcisTarget/inst/examples/motifEnrichmentTable.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCM/data/Zeller.RData: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCM/inst/fits/zellerFits.RData: load().. ok [6 object(s)]; updateObject(RCM, check=FALSE).. no match, no-op; updateObject(RCM, check=FALSE).. no match, no-op; updateObject(RCM, check=FALSE).. no match, no-op; updateObject(RCM, check=FALSE).. no match, no-op; updateObject(RCM, check=FALSE).. no match, no-op; updateObject(RCM, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AA2DACOR.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AA3DMoRSE.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAACF.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AABLOSUM100.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AABLOSUM45.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AABLOSUM50.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AABLOSUM62.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AABLOSUM80.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AABurden.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAConn.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAConst.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AACPSA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AADescAll.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAEdgeAdj.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAEigIdx.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAFGC.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAGeom.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAGETAWAY.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAindex.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAInfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAMetaInfo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAMOE2D.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAMOE3D.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAMolProp.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAPAM120.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAPAM250.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAPAM30.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAPAM40.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAPAM70.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AARandic.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AARDF.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AATopo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AATopoChg.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAWalk.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/data/AAWHIM.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/inst/sysdata/CTDict.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/inst/sysdata/CTIndex.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rcpi/inst/sysdata/TCDict.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCSL/data/yan.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCyjs/inst/extdata/graph.11nodes.14edges.RData: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCyjs/inst/extdata/graph.1669nodes_3260edges_challenge_for_converting_to_json.RData: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCyjs/inst/extdata/hypoxiaLayout.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCyjs/inst/unitTests/gridLayout.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCyjs/inst/unitTests/junk.RData: load().. ok [2 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCyjs/inst/unitTests/layout.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RCyjs/inst/unitTests/testLayout.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ReactomeGraph4R/tests/testthat/for.test.results.Rdata: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ReactomeGraph4R/vignettes/data/vignette.Rdata: load().. ok [16 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.table, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File REBET/data/data.rda: load().. ok [3 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File receptLoss/data/nhrs.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File reconsi/data/VandeputteData.RData: load().. ok [1 object(s)]; updateObject(phyloseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File recount/data/recount_abstract.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File recount/data/recount_exons.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File recount/data/recount_genes.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File recount/data/recount_url.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File recount/data/rse_gene_SRP009615.RData: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File recountmethylation/inst/extdata/remethdb-h5se_gr-test_0-0-1_1590090412/se.rds: readRDS().. ok; updateObject(GenomicRatioSet, check=FALSE).. no match, no-op ==> 0
File recountmethylation/inst/extdata/data_analyses/data_analyses.RData: load().. ok [19 object(s)]; updateObject(function, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(DFrame, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File recountmethylation/inst/extdata/gsm_metadata/md_final_hm450k_0-0-1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File recountmethylation/inst/extdata/servermatrix_rda/servermatrix_1607018051.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File recoup/data/recoup_test_data.rda: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RedeR/data/Carroll2006.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RedeR/data/ER.deg.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RedeR/data/ER.limma.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RedeR/data/hs.inter.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File REDseq/data/example.assignedREDseq.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File REDseq/data/example.map.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File REDseq/data/example.REDseq.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File RegEnrich/data/Lyme_GSE63085.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RegEnrich/data/TFs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File REMP/data/Alu.hg19.demo.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File REMP/data/Alu.hg38.demo.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File Repitools/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File Repitools/data/expr.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Repitools/data/hcRegions.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File Repitools/data/samplesList.RData: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File ReportingTools/data/mockRnaSeqData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rexposome/data/eclust.rda: load().. ok [1 object(s)]; updateObject(ExposomeClust, check=FALSE).. no match, no-op; nothing to update ==> 0
File rexposome/data/ex_imp.rda: load().. ok [1 object(s)]; updateObject(imExposomeSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File rexposome/data/exposome.rda: load().. ok [1 object(s)]; updateObject(ExposomeSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File rexposome/data/me.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rfPred/data/example_GRanges.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File rfPred/data/variant_list_Y.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rgraphviz/inst/usecases/droso_ppi.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rGREAT/inst/extdata/job.rds: readRDS().. ok; updateObject(GreatJob, check=FALSE).. no match, no-op ==> 0
File RGSEA/data/cmap.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File RGSEA/data/e1.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File RGSEA/data/e2.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rhisat2/inst/extdata/refs/genes.granges.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File RiboCrypt/inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_cds.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File RiboCrypt/inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_leaders.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File RiboCrypt/inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_mrna.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File RiboCrypt/inst/extdata/Homo_sapiens_sample/QC_STATS/countTable_trailers.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File RiboDiPA/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File RiboDiPA/data/data.binned.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RiboDiPA/data/data.psite.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RiboDiPA/data/result.exon.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RiboDiPA/data/result.pst.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RiboProfiling/data/cdsPosTransc.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RiboProfiling/data/codonDataCtrl.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RiboProfiling/data/codonIndexCovCtrl.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RiboProfiling/data/ctrlGAlignments.rda: load().. ok [1 object(s)]; updateObject(GAlignments, check=FALSE).. no match, no-op; nothing to update ==> 0
File ribosomeProfilingQC/inst/extdata/CDS.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File ribosomeProfilingQC/inst/extdata/cnts.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File ribosomeProfilingQC/inst/extdata/danrer10.annotations.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File ribosomeProfilingQC/inst/extdata/samplePc.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/dm.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppdm.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppta.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppti.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppts.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppzb.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/suppzc.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/ta.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/ti.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/ts.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/zb.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY139/zc.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/dm.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppdm.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppta.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppti.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppts.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppza.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppzb.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/suppzd.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/ta.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/ti.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/ts.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/za.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/zb.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RImmPort/inst/extdata/ImmPortStudies/Rds/SDY208/zd.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Ringo/inst/agilentData/mm9chr17.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Ringo/inst/exData/exampleProbeAnno.rda: load().. ok [2 object(s)]; updateObject(probeAnno, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Ringo/inst/exData/exampleX.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Ringo/inst/exData/reportersInexactMatchesHg18.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RIPAT/inst/extdata/GRCh37_chrom.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RIPAT/inst/extdata/GRCh38_chrom.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File RIPAT/data/blast_gene.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RIPAT/data/blast_obj.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RIPAT/data/cpg_exam_db.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RIPAT/data/gene_exam_db.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RIPAT/data/micro_exam_db.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RIPAT/data/repeat_exam_db.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RIPAT/data/tss_exam_db.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RIPAT/data/var_exam_db.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RITAN/data/vac1.day0vs31.de.genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File RITAN/data/vac1.day0vs56.de.genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File RITAN/data/vac2.day0vs31.de.genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File RITAN/data/vac2.day0vs56.de.genes.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_1.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_10.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_11.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_2.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_3.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_4.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_5.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_6.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_7.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_8.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/demo_vignette/segmentResult_9.rds: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/RJMCMC_seg_01.RDS: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/RJMCMC_seg_02.RDS: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/inst/extdata/RJMCMC_seg_03.RDS: readRDS().. ok; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op ==> 0
File RJMCMCNucleosomes/data/reads_demo_01.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File RJMCMCNucleosomes/data/reads_demo_02.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File RJMCMCNucleosomes/data/RJMCMC_result.RData: load().. ok [1 object(s)]; updateObject(rjmcmcNucleosomes, check=FALSE).. no match, no-op; nothing to update ==> 0
File RJMCMCNucleosomes/data/syntheticNucleosomeReads.RData: load().. ok [1 object(s)]; updateObject(syntheticNucReads, check=FALSE).. no match, no-op; nothing to update ==> 0
File RLassoCox/data/dGMMirGraph.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File RLassoCox/data/mRNA_matrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File RLassoCox/data/survData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RLSeq/inst/extdata/rlrsmall.rds: readRDS().. ok; updateObject(RLRanges, check=FALSE).. no match, no-op ==> 0
File RLSeq/data/auxdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RLSeq/data/available_genomes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RLSeq/data/genomeMasks.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rmagpie/data/vV70genesDataset.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File RmiR/data/RmiR.rda: load().. ok [6 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAAgeCalc/data/countExample.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAAgeCalc/data/fpkmExample.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAAgeCalc/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAdecay/data/decay_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAdecay/data/models.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAdecay/data/results.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAdecay/data/RPMs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rnaEditr/inst/extdata/hg19_annoGene_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File rnaEditr/inst/extdata/hg38_annoGene_gr.RDS: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File rnaEditr/inst/extdata/pheno_df.RDS: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File rnaEditr/data/rnaedit_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rnaEditr/data/t_rnaedit_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAinteract/data/sgi.rda: load().. ok [1 object(s)]; updateObject(RNAinteract, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/csd.rda: load().. ok [1 object(s)]; updateObject(CoverageSequenceData, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/e3sd.rda: load().. ok [1 object(s)]; updateObject(End3SequenceData, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/e5sd.rda: load().. ok [1 object(s)]; updateObject(End5SequenceData, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/esd.rda: load().. ok [1 object(s)]; updateObject(EndSequenceData, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/msi.rda: load().. ok [1 object(s)]; updateObject(ModSetInosine, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/ne3sd.rda: load().. ok [1 object(s)]; updateObject(NormEnd3SequenceData, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/ne5sd.rda: load().. ok [1 object(s)]; updateObject(NormEnd5SequenceData, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/pesd.rda: load().. ok [1 object(s)]; updateObject(ProtectedEndSequenceData, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/psd.rda: load().. ok [1 object(s)]; updateObject(PileupSequenceData, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/sdl.rda: load().. ok [1 object(s)]; updateObject(SequenceDataList, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR/data/sds.rda: load().. ok [1 object(s)]; updateObject(SequenceDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR.AlkAnilineSeq/data/msaas.rda: load().. ok [1 object(s)]; updateObject(ModSetAlkAnilineSeq, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR.ML/data/dmod.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR.ML/data/me.rda: load().. ok [1 object(s)]; updateObject(ModMLExample, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR.ML/data/mod7.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR.ML/data/model.rda: load().. ok [1 object(s)]; updateObject(ranger, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAmodR.RiboMethSeq/data/msrms.rda: load().. ok [1 object(s)]; updateObject(ModSetRiboMethSeq, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNAsense/data/MZsox.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File rnaseqcomp/data/simdata.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RNASeqR/data/yeast.RData: load().. ok [1 object(s)]; updateObject(RNASeqRParam, check=FALSE).. no match, no-op; nothing to update ==> 0
File RnBeads/data/lump.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rnits/data/yeastchemostat.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
Skip package ROntoTools ==> -3
File ropls/data/cellulose.rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ropls/data/sacurine.rdata: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ROSeq/data/L_Tung_single.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ROTS/data/affySpikeIn.RData: load().. ok [4 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File ROTS/data/upsSpikeIn.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File rprimer/data/exampleRprimerAlignment.RData: load().. ok [1 object(s)]; updateObject(DNAMultipleAlignment, check=FALSE).. no match, no-op; nothing to update ==> 0
File rprimer/data/exampleRprimerAssay.RData: load().. ok [1 object(s)]; updateObject(RprimerAssay, check=FALSE).. no match, no-op; nothing to update ==> 0
File rprimer/data/exampleRprimerMatchAssay.RData: load().. ok [1 object(s)]; updateObject(RprimerMatchAssay, check=FALSE).. no match, no-op; nothing to update ==> 0
File rprimer/data/exampleRprimerMatchOligo.RData: load().. ok [1 object(s)]; updateObject(RprimerMatchOligo, check=FALSE).. no match, no-op; nothing to update ==> 0
File rprimer/data/exampleRprimerOligo.RData: load().. ok [1 object(s)]; updateObject(RprimerOligo, check=FALSE).. no match, no-op; nothing to update ==> 0
File rprimer/data/exampleRprimerProfile.RData: load().. ok [1 object(s)]; updateObject(RprimerProfile, check=FALSE).. no match, no-op; nothing to update ==> 0
File rprimer/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rqc/inst/extdata/Rqc.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File rqt/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RRHO/data/lists.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rsamtools/inst/extdata/olaps.Rda: load().. ok [1 object(s)]; updateObject(SimpleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File rsemmed/data/g_mini.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File rsemmed/data/g_small.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File RSVSim/data/segmentalDuplications.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File RSVSim/data/weightsMechanisms.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RSVSim/data/weightsRepeats.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTCGAToolbox/data/accmini.rda: load().. ok [1 object(s)]; updateObject(FirehoseData, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTN/data/pksData.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTN/data/stni.RData: load().. ok [1 object(s)]; updateObject(TNI, check=FALSE).. returned an error ==> -1
File RTN/data/tfsData.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTN/data/tnaData.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTN/data/tniData.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTNsurvival/data/survival.data.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTopper/data/exampleData.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTopper/data/fgsList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTopper/data/gseResultsSep.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTopper/data/intScores.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RTopper/data/sepScores.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rtpca/data/ori_et_al_complex_ppis.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rtpca/data/ori_et_al_complexes_df.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rtpca/data/string_ppi_df.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File rtracklayer/data/cpneTrack.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File rtracklayer/data/targets.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Rtreemix/data/hiv.data.RData: load().. ok [1 object(s)]; updateObject(RtreemixData, check=FALSE).. no match, no-op; nothing to update ==> 0
File rTRM/data/biogrid_hs.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File rTRM/data/biogrid_mm.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File rTRM/inst/extra/example.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File rTRM/inst/extra/pwm_mm_logn.rda: load().. ok [1 object(s)]; updateObject(PWMLognBackground, check=FALSE).. no match, no-op; nothing to update ==> 0
File rTRM/inst/extra/sox2_enr.rda: load().. ok [1 object(s)]; updateObject(MotifEnrichmentResults, check=FALSE).. no match, no-op; nothing to update ==> 0
File rTRM/inst/extra/sox2_motif_list.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File RVS/data/ex.ped.mat.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File RVS/data/famVCF.RData: load().. ok [2 object(s)]; updateObject(CollapsedVCF, check=FALSE).. no match, no-op; updateObject(CollapsedVCF, check=FALSE).. no match, no-op; nothing to update ==> 0
File RVS/data/samplePedigrees.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File RVS/data/snpMat.RData: load().. ok [1 object(s)]; updateObject(SnpMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File safe/data/p53.stat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SAIGEgds/inst/extdata/v_glmm.rds: readRDS().. ok; updateObject(ClassSAIGE_NullModel, check=FALSE).. no match, no-op ==> 0
File SAIGEgds/inst/unitTests/saige_model_quant.rds: readRDS().. ok; updateObject(ClassSAIGE_NullModel, check=FALSE).. no match, no-op ==> 0
File SAIGEgds/inst/unitTests/saige_model.rds: readRDS().. ok; updateObject(ClassSAIGE_NullModel, check=FALSE).. no match, no-op ==> 0
File SAIGEgds/inst/unitTests/saige_pval_quant.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File SAIGEgds/inst/unitTests/saige_pval.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File SamSPECTRAL/data/eigen.values.10.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SamSPECTRAL/data/eigen.values.1000.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SamSPECTRAL/data/small_data.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SamSPECTRAL/data/stm.RData: load().. ok [1 object(s)]; updateObject(flowFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sangeranalyseR/data/qualityReportData.RData: load().. ok [1 object(s)]; updateObject(QualityReport, check=FALSE).. returned an error ==> -1
File sangeranalyseR/data/sangerAlignmentData.RData: load().. ok [1 object(s)]; updateObject(SangerAlignment, check=FALSE).. returned an error ==> -1
File sangeranalyseR/data/sangerContigData.RData: load().. ok [1 object(s)]; updateObject(SangerContig, check=FALSE).. returned an error ==> -1
File sangeranalyseR/data/sangerReadFData.RData: load().. ok [1 object(s)]; updateObject(SangerRead, check=FALSE).. returned an error ==> -1
File sangeranalyseR/sangerAlignmentData.RData: load().. ok [1 object(s)]; updateObject(SangerAlignment, check=FALSE).. returned an error ==> -1
File sangerseqR/inst/testData/heterozygousabif.rds: readRDS().. ok; updateObject(sangerseq, check=FALSE).. no match, no-op ==> 0
File sangerseqR/inst/testData/heterozygousscf.rds: readRDS().. ok; updateObject(sangerseq, check=FALSE).. no match, no-op ==> 0
File sangerseqR/inst/testData/noprintabif.rds: readRDS().. ok; updateObject(sangerseq, check=FALSE).. no match, no-op ==> 0
File SANTA/data/edgelist.humannet.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SANTA/data/edgelist.intact.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SANTA/data/g.bandyopadhyay.treated.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File SANTA/data/g.bandyopadhyay.untreated.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File SANTA/data/g.costanzo.cor.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File SANTA/data/g.costanzo.raw.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File SANTA/data/g.srivas.high.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File SANTA/data/g.srivas.untreated.RData: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File SANTA/data/go.entrez.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File SANTA/data/rnai.cheung.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File sarks/data/simulatedScores.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File sarks/data/simulatedSeqs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File satuRn/data/sumExp_example.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File satuRn/data/Tasic_counts_vignette.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File satuRn/data/Tasic_metadata_vignette.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SBGNview/data/mapped.ids.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SBGNview/data/pathways.info.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SBGNview/data/pathways.stats.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SBGNview/data/SBGNhub.id.mapping.tables.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SC3/data/yan.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Scale4C/data/liverData.RData: load().. ok [1 object(s)]; updateObject(Scale4C, check=FALSE).. no match, no-op; nothing to update ==> 0
File Scale4C/data/liverDataVP.RData: load().. ok [1 object(s)]; updateObject(Scale4C, check=FALSE).. no match, no-op; nothing to update ==> 0
File scAlign/data/cellbench.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File scanMiR/data/SampleKdModel.RData: load().. ok [1 object(s)]; updateObject(KdModel, check=FALSE).. no match, no-op; nothing to update ==> 0
File scanMiR/data/SampleTranscript.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File scAnnotatR/data/tirosh_mel80_example.rda: load().. ok [1 object(s)]; updateObject(Seurat, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCANVIS/data/SCANVISexamples.RData: load().. ok [6 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCArray/inst/extdata/LaMannoBrainSub.rds: readRDS().. ok; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op ==> 0
File scatterHatch/data/pdacData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scBFA/data/celltype_toy.rda: load().. ok [1 object(s)]; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File scBFA/data/celltype.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File scBFA/data/disperPlot.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scBFA/data/exprdata.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File scBFA/data/zinb_toy.rda: load().. ok [1 object(s)]; updateObject(ZinbModel, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCBN/data/orthgenes.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCBN/data/sim_data.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scCB2/data/mbrainSub.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File scClassify/data/scClassify_example.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scClassify/data/trainClassExample_wang.rda: load().. ok [1 object(s)]; updateObject(scClassifyTrainModel, check=FALSE).. no match, no-op; nothing to update ==> 0
File scClassify/data/trainClassExample_xin.rda: load().. ok [1 object(s)]; updateObject(scClassifyTrainModel, check=FALSE).. no match, no-op; nothing to update ==> 0
File sccomp/data/counts_obj.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File sccomp/data/glm_dirichlet_multinomial_generate_quantities.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File sccomp/data/glm_dirichlet_multinomial_imputation.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File sccomp/data/glm_dirichlet_multinomial.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File sccomp/data/glm_multi_beta_generate_data.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File sccomp/data/glm_multi_beta.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File sccomp/data/sce_obj.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File sccomp/data/seurat_obj.rda: load().. ok [1 object(s)]; updateObject(Seurat, check=FALSE).. no match, no-op; nothing to update ==> 0
File scDataviz/inst/extdata/complosome.rdata: load().. ok [7 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File scDblFinder/data/doubletsComparison.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scDD/data/scDatEx.RData: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File scDD/data/scDatExList.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scDD/data/scDatExSim.RData: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File scde/data/es.mef.small.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scde/data/knn.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scde/data/o.ifm.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scde/data/pollen.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File scde/data/scde.edff.rda: load().. ok [1 object(s)]; updateObject(gam, check=FALSE).. no match, no-op; nothing to update ==> 0
File scds/data/sce_chcl.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCFA/data/GBM.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scFeatureFilter/data/scData_hESC.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File scGPS/data/day_2_cardio_cell_sample.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scGPS/data/day_5_cardio_cell_sample.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scGPS/data/training_gene_sample.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scHOT/data/liver.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scHOT/data/MOB_subset.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/arp23.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/arp23G.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/arp23Orf.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/arp23Y2HG.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/cfia.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/cfiaOrf.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/dataS.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/eAt.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/eAt2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/egEBI16112.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/expStats.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/gavin2mergeMG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/ho2mergeMGG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/krogan2mergeMGGH.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/locScISI.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/mapping2SysG.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/mappingsG.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/mips2go.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/nAt.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/nAtMap.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/nonGenes.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/nucComp.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/redundantM.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/ScISI.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/ScISIC.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/ScISIverified.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/subCompM.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/unwanted.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/data/xtraGO.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/arp23AM.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/arp23BP.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/arp23BPG.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/arp23CMG.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/arp23CMM.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/arp23G.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/cfiaAM.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/cfiaCMG.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/cfiaCMM.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/cfiaG.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/ppi1.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/ppi1G.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/ppi2.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/graphs/ppi2G.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/pathway/keggM.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/extdata/pathway/sgdPathM.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ScISI/inst/Scripts/C1G.rda: load().. ok [1 object(s)]; updateObject(graphNEL, check=FALSE).. no match, no-op; nothing to update ==> 0
File scMAGeCK/inst/extdata/singles_dox_mki67_v3.RDS: readRDS().. ok; updateObject(Seurat, check=FALSE).. no match, no-op ==> 0
File scmap/data/yan.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scMerge/data/example_sce.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File scMerge/data/segList_ensemblGeneID.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scMerge/data/segList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scmeth/inst/extdata/bismark_data/se.rds: readRDS().. ok; updateObject(BSseq, check=FALSE).. no match, no-op ==> 0
File scmeth/inst/extdata/bsObject.rda: load().. ok [1 object(s)]; updateObject(BSseq, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCnorm/data/ExampleSimSCData.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File scone/data/cellcycle_genes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scone/data/cortical_markers.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scone/data/housekeeping_revised.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scone/data/housekeeping.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/bz.gmcsf.final.norm.scale.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/bz.gmcsf.final.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/exist.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/funct.markers.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/input.markers.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/markers.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/wand.combined.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/wand.final.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/wand.ideal.k.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/wand.il7.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sconify/data/wand.scone.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCOPE/data/coverageObj.scopeDemo.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCOPE/data/demo.rda: load().. ok [2 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCOPE/data/iCN_sim.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCOPE/data/normObj.scopeDemo.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCOPE/data/QCmetric.scopeDemo.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SCOPE/data/ref.scopeDemo.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File scoreInvHap/data/hetRefs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scoreInvHap/data/info.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scoreInvHap/data/inversionGR.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File scoreInvHap/data/Refs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scoreInvHap/data/SNPsR2.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scp/data/mqScpData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scp/data/sampleAnnotation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scp/data/scp1.rda: load().. ok [1 object(s)]; updateObject(QFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File scPCA/data/background_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scPCA/data/toy_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scPipe/data/sc_sample_data.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File scPipe/data/sc_sample_qc.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scran/inst/exdata/human_cycle_markers.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File scran/inst/exdata/mouse_cycle_markers.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File scReClassify/data/gse87795_subset_sce.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File scRecover/data/scRecoverTest.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File scRepertoire/data/contig_list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scRepertoire/data/screp_example.rda: load().. ok [1 object(s)]; updateObject(Seurat, check=FALSE).. no match, no-op; nothing to update ==> 0
File scruff/data/bamExample.rda: load().. ok [1 object(s)]; updateObject(GAlignments, check=FALSE).. no match, no-op; nothing to update ==> 0
File scruff/data/barcodeExample.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File scruff/data/cbtop10000.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File scruff/data/sceExample.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File scruff/data/validCb.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File scShapes/data/scData.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scTensor/data/GermMale.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File scTensor/data/labelGermMale.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File scTensor/data/m.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File scTensor/data/tsneGermMale.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File scTensor/data/v.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File scTGIF/data/DistalLungEpithelium.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File scTGIF/data/label.DistalLungEpithelium.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File scTGIF/data/pca.DistalLungEpithelium.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File scTHI/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SDAMS/data/exampleSingleCell.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File SDAMS/data/exampleSumExp.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File sechm/data/Chen2017.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File segmenter/data/test_obj.rda: load().. ok [1 object(s)]; updateObject(segmentation, check=FALSE).. no match, no-op; nothing to update ==> 0
File segmenter/data/test_objs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File segmentSeq/data/hSL.RData: load().. ok [1 object(s)]; updateObject(lociData, check=FALSE).. no match, no-op; nothing to update ==> 0
File selectKSigs/inst/extdata/sample.rdata: load().. ok [1 object(s)]; updateObject(MutationFeatureData, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_anopheles_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_anopheles_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_anopheles_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_arabidopsis_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_arabidopsis_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_arabidopsis_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_bovine_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_bovine_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_bovine_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_canine_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_canine_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_canine_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_chicken_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_chicken_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_chicken_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_chimp_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_chimp_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_chimp_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_ecolik12_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_ecolik12_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_ecolik12_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_fly_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_fly_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_fly_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_human_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_human_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_human_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_malaria_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_malaria_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_malaria_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_mouse_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_mouse_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_mouse_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_pig_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_pig_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_pig_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_rat_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_rat_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_rat_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_rhesus_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_rhesus_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_rhesus_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_worm_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_worm_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_worm_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_xenopus_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_xenopus_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_xenopus_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_yeast_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_yeast_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_yeast_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_zebrafish_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_zebrafish_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Info_Accretion_zebrafish_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_anopheles_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_anopheles_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_anopheles_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_arabidopsis_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_arabidopsis_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_arabidopsis_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_bovine_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_bovine_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_bovine_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_canine_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_canine_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_canine_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_chicken_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_chicken_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_chicken_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_chimp_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_chimp_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_chimp_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_ecolik12_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_ecolik12_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_ecolik12_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_fly_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_fly_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_fly_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_human_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_human_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_human_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_malaria_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_malaria_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_malaria_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_mouse_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_mouse_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_mouse_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_pig_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_pig_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_pig_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_rat_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_rat_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_rat_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_rhesus_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_rhesus_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_rhesus_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_worm_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_worm_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_worm_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_xenopus_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_xenopus_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_xenopus_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_yeast_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_yeast_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_yeast_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_zebrafish_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_zebrafish_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Parent_Count_zebrafish_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_anopheles_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_anopheles_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_anopheles_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_arabidopsis_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_arabidopsis_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_arabidopsis_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_bovine_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_bovine_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_bovine_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_canine_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_canine_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_canine_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_chicken_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_chicken_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_chicken_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_chimp_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_chimp_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_chimp_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_ecolik12_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_ecolik12_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_ecolik12_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_fly_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_fly_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_fly_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_human_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_human_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_human_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_malaria_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_malaria_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_malaria_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_mouse_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_mouse_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_mouse_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_pig_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_pig_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_pig_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_rat_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_rat_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_rat_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_rhesus_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_rhesus_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_rhesus_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_worm_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_worm_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_worm_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_xenopus_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_xenopus_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_xenopus_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_yeast_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_yeast_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_yeast_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_zebrafish_BP.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_zebrafish_CC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/data/Term_Count_zebrafish_MF.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SemDist/inst/extdata/myIA.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File semisup/data/table.rda: load().. ok [1 object(s)]; updateObject(NULL, check=FALSE).. no match, no-op; nothing to update ==> 0
File semisup/data/toydata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SEPIRA/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File SEPIRA/data/GeneExp.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SEPIRA/data/LUSCexp.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SEPIRA/data/LUSCmeth.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SEPIRA/data/TFeid.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File SEPIRA/data/VALexp.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File seq2pathway/Meta/data.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File seq2pathway/Meta/features.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File seq2pathway/Meta/hsearch.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File seq2pathway/Meta/links.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File seq2pathway/Meta/nsInfo.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File seq2pathway/Meta/package.rds: readRDS().. ok; updateObject(packageDescription2, check=FALSE).. no match, no-op ==> 0
File seq2pathway/Meta/Rd.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File seq2pathway/Meta/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File seq2pathway/data/Chipseq_Peak_demo.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File seq2pathway/data/dat_chip.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File seq2pathway/data/dat_RNA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File seq2pathway/data/GRanges_demo.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqArray/data/KG_P1_SampData.RData: load().. ok [1 object(s)]; updateObject(AnnotatedDataFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqArray/inst/unitTests/data/Valid.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqCAT/data/test_comparison.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqCAT/data/test_profile_1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqCAT/data/test_profile_2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqCAT/data/test_profile_3.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqCAT/data/test_similarities.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqCAT/data/test_variant_list.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqGate/data/data_MiTF_1000genes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqGSEA/data/DEscore.perm.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqGSEA/data/DEscore.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqGSEA/data/DSscore.perm.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqGSEA/data/DSscore.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqGSEA/data/GS_example.RData: load().. ok [1 object(s)]; updateObject(SeqGeneSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqGSEA/data/RCS_example.RData: load().. ok [1 object(s)]; updateObject(ReadCountSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqPattern/data/TBPpwm.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqPattern/data/zebrafishPromoters.RData: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqPattern/data/zebrafishPromoters24h.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/Bcell_peaks.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/chromHMM_demo_bw_states_gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/chromHMM_demo_chain_url.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/chromHMM_demo_overlaps_gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/chromHMM_demo_segmentation_url.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/chromHMM_demo_state_colors.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/chromHMM_demo_state_total_widths.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/CTCF_in_10a_bigWig_urls.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/CTCF_in_10a_narrowPeak_grs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/CTCF_in_10a_narrowPeak_urls.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/CTCF_in_10a_overlaps_gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/CTCF_in_10a_profiles_dt.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/CTCF_in_10a_profiles_gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqsetvis/data/test_peaks.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqSQC/inst/extdata/example.seqfile.Rdata: load().. ok [1 object(s)]; updateObject(SeqSQC, check=FALSE).. no match, no-op; nothing to update ==> 0
File seqTools/inst/extdata/test_res.RData: load().. ok [11 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SeqVarTools/data/pedigree.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SEtools/data/SE.RData: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File sevenC/data/cutoffBest10.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File sevenC/data/cutoffByTF.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File sevenC/data/modelBest10Avg.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sevenC/data/motif.hg19.CTCF.chr22.cov.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File sevenC/data/motif.hg19.CTCF.chr22.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File sevenC/data/motif.hg19.CTCF.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File sevenC/data/TFspecificModels.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/sgf_ann.rda: load().. ok [1 object(s)]; updateObject(SGFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/sgf_pred.rda: load().. ok [1 object(s)]; updateObject(SGFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/sgfc_ann.rda: load().. ok [1 object(s)]; updateObject(SGFeatureCounts, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/sgfc_pred.rda: load().. ok [1 object(s)]; updateObject(SGFeatureCounts, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/sgv_ann.rda: load().. ok [1 object(s)]; updateObject(SGVariants, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/sgv_pred.rda: load().. ok [1 object(s)]; updateObject(SGVariants, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/sgvc_ann_from_bam.rda: load().. ok [1 object(s)]; updateObject(SGVariantCounts, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/sgvc_ann.rda: load().. ok [1 object(s)]; updateObject(SGVariantCounts, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/sgvc_pred_from_bam.rda: load().. ok [1 object(s)]; updateObject(SGVariantCounts, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/sgvc_pred.rda: load().. ok [1 object(s)]; updateObject(SGVariantCounts, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/si.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/tx.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/txf_ann.rda: load().. ok [1 object(s)]; updateObject(TxFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File SGSeq/data/txf_pred.rda: load().. ok [1 object(s)]; updateObject(TxFeatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File shinyMethyl/inst/unitTests/testDigests.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File ShortRead/vignettes/qa_E-MTAB-1147.Rda: load().. ok [1 object(s)]; updateObject(FastqQA, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIAMCAT/data/feat_crc_zeller.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIAMCAT/data/meta_crc_zeller.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIAMCAT/data/siamcat_example.RData: load().. ok [1 object(s)]; updateObject(siamcat, check=FALSE).. no match, no-op; nothing to update ==> 0
File SigCheck/data/classifyResults.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SigCheck/data/knownSignatures.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SigCheck/data/nkiResults.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File sigFeature/data/ExampleRawData.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File sigFeature/data/featsweepSigFe.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File sigFeature/data/featureRankedList.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File sigFeature/data/results.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File sigFeature/data/sigfeatureRankedList.rda: load().. ok [1 object(s)]; updateObject(integer, check=FALSE).. no match, no-op; nothing to update ==> 0
File SigFuge/data/geneAnnot.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File SigFuge/data/geneDepth.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sights/data/ex_dataMatrix.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sights/data/inglese.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sights/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sights/tests/testthat/inglese_results.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sights/tests/testthat/inglese.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File signatureSearch/data/cell_info.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File signatureSearch/data/chembl_moa_list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File signatureSearch/data/clue_moa_list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File signatureSearch/data/drugs10.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File signatureSearch/data/lincs_expr_inst_info.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File signatureSearch/data/lincs_pert_info.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File signatureSearch/data/lincs_pert_info2.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File signatureSearch/data/lincs_sig_info.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File signatureSearch/data/targetList.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File signatureSearch/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File sigPathway/data/MuscleExample.RData: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SigsPack/data/cosmicSigs.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SigsPack/data/hg19context_freq.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SigsPack/data/sigProfiler20190522.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SigsPack/data/sigProfilerExome.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File sigsquared/data/BrCa443.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIM/data/acgh.data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIM/data/chrom.table.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIM/data/expr.data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIM/data/samples.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIMAT/data/Library.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIMAT/data/RItable.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIMAT/data/Run.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIMAT/data/target.table.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIMAT/data/Targets.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SimBindProfiles/data/precomputed.RData: load().. ok [3 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SimBindProfiles/data/SGR.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIMD/data/example_data.RData: load().. ok [7 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File similaRpeak/data/chr7Profiles.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File similaRpeak/data/demoProfiles.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIMLR/data/BuettnerFlorian.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SIMLR/data/ZeiselAmit.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File simplifyEnrichment/inst/extdata/GO_global_word_freq.rds: readRDS().. ok; updateObject(array, check=FALSE).. no match, no-op ==> 0
File simplifyEnrichment/inst/extdata/pathway_network_kegg.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File simplifyEnrichment/inst/extdata/pathway_network_panther.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File simplifyEnrichment/inst/extdata/pathway_network_pathbank.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File simplifyEnrichment/inst/extdata/pathway_network_reactome.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File simplifyEnrichment/inst/extdata/random_GO_BP_sim_mat_clt.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File simplifyEnrichment/inst/extdata/random_GO_BP_sim_mat.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File simplifyEnrichment/inst/extdata/refseq_gene_desc_human.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File simplifyEnrichment/inst/extdata/tdm_GO.rds: readRDS().. ok; updateObject(TermDocumentMatrix, check=FALSE).. no match, no-op ==> 0
File simplifyEnrichment/inst/extdata/golub_sig_go.RData: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(integer, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File sincell/data/ExpressionMatrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File sincell/data/geneset.list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SingleCellSignalR/data/example_dataset.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SingleCellSignalR/data/LRdb.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SingleCellSignalR/data/markers_default.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SingleCellSignalR/data/mm2Hs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SingleCellSignalR/data/PwC_ReactomeKEGG.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File singleCellTK/inst/extdata/dropEst_scg71/cell.counts.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File singleCellTK/data/MitoGenes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File singleCellTK/data/mouseBrainSubsetSCE.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File singleCellTK/data/msigdb_table.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File singleCellTK/data/sceBatches.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File singleCellTK/data/scExample.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File singleCellTK/data/SEG.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File singleCellTK/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SingleMoleculeFootprinting/inst/extdata/vignette_ConversionRatePrecision.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File singscore/data/scoredf_ccle_epi.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File singscore/data/scoredf_ccle_mes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File singscore/data/scoredf_tcga_epi.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File singscore/data/scoredf_tcga_mes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File singscore/data/tgfb_expr_10_se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File singscore/data/tgfb_gs_dn.rda: load().. ok [1 object(s)]; updateObject(GeneSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File singscore/data/tgfb_gs_up.rda: load().. ok [1 object(s)]; updateObject(GeneSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File singscore/data/toy_expr_se.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File singscore/data/toy_gs_dn.rda: load().. ok [1 object(s)]; updateObject(GeneSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File singscore/data/toy_gs_up.rda: load().. ok [1 object(s)]; updateObject(GeneSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File singscore/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SISPA/data/data.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SISPA/vignettes/data.rda: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sitePath/data/h3n2_align_reduced.rda: load().. ok [1 object(s)]; updateObject(alignment, check=FALSE).. no match, no-op; nothing to update ==> 0
File sitePath/data/h3n2_align.rda: load().. ok [1 object(s)]; updateObject(alignment, check=FALSE).. no match, no-op; nothing to update ==> 0
File sitePath/data/h3n2_tree_reduced.rda: load().. ok [1 object(s)]; updateObject(phylo, check=FALSE).. no match, no-op; nothing to update ==> 0
File sitePath/data/h3n2_tree.rda: load().. ok [1 object(s)]; updateObject(phylo, check=FALSE).. no match, no-op; nothing to update ==> 0
File sitePath/data/sars2_align.rda: load().. ok [1 object(s)]; updateObject(alignment, check=FALSE).. no match, no-op; nothing to update ==> 0
File sitePath/data/sars2_tree.rda: load().. ok [1 object(s)]; updateObject(phylo, check=FALSE).. no match, no-op; nothing to update ==> 0
File sitePath/data/zikv_align_reduced.rda: load().. ok [1 object(s)]; updateObject(alignment, check=FALSE).. no match, no-op; nothing to update ==> 0
File sitePath/data/zikv_align.rda: load().. ok [1 object(s)]; updateObject(alignment, check=FALSE).. no match, no-op; nothing to update ==> 0
File sitePath/data/zikv_tree_reduced.rda: load().. ok [1 object(s)]; updateObject(phylo, check=FALSE).. no match, no-op; nothing to update ==> 0
File sitePath/data/zikv_tree.rda: load().. ok [1 object(s)]; updateObject(phylo, check=FALSE).. no match, no-op; nothing to update ==> 0
File slalom/inst/extdata/sim_N_20_v3.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File slalom/data/mesc.RData: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
Skip package SLGI ==> -3
File slingshot/data/slingshotExample.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SLqPCR/data/SLqPCRdata.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SLqPCR/data/vandesompele.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SMAD/data/TestDatInput.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SMAP/data/GBM.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SMITE/data/curated_expressiondata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SMITE/data/genes_for_conversiontest.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SMITE/data/hg19_genes_bed.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SMITE/data/histone_h3k4me1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SMITE/data/methylationdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SMITE/data/Reactome.Symbol.Igraph.rda: load().. ok [1 object(s)]; updateObject(igraph, check=FALSE).. no match, no-op; nothing to update ==> 0
File SMITE/data/test_annotation_score_data.rda: load().. ok [1 object(s)]; updateObject(PvalueAnnotation, check=FALSE).. no match, no-op; nothing to update ==> 0
File snapCGH/inst/extdata/non.zero.length.distr.non.tiled.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File snapCGH/inst/extdata/non.zero.length.distr.tiled.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File snapCGH/inst/extdata/zero.length.distr.non.tiled.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File snapCGH/inst/extdata/zero.length.distr.tiled.rds: readRDS().. ok; updateObject(numeric, check=FALSE).. no match, no-op ==> 0
File snapcount/inst/testdata/test_jir_output.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File snapcount/inst/testdata/test_junction_intersection_output.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File snapcount/inst/testdata/test_junction_union_output.rds: readRDS().. ok; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File snapcount/inst/testdata/test_psi_output.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File snapcount/inst/testdata/test_ssc_output.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
File snapcount/inst/testdata/test_ts_output.rds: readRDS().. ok; updateObject(data.table, check=FALSE).. no match, no-op ==> 0
Skip package SNPhood ==> -3
File SNPRelate/data/hapmap_geno.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SNPRelate/inst/unitTests/valid/Validate.Beta.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SNPRelate/inst/unitTests/valid/Validate.EIGMIX.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SNPRelate/inst/unitTests/valid/Validate.IBS.RData: load().. ok [1 object(s)]; updateObject(snpgdsIBSClass, check=FALSE).. no match, no-op; nothing to update ==> 0
File SNPRelate/inst/unitTests/valid/Validate.KING.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SNPRelate/inst/unitTests/valid/Validate.MoM.RData: load().. ok [1 object(s)]; updateObject(snpgdsIBDClass, check=FALSE).. no match, no-op; nothing to update ==> 0
File SNPRelate/inst/unitTests/valid/Validate.PCA.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File snpStats/data/families.RData: load().. ok [2 object(s)]; updateObject(SnpMatrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File snpStats/data/for.exercise.RData: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(SnpMatrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File snpStats/data/ld.example.RData: load().. ok [3 object(s)]; updateObject(SnpMatrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(SnpMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File snpStats/data/testdata.RData: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(SnpMatrix, check=FALSE).. no match, no-op; updateObject(XSnpMatrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File soGGi/data/chipExampleBig.rda: load().. ok [1 object(s)]; updateObject(ChIPprofile, check=FALSE).. no match, no-op; nothing to update ==> 0
File soGGi/data/ik_Example.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File soGGi/data/ik_Profiles.rda: load().. ok [1 object(s)]; updateObject(ChIPprofile, check=FALSE).. no match, no-op; nothing to update ==> 0
File soGGi/data/pwmCov.rda: load().. ok [1 object(s)]; updateObject(SimpleRleList, check=FALSE).. no match, no-op; nothing to update ==> 0
File soGGi/data/singleGRange.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File SomaticSignatures/data/kmers.rda: load().. ok [2 object(s)]; updateObject(array, check=FALSE).. no match, no-op; updateObject(table, check=FALSE).. no match, no-op; nothing to update ==> 0
File SomaticSignatures/data/sca_mm.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SomaticSignatures/data/sca_motifs_tiny.rda: load().. ok [1 object(s)]; updateObject(VRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File SomaticSignatures/data/sca_sigs.rda: load().. ok [2 object(s)]; updateObject(MutationalSignatures, check=FALSE).. no match, no-op; updateObject(MutationalSignatures, check=FALSE).. no match, no-op; nothing to update ==> 0
File SomaticSignatures/data/signatures21.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SOMNiBUS/tests/testthat/data/ref_input_binomRegMethModelSummary.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File SOMNiBUS/tests/testthat/data/ref_input_BSMethEMUpdate.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File SOMNiBUS/tests/testthat/data/ref_input_hessianComp.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File SOMNiBUS/tests/testthat/data/ref_results.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File SOMNiBUS/tests/testthat/data/ref_resultsV2.RDS: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File SOMNiBUS/data/RAdat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SOMNiBUS/data/RAdat2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Spaniel/inst/extdata/counts.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File Spaniel/inst/extdata/image.rds: readRDS().. ok; updateObject(rastergrob, check=FALSE).. no match, no-op ==> 0
File Spaniel/inst/extdata/sceData.rds: readRDS().. ok; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op ==> 0
File sparrow/inst/extdata/testdata/genesets-sparrow-list-of-lists.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File sparrow/inst/extdata/testdata/TCGA-BRCA-some.DGEList.rds: readRDS().. ok; updateObject(DGEList, check=FALSE).. no match, no-op ==> 0
File sparrow/inst/extdata/testdata/test-SparrowResult.rds: readRDS().. ok; updateObject(SparrowResult, check=FALSE).. no match, no-op ==> 0
File sparsenetgls/data/bandprec.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SparseSignatures/data/background.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SparseSignatures/data/background2.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SparseSignatures/data/cv_example.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SparseSignatures/data/imported_data.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SparseSignatures/data/lambda_range_example.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SparseSignatures/data/mutation_categories.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File SparseSignatures/data/nmf_LassoK_example.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SparseSignatures/data/patients.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SparseSignatures/data/ssm560_reduced.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File SparseSignatures/data/starting_betas_example.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatialDE/data/MOB_sample_info.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatialDE/data/Rep11_MOB_0.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpatialDecon/data/cellcols.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpatialDecon/data/mean.resid.sd.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpatialDecon/data/mini_geomx_dataset.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpatialDecon/data/mini_singleCell_dataset.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpatialDecon/data/nsclc.RData: load().. ok [1 object(s)]; updateObject(NanoStringGeoMxSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpatialDecon/data/safeTME.matches.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpatialDecon/data/safeTME.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpatialDecon/tests/testthat/expectedtestresults.RData: load().. ok [5 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpatialDecon/tests/testthat/testdata.RData: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatialHeatmap/data/aSVG.remote.repo.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatialHeatmap/data/deg.table.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatialHeatmap/data/lis.deg.up.down.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/anchor_pair_example_count.rda: load().. ok [1 object(s)]; updateObject(interactionData, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/anchor_pair_example_match.rda: load().. ok [1 object(s)]; updateObject(interactionData, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/anchor_pair_example_score.rda: load().. ok [1 object(s)]; updateObject(interactionData, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/compare_pairs_example.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/filter_pairs_example.rda: load().. ok [1 object(s)]; updateObject(interactionData, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/int_data_k562.rda: load().. ok [1 object(s)]; updateObject(interactionData, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/int_data_mslcl.rda: load().. ok [1 object(s)]; updateObject(interactionData, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/int_data_yy1.rda: load().. ok [1 object(s)]; updateObject(interactionData, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/interactions_yy1_enhancer.rda: load().. ok [1 object(s)]; updateObject(GenomicInteractions, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/interactions_yy1_ep.rda: load().. ok [1 object(s)]; updateObject(GenomicInteractions, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/interactions_yy1_promoter.rda: load().. ok [1 object(s)]; updateObject(GenomicInteractions, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/interactions_yy1.rda: load().. ok [1 object(s)]; updateObject(GenomicInteractions, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/scan_interactions_example_filtered.rda: load().. ok [1 object(s)]; updateObject(interactionData, check=FALSE).. no match, no-op; nothing to update ==> 0
File spatzie/data/scan_interactions_example.rda: load().. ok [1 object(s)]; updateObject(interactionData, check=FALSE).. no match, no-op; nothing to update ==> 0
File specL/data/iRTpeptides.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File specL/data/ms1_p2069.RData: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File specL/data/peptideStd.RData: load().. ok [2 object(s)]; updateObject(psmSet, check=FALSE).. no match, no-op; updateObject(psmSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpeCond/data/expressionSpeCondExample.rdata: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpeCond/data/expSetSpeCondExample.rdata: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpeCond/data/simulatedSpeCondData.rdata: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Spectra/data/fft_spectrum.RData: load().. ok [1 object(s)]; updateObject(Spectra, check=FALSE).. no match, no-op; nothing to update ==> 0
File SpectralTAD/data/rao_chr20_25_rep.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPEM/data/sos.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPIA/data/colorectalcancer.RData: load().. ok [3 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPIA/data/Vessels.RData: load().. ok [2 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPIA/inst/extdata/hsaSPIA.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPIA/inst/extdata/mmuSPIA.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File spicyR/data/diabetesData.rda: load().. ok [1 object(s)]; updateObject(SegmentedCells, check=FALSE).. no match, no-op; nothing to update ==> 0
File spicyR/data/spicyTest.rda: load().. ok [1 object(s)]; updateObject(SpicyResults, check=FALSE).. no match, no-op; nothing to update ==> 0
File spicyR/data/spicyTestBootstrap.rda: load().. ok [1 object(s)]; updateObject(SpicyResults, check=FALSE).. no match, no-op; nothing to update ==> 0
File spikeLI/data/conc133.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File spikeLI/data/conc95.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File spikeLI/data/hgu.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File spikeLI/data/SPIKE_IN.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File spikeLI/data/SPIKE_IN95.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File spikeLI/data/SPIKE_INA.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File spikeLI/data/SPIKE_INB.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File spikeLI/data/SPIKE_INH.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File spiky/data/dedup.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File spiky/data/genbank_mito.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File spiky/data/phage.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File spiky/data/spike_cram_counts.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File spiky/data/spike_read_counts.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File spiky/data/spike.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File spiky/data/ssb_res.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File spiky/data/testGR.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File spkTools/data/affy.rda: load().. ok [1 object(s)]; updateObject(SpikeInExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File SplicingFactory/data/tcga_brca_luma_dataset.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SplicingGraphs/inst/extdata/TSPCsg.rda: load().. ok [1 object(s)]; updateObject(SplicingGraphs, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File SplicingGraphs/vignettes/precomputed_results/sg_with_bubbles.rda: load().. ok [1 object(s)]; updateObject(SplicingGraphs, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File SplicingGraphs/vignettes/precomputed_results/sg_with_reads.rda: load().. ok [1 object(s)]; updateObject(SplicingGraphs, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File splineTimeR/data/TCsimData.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/acceptor.m.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/compatible_cds.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/compatible_tx.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/donor.m.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/pcr_result1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/primers.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/region_minus_exon.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/roi.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/splice_data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/splice_fasta.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/thecds.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/theexons.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/valid_cds.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPLINTER/data/valid_tx.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPONGE/data/ceRNA_interactions.RData: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPONGE/data/gene_expr.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPONGE/data/mir_expr.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPONGE/data/mir_interactions.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPONGE/data/mircode.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPONGE/data/precomputed_null_model.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPONGE/data/scor_simulation_cov_matrices.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPONGE/data/targetscan.RData: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File spqn/inst/unitTests/cor_m_spqn_sample.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File spqn/inst/unitTests/grp_loc_target.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPsimSeq/data/scNGP.data.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File SPsimSeq/data/zhang.data.sub.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File sRACIPE/data/configData.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File sRACIPE/data/CoupledToggleSwitchSA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sRACIPE/data/demoCircuit.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sRACIPE/data/EMT1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sRACIPE/data/EMT2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File srnadiff/inst/extdata/srnadiffExample.rda: load().. ok [1 object(s)]; updateObject(srnadiffExp, check=FALSE).. no match, no-op; nothing to update ==> 0
File sSeq/data/countsTable.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File sSeq/data/Hammer2months.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File sSeq/data/Sultan.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File sSeq/data/Tuch.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssize/data/exp.sd.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssPATHS/data/expected_score_output.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssPATHS/data/gene_weights_reference.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssPATHS/data/new_samp_df.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssPATHS/data/tcga_expr_df.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssrch/data/docset_cancer68.rda: load().. ok [1 object(s)]; updateObject(DocSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssrch/data/study_publ_dates.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssrch/data/titles68.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssrch/data/urls68.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssrch/inst/rda/ds_can1009b.rda: load().. ok [1 object(s)]; updateObject(DocSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File ssviz/data/ssviz.rda: load().. ok [5 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; updateObject(DFrame, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(DFrame, check=FALSE).. no match, no-op; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File stageR/data/esetProstate.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File stageR/data/hammer.eset.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File STAN/data/example.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File STAN/data/pilot.hg19.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File STAN/data/trainRegions.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File STAN/data/ucscGenes.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File STAN/data/yeastTF_databychrom_ex.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File STAN/data/yeastTF_SGDGenes.rda: load().. ok [1 object(s)]; updateObject(GeneRegionTrack, check=FALSE).. no match, no-op; nothing to update ==> 0
File staRank/data/salmonellaInfection.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File staRank/data/salmonellaStability.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File StarBioTrek/data/Data_CANCER_normUQ_fil.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File StarBioTrek/data/netw_IPPI.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File StarBioTrek/data/netw.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File StarBioTrek/data/norm.rda: load().. ok [1 object(s)]; updateObject(function, check=FALSE).. no match, no-op; nothing to update ==> 0
File StarBioTrek/data/path.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. returned an error ==> -1
File StarBioTrek/data/pathway_matrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File StarBioTrek/data/pathway.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File StarBioTrek/data/score_euc_dista.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File StarBioTrek/data/tumo.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File STATegRa/data/STATegRa_S1.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STATegRa/data/STATegRa_S2.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STATegRa/data/STATegRa_S3.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STATegRa/data/TCGA_BRCA_Batch_93.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File STRINGdb/data/diff_exp_example1.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STRINGdb/data/interactions_example.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STROMA4/data/B.stroma.property.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STROMA4/data/BL1.property.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STROMA4/data/BL2.property.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STROMA4/data/D.stroma.property.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STROMA4/data/E.stroma.property.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STROMA4/data/IM.property.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STROMA4/data/LAR.property.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STROMA4/data/M.property.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STROMA4/data/MSL.property.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File STROMA4/data/T.stroma.property.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Structstrings/data/dbs.rda: load().. ok [1 object(s)]; updateObject(DotBracketStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Structstrings/data/nseq.rda: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File structToolbox/R/sysdata.rda: load().. ok [3 object(s)]; updateObject(DatasetExperiment, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File SubCellBarCode/data/hcc827Ctrl.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SubCellBarCode/data/hcc827CtrlPSMCount.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SubCellBarCode/data/hcc827exon.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SubCellBarCode/data/hcc827GEF.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SubCellBarCode/data/hcc827GEFClass.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SubCellBarCode/data/hcc827GefPSMCount.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SubCellBarCode/data/markerProteins.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File subSeq/data/hammer.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File subSeq/data/ss.rda: load().. ok [1 object(s)]; updateObject(subsamples, check=FALSE).. no match, no-op; nothing to update ==> 0
File SummarizedBenchmark/data/quantSB.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File SummarizedBenchmark/data/sb.RData: load().. ok [1 object(s)]; updateObject(SummarizedBenchmark, check=FALSE).. no match, no-op; nothing to update ==> 0
File SummarizedBenchmark/data/soneson2016.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File SummarizedBenchmark/data/tdat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Summix/data/ancestryData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File supersigs/data/example_dt.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File supersigs/data/supersig_ls.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File supersigs/R/sysdata.rda: load().. ok [12 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File supraHex/data/Fang.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File supraHex/data/Golub.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File supraHex/data/Xiang.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File surfaltr/data/Crb1.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File surfaltr/data/hpa_genes.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File surfaltr/data/hpa_mouse_genes.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File surfaltr/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File surfaltr/tests/testthat/sysdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File survcomp/data/breastCancerData.RData: load().. ok [6 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_5C.bedpe.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_ChIAPET_pol2.bedpe.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_ChIPExo_CTCF.bedgraph.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_ChIPSeq_CTCF.bedgraph.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_ChIPSeq_pol2.bed.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_ChIPSeq_pol2.bedgraph.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_ChIPSeq_severalfactors.bed.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_DNaseI.bedgraph.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_genes.bed.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_GWAS.bed.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_hg18_genome.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_HiC.matrix.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_RNASeq_K562.bedgraph.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Sushi/data/Sushi_transcripts.bed.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File sva/src/symbols.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File SWATH2stats/data/Spyogenes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SwathXtend/data/ionCorGS.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File swfdr/data/BMI_GIANT_GWAS_sample.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File swfdr/data/journals_pVals.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File switchBox/data/testingData.rda: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File switchBox/data/trainingData.rda: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File switchde/data/ex_pseudotime.rda: load().. ok [1 object(s)]; updateObject(array, check=FALSE).. no match, no-op; nothing to update ==> 0
File switchde/data/synth_gex.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File synapter/data/synapterTiny.rda: load().. ok [1 object(s)]; updateObject(Synapter, check=FALSE).. returned an error ==> -1
File synergyfinder/data/mathews_screening_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File synergyfinder/data/NCATS_screening_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File synergyfinder/data/ONEIL_screening_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File SynExtend/data/Generic.RData: load().. ok [1 object(s)]; updateObject(glm, check=FALSE).. no match, no-op; nothing to update ==> 0
File synlet/data/exampleDat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TADCompare/data/GM12878.40kb.raw.chr2.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TADCompare/data/IMR90.40kb.raw.chr2.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TADCompare/data/rao_chr22_prim.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TADCompare/data/rao_chr22_rep.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TADCompare/data/time_mats.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TAPseq/data/bone_marrow_genex.rda: load().. ok [1 object(s)]; updateObject(Seurat, check=FALSE).. no match, no-op; nothing to update ==> 0
File TAPseq/data/chr11_genes.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File TAPseq/data/chr11_polyA_sites.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File TAPseq/data/chr11_primers.rda: load().. ok [1 object(s)]; updateObject(TsIOList, check=FALSE).. no match, no-op; nothing to update ==> 0
File TAPseq/data/chr11_truncated_txs_seq.rda: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File TAPseq/data/chr11_truncated_txs.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File TAPseq/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File target/data/real_peaks.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File target/data/real_transcripts.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File target/data/sim_peaks.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File target/data/sim_transcripts.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File TargetDecoy/data/ModSwiss.rda: load().. ok [1 object(s)]; updateObject(mzID, check=FALSE).. no match, no-op; nothing to update ==> 0
File TargetDecoy/data/ModSwissXT.rda: load().. ok [1 object(s)]; updateObject(mzID, check=FALSE).. no match, no-op; nothing to update ==> 0
File TargetScore/inst/extdata/realtestdata.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TargetSearch/data/TSExample.rda: load().. ok [7 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(tsProfile, check=FALSE).. no match, no-op; updateObject(tsMSdata, check=FALSE).. no match, no-op; updateObject(tsLib, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(tsRim, check=FALSE).. no match, no-op; updateObject(tsSample, check=FALSE).. no match, no-op; nothing to update ==> 0
File TarSeqQC/data/ampliPanel.rda: load().. ok [1 object(s)]; updateObject(TargetExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TarSeqQC/data/ampliPanel2.rda: load().. ok [1 object(s)]; updateObject(TargetExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TarSeqQC/data/myCounts.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TarSeqQC/data/TEList.rda: load().. ok [1 object(s)]; updateObject(TargetExperimentList, check=FALSE).. no match, no-op; nothing to update ==> 0
File TBSignatureProfiler/data/common_sigAnnotData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TBSignatureProfiler/data/COVIDsignatures.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TBSignatureProfiler/data/OriginalTrainingData.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TBSignatureProfiler/data/sigAnnotData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TBSignatureProfiler/data/TB_hiv.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TBSignatureProfiler/data/TB_indian.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TBSignatureProfiler/data/TBcommon.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TBSignatureProfiler/data/TBsignatures.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TBSignatureProfiler/data/TBsignaturesSplit.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCC/data/arab.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCC/data/hypoData_mg.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCC/data/hypoData_ts.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCC/data/hypoData.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCC/data/nakai.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/chol_maf.rda: load().. ok [1 object(s)]; updateObject(MAF, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/clinical.biotab.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/dataBRCA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/dataDEGsFiltLevel.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/dataREAD_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/dataREAD.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/gbm.exp.harmonized.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/gbm.exp.legacy.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/geneInfo.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/geneInfoHT.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/met.gbm.27k.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/msi_results.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/PCBC_stemSig.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/TabSubtypesCol_merged.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/tabSurvKMcompleteDEGs.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/data/Tumor.purity.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAbiolinks/R/sysdata.rda: load().. ok [40 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAutils/data/clinicalNames.rda: load().. ok [1 object(s)]; updateObject(CompressedCharacterList, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAutils/data/diseaseCodes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCGAutils/data/sampleTypes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCseq/data/countsTable.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCseq/data/experiment_BAMfile.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCseq/data/experiment.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCseq/data/genomicIntervals.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TCseq/data/tca_ATAC.rda: load().. ok [1 object(s)]; updateObject(TCA, check=FALSE).. no match, no-op; nothing to update ==> 0
File TDARACNE/data/dataIRMAoff.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File TDARACNE/data/dataIRMAon.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File TDARACNE/data/dataSOSmean.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File TDARACNE/data/dataYeast.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File TDARACNE/data/threshIRMAon.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TDARACNE/data/threshSOSmean.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TDARACNE/data/threshYeast.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File tenXplore/data/CellTypes.rda: load().. ok [1 object(s)]; updateObject(TermSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File tenXplore/data/tenx500.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFARM/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TFARM/data/data_man.rda: load().. ok [10 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFARM/data/MCF7_chr1.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFBSTools/data/MA0003.2.rda: load().. ok [1 object(s)]; updateObject(PFMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFBSTools/data/MA0004.1.rda: load().. ok [1 object(s)]; updateObject(PFMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFBSTools/data/MA0043.rda: load().. ok [1 object(s)]; updateObject(PFMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFBSTools/data/MA0048.rda: load().. ok [1 object(s)]; updateObject(PFMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/ARNT.metadata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/ARNT.peaks.bed.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/DnaseHS_db.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/Entrez.gene.IDs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/Genes.Upreg.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/gr.list.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/GSEA.result.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/hypoxia_DESeq.rda: load().. ok [1 object(s)]; updateObject(DESeqResults, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/hypoxia.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/log2.FC.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/Mat01.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/MetaData.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFEA.ChIP/data/tfbs.database.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFHAZ/data/data_man.rda: load().. ok [8 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFHAZ/data/Ishikawa.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/inst/fimoser/fimo16rr.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TFutils/data/cisbpTFcat_2.0.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/cisbpTFcat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/demo_fimo_granges.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/encode690.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/fimo16.rda: load().. ok [1 object(s)]; updateObject(GenomicFiles, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/fimoMap.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/gwascat_hg19_chr17.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/hocomoco.mono.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/hocomoco.mono.sep2018.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/lambert_snps.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/metadata_tf.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/named_tf.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/seqinfo_hg19_chr17.rda: load().. ok [1 object(s)]; updateObject(Seqinfo, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/tfhash.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/tftColl.rda: load().. ok [1 object(s)]; updateObject(GeneSetCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File TFutils/data/tftCollMap.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/dev/benchmark/stats_pasilla_standard.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File tidybulk/dev/benchmark/stats_pasilla_ttBulk.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File tidybulk/dev/benchmark/stats_TCGA_standard.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File tidybulk/dev/benchmark/stats_TCGA_ttBulk.rds: readRDS().. ok; updateObject(tbl_df, check=FALSE).. no match, no-op ==> 0
File tidybulk/data/breast_tcga_mini_SE.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/counts_ensembl.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/counts_SE.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/ensembl_symbol_mapping.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/flybaseIDs.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/se_mini.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/se.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/test_deseq2_df.rda: load().. ok [1 object(s)]; updateObject(DESeqDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/vignette_manuscript_signature_boxplot.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/vignette_manuscript_signature_tsne.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/vignette_manuscript_signature_tsne2.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidybulk/data/X_cibersort.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidySingleCellExperiment/data/cell_type_df.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidySingleCellExperiment/data/pbmc_small_nested_interactions.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidySingleCellExperiment/data/pbmc_small.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidySummarizedExperiment/data/pasilla.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File tidySummarizedExperiment/data/se.rda: load().. ok [1 object(s)]; updateObject(RangedSummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File tigre/data/drosophila_gpsim_fragment.RData: load().. ok [1 object(s)]; updateObject(ExpressionTimeSeries, check=FALSE).. no match, no-op; nothing to update ==> 0
File tigre/data/drosophila_mmgmos_fragment.RData: load().. ok [1 object(s)]; updateObject(exprReslt, check=FALSE).. returned an error ==> -1
File tilingArray/data/gffSub.rda: load().. ok [1 object(s)]; updateObject(GenomeFeature, check=FALSE).. no match, no-op; nothing to update ==> 0
File tilingArray/data/segnf.rda: load().. ok [1 object(s)]; updateObject(environment, check=FALSE).. no match, no-op; nothing to update ==> 0
File timecourse/data/fruitfly.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File timeOmics/inst/extdata/data_silhouette.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File timeOmics/data-raw/kidneySimTimeGroup.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File timeOmics/data-raw/lmms.test.data.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File timeOmics/data-raw/timeOmics.simdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File timeOmics/data/timeOmics.simdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File timeOmics/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimeSeriesExperiment/vignettes/de_trajectory_cop1.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TimeSeriesExperiment/vignettes/enrich_res_cop1.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TimeSeriesExperiment/data/endoderm_small.rda: load().. ok [1 object(s)]; updateObject(TimeSeriesExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/tests/testthat/Clusters.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File TimiRGeN/tests/testthat/corrmat.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/EnrichWiki.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/filt_df.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/filtered_genelist_c.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/filtered_genelist_s.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/gene_entrez_c.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/genelist_s.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/geneslist_c.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/GenesofInterest.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/genetic_data.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/IDs_mouse_miR.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/IDs_mouse_mRNA.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File TimiRGeN/tests/testthat/interactions.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/log2fc.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/MAE_mm.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/MAE_Prefix.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/MiningMatrix.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/miRDB_resuts.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/miRTarBase_results.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/net.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/TargetScans_results.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/wikimatrix.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/tests/testthat/wpdata.rds: readRDS().. ok; updateObject(MultiAssayExperiment, check=FALSE).. no match, no-op ==> 0
File TimiRGeN/data/e_list_mouse.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/data/hs_miR.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/data/hs_mRNA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/data/hs_probes.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/data/long_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/data/miRTarBase.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/data/mm_miR.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/data/mm_mRNA.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/data/UUO_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/data/w_list_mouse.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/inst/extdata/clusterdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/inst/extdata/clusters.rda: load().. ok [1 object(s)]; updateObject(fclust, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/inst/extdata/hs_gmt.rda: load().. ok [1 object(s)]; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File TimiRGeN/inst/extdata/Int_data.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/inst/extdata/mfuzzdata.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TimiRGeN/inst/extdata/mm_gmt.rda: load().. ok [1 object(s)]; updateObject(MultiAssayExperiment, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File TimiRGeN/inst/extdata/w_list_human.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TIN/data/geneAnnotation.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TIN/data/geneSets.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TIN/data/sampleSetFirmaScores.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TIN/data/sampleSetGeneSummaries.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TIN/data/splicingFactors.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TissueEnrich/inst/extdata/combine-expression.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TitanCNA/data/EMresults.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File TitanCNA/inst/extdata/Seqinfo_hg19.rda: load().. failed! ==> -2
File tLOH/data/humanGBMsampleAC.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TMixClust/data/best_clust_toy_obj.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TMixClust/data/best_clust_yeast_obj.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TMixClust/data/toy_data_df.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TNBC.CMS/data/GSE25055.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TNBC.CMS/R/sysdata.rda: load().. ok [9 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(svm, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TOAST/data/beta_emp.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TOAST/data/CBS_PBMC_array.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TOAST/data/RA_100samples.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File tomoda/data/zh.data.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File topdownr/data/tds.RData: load().. ok [1 object(s)]; updateObject(TopDownSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File topdownr/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File topGO/data/geneList.rda: load().. ok [3 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(function, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File topGO/data/GOdata.rda: load().. ok [1 object(s)]; updateObject(topGOdata, check=FALSE).. returned an error ==> -1
File topGO/data/results.tGO.rda: load().. ok [2 object(s)]; updateObject(topGOresult, check=FALSE).. no match, no-op; updateObject(topGOresult, check=FALSE).. no match, no-op; nothing to update ==> 0
File ToxicoGx/tests/testthat/annotation.TGGATESsmall.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/cellInfo.TGGATESsmall.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/cellNames.TGGATESsmall.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/curation.TGGATESsmall.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/drugInfo.TGGATESsmall.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/drugNames.TGGATESsmall.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/mDataNames.TGGATESsmall.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/name.TGGATESsmall.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/pertNumber.TGGATESsmall.rds: readRDS().. ok; updateObject(array, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/perturbation.TGGATESsmall.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/rna.featureInfo.TGGATESsmall.rds: readRDS().. ok; updateObject(DFrame, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/rna.fNames.TGGATESsmall.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/rna.molecularProfiles.TGGATESsmall.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/rna.phenoData.TGGATESsmall.rds: readRDS().. ok; updateObject(DFrame, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/sensitivitProfiles.TGGATESsmall.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/sensitivityInfo.TGGATESsmall.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/sensitivityMeasures.TGGATESsmall.rds: readRDS().. ok; updateObject(character, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/sensNumber.TGGATESsmall.rds: readRDS().. ok; updateObject(matrix, check=FALSE).. no match, no-op ==> 0
File ToxicoGx/tests/testthat/subsetTo.TGGATESsmall.rds: readRDS().. ok; updateObject(ToxicoSet, check=FALSE).. returned an error ==> -1
File ToxicoGx/data/HCC_sig.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File ToxicoGx/data/TGGATESsmall.rda: load().. ok [1 object(s)]; updateObject(ToxicoSet, check=FALSE).. returned an error ==> -1
File TPP/inst/test_data/panobinostat_2D_fcResults.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/inst/test_data/panobinostat_2D_fcResults2.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/inst/test_data/panobinostat_2D_fitResults.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/inst/test_data/panobinostat_2D_fitResults2.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/inst/test_data/panobinostat_2D_fitResults3.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/inst/test_data/panobinostat_2D_importResults.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/inst/test_data/panobinostat_2D_importResults2.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/inst/test_data/panobinostat_2D_normResults.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/inst/test_data/panobinostat_2D_normResults2.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/inst/test_data/panobinostat_2D_normResults3.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/inst/test_data/panobinostat_CCR_fitResults.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TPP/data/hdacCCR_smallExample.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/data/hdacTR_resultsTable_smallExample.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/data/hdacTR_smallExample.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/data/panobinostat_2DTPP_smallExample.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/data/TPPTR_reference_results_HepG2.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/inst/example_data/2D_example_data/fractAbundInData.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/inst/example_data/2D_example_data/referenceNormData.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/inst/example_data/2D_example_data/shortCCRresults.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/inst/example_data/2D_example_data/shortData2d.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/inst/extdata/randomESet.Rdata: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/inst/extdata/validationData_meltCurveFilter.Rdata: load().. ok [5 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(logical, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/inst/extdata/validationData_pvalBinning.Rdata: load().. ok [2 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/inst/extdata/validationData_pvalComputation.Rdata: load().. ok [9 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(numeric, check=FALSE).. no match, no-op; updateObject(logical, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP/inst/test_data/panobinostat_2DTPP_smallExample.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP2D/data/config_tab.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP2D/data/raw_dat_list.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP2D/data/simulated_cell_extract_df.RData: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File TPP2D/R/sysdata.rda: load().. ok [1 object(s)]; updateObject(lda, check=FALSE).. no match, no-op; nothing to update ==> 0
File tracktables/data/Intervals.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File trackViewer/inst/extdata/ctcf.sample.rds: readRDS().. ok; updateObject(track, check=FALSE).. no match, no-op ==> 0
File trackViewer/inst/extdata/gi.rds: readRDS().. ok; updateObject(GInteractions, check=FALSE).. no match, no-op ==> 0
File trackViewer/inst/extdata/ideo.hg38.rds: readRDS().. ok; updateObject(GRanges, check=FALSE).. no match, no-op ==> 0
File trackViewer/inst/extdata/nij.chr6.51120000.53200000.gi.rds: readRDS().. ok; updateObject(GInteractions, check=FALSE).. no match, no-op ==> 0
File tradeSeq/data/celltype.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File tradeSeq/data/countMatrix.rda: load().. ok [1 object(s)]; updateObject(dgCMatrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File tradeSeq/data/crv.rda: load().. ok [1 object(s)]; updateObject(SlingshotDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File tradeSeq/data/gamList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File tradeSeq/data/sds.rda: load().. ok [1 object(s)]; updateObject(SlingshotDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/chol_answers.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/chol_attributes.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/chol_branch_point_results.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/chol_pseudo_time_normalised.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/chol_pseudo_time.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/crooked_path_center.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/crooked_path_projection.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/crooked_path_radius.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/crooked_path.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/hep_answers.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/hep_attributes.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/hep_pseudo_time_normalised.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/hep_pseudo_time.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/oscillation.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/single_cell_matrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/straight_path_center.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/straight_path_projection.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/straight_path_radius.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File TrajectoryGeometry/data/straight_path.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/association.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/DEsymbols.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/GPL570.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/GSE9988.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Hs700.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Hs800.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Hs900.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/HsBPTerms.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Mm700.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Mm800.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Mm900.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Rn700.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Rn800.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Rn900.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Sc700.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Sc800.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/data/Sc900.RData: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptogramer/vignettes/terms.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptR/data/annot.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptR/data/cds.rda: load().. ok [1 object(s)]; updateObject(ChipDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File transcriptR/data/tds.rda: load().. ok [1 object(s)]; updateObject(TranscriptionDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File transite/data/ge.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File transite/data/kmers_enrichment.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File transite/data/motifs.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File transite/data/toy_motif_matrix.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File tRanslatome/data/tRanslatomeSampleData.RData: load().. ok [7 object(s)]; updateObject(GOsims, check=FALSE).. no match, no-op; updateObject(GOsets, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(DEGs, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(TranslatomeDataset, check=FALSE).. no match, no-op; nothing to update ==> 0
File TraRe/inst/extdata/ChIP/Tumor_OV50.tar8855_reg638.VBSR.m100_b10.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/graph_netrun_example.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/linker_phaseone_example.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/linker_rewiring_example.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/prepared_rewiring_example.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/refinedsumm.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/targets_linker_example.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/tfs_linker_example_eg.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/tfs_linker_example.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/VignetteFiles/graph_netrun_vignette.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/VignetteFiles/linker_output_vignette.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File TraRe/inst/extdata/VignetteFiles/SEObject.rds: readRDS().. ok; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op ==> 0
File traseR/data/CEU.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File traseR/data/taSNP.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File traseR/data/taSNPLD.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File traseR/data/Tcell.RData: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File traviz/data/counts.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File traviz/data/crv.rda: load().. ok [1 object(s)]; updateObject(SlingshotDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File traviz/data/sce.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TreeAndLeaf/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TreeAndLeaf/data/phylo_species.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TreeAndLeaf/data/phylo_tree.RData: load().. ok [1 object(s)]; updateObject(phylo, check=FALSE).. no match, no-op; nothing to update ==> 0
File TreeAndLeaf/data/spdata.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File treekoR/data/COVIDSampleData.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File TreeSummarizedExperiment/data/tinyTree.RData: load().. ok [1 object(s)]; updateObject(phylo, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/inst/extdata/ampAD.154genes.mef2cTFs.278samples.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/inst/extdata/ampAD.58genes.mef2cTFs.278samples.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/inst/extdata/brand.tbl.model.trimmed.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/inst/extdata/human.regulatory.genes.RData: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/inst/extdata/tbl.mef2c.model.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/inst/extdata/xgboost.sample.RData: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/inst/extdata/yeast-53genes-536-samples.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/inst/unitTests/tbl.snps.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/misc/nfe2/brand/trena.model.fimo.phast7.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/misc/nfe2/brand/trena.models.brand.noDNA.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/misc/nfe2/gtex-blood/trena.models.fimo.phast7.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File trena/misc/nfe2/tbls.motifs.RData: load().. ok [2 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Trendy/data/trendyExampleData.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRESS/data/Basal.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRESS/data/DMR_M3vsWT.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRESS/data/DMR_SixWeekvsTwoWeek.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRESS/inst/extdata/examplebyBam.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(Rle, check=FALSE).. no match, no-op; nothing to update ==> 0
File tricycle/data/neuroRef.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File tricycle/data/neurosphere_example.rda: load().. ok [1 object(s)]; updateObject(SingleCellExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File tricycle/data/RevelioGeneList.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File trigger/data/yeast.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File trio/data/trio.data.RData: load().. ok [12 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File tRNA/data/gr_eco.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File tRNA/data/gr_human.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File tRNA/data/gr_human2.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File tRNA/data/gr.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRONCO/data/aCML.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRONCO/data/crc_gistic.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRONCO/data/crc_maf.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRONCO/data/crc_plain.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRONCO/data/muts.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRONCO/data/stage.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRONCO/data/test_dataset_no_hypos.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRONCO/data/test_dataset.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRONCO/data/test_model_kfold.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TRONCO/data/test_model.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File TSCAN/data/lpsdata.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File tscR/data/tscR.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File tspair/data/tspdata.rda: load().. ok [5 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(ExpressionSet, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File TSRchitect/inst/extdata/tssObjectExample.RData: load().. ok [1 object(s)]; updateObject(tssObject, check=FALSE).. no match, no-op; nothing to update ==> 0
File TurboNorm/data/methylation.RData: load().. ok [1 object(s)]; updateObject(RGList, check=FALSE).. no match, no-op; nothing to update ==> 0
File TVTB/inst/misc/motivations_rules.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File TVTB/inst/shinyApp/rds/parallel.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File tweeDEseq/data/seizure.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File twilight/data/exfdr.rda: load().. ok [1 object(s)]; updateObject(twilight, check=FALSE).. no match, no-op; nothing to update ==> 0
File twilight/data/expval.rda: load().. ok [1 object(s)]; updateObject(twilight, check=FALSE).. no match, no-op; nothing to update ==> 0
File twoddpcr/data/KRAScounts.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File twoddpcr/data/KRAScountsQS.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File twoddpcr/data/KRAScountsWellCol.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File twoddpcr/data/KRASdata.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File Ularcirc/inst/extdata/TwoSzabo.RData: load().. ok [3 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File UMI4Cats/data/ex_ciita_umi4c.rda: load().. ok [1 object(s)]; updateObject(UMI4C, check=FALSE).. no match, no-op; nothing to update ==> 0
File UNDO/data/BiologicalMixMCF7HS27.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File UNDO/data/NumericalMixingMatrix.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File UNDO/data/NumericalMixMCF7HS27.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File UNDO/data/PureMCF7HS27.rda: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File unifiedWMWqPCR/data/NBdata.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File unifiedWMWqPCR/data/NBmat.rda: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(factor, check=FALSE).. no match, no-op; nothing to update ==> 0
File Uniquorn/inst/Libraries_Ref_gen_GRCH37_Uniquorn_DB.RData: load().. failed! ==> -2
File Uniquorn/inst/Libraries/GRCH37/CELLMINER/CCL_List_Uniquorn_DB.RData: load().. failed! ==> -2
File Uniquorn/inst/Libraries/GRCH37/CELLMINER/W0_Uniquorn_DB.RData: load().. failed! ==> -2
File Uniquorn/inst/Libraries/GRCH37/CELLMINER/W0.25_Uniquorn_DB.RData: load().. failed! ==> -2
File Uniquorn/inst/Libraries/GRCH37/CELLMINER/W0.5_Uniquorn_DB.RData: load().. failed! ==> -2
File Uniquorn/inst/Libraries/GRCH37/CELLMINER/W0.excluded_variants_Uniquorn_DB.RData: load().. failed! ==> -2
File Uniquorn/inst/Libraries/GRCH37/CELLMINER/W1_Uniquorn_DB.RData: load().. failed! ==> -2
File universalmotif/data/ArabidopsisMotif.rda: load().. ok [1 object(s)]; updateObject(universalmotif, check=FALSE).. no match, no-op; nothing to update ==> 0
File universalmotif/data/ArabidopsisPromoters.rda: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File universalmotif/data/examplemotif.rda: load().. ok [1 object(s)]; updateObject(universalmotif, check=FALSE).. no match, no-op; nothing to update ==> 0
File universalmotif/data/examplemotif2.rda: load().. ok [1 object(s)]; updateObject(universalmotif, check=FALSE).. no match, no-op; nothing to update ==> 0
File universalmotif/data/fontDFroboto.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File universalmotif/data/JASPAR2018_CORE_DBSCORES.rda: load().. ok [1 object(s)]; updateObject(DFrame, check=FALSE).. no match, no-op; nothing to update ==> 0
File VanillaICE/data/snp_exp.rda: load().. ok [1 object(s)]; updateObject(SnpArrayExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File VanillaICE/inst/extdata/snp_exp.rda: load().. ok [1 object(s)]; updateObject(SnpArrayExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File VarCon/data/gene2transcript.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File VarCon/data/hbg.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File VarCon/data/hex.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File VarCon/data/referenceDnaStringSet.rda: load().. ok [1 object(s)]; updateObject(DNAStringSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File VarCon/data/transCoord.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File VarCon/R/sysdata.rda: load().. ok [5 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(tbl_df, check=FALSE).. no match, no-op; updateObject(DNAStringSet, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File variancePartition/data/varPartData.rda: load().. ok [3 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File variancePartition/data/varPartDEdata.rda: load().. ok [2 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File VariantFiltering/inst/extdata/sequence_variant.gSOXPapril2016.rds: readRDS().. ok; updateObject(graphNEL, check=FALSE).. no match, no-op ==> 0
File VariantFiltering/inst/extdata/uind.rds: readRDS().. ok; updateObject(VariantFilteringResults, check=FALSE).. returned an error ==> -1
File VariantFiltering/inst/extdata/humanEnsGenePhylostrata.rda: load().. ok [2 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File VariantTools/data/vignette.rda: load().. ok [6 object(s)]; updateObject(SimpleRleList, check=FALSE).. no match, no-op; updateObject(SimpleRleList, check=FALSE).. no match, no-op; updateObject(DNAStringSet, check=FALSE).. no match, no-op; updateObject(GRanges, check=FALSE).. no match, no-op; updateObject(VRanges, check=FALSE).. no match, no-op; updateObject(VRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File VaSP/data/rice.bg.RData: load().. ok [1 object(s)]; updateObject(ballgown, check=FALSE).. no match, no-op; nothing to update ==> 0
File vbmp/data/BRCA12.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File veloviz/data/pancreas.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File veloviz/data/vel.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File VennDetail/data/T2DM.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File VERSO/data/inference.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File VERSO/data/variants.RData: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File vidger/data/df.cuff.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File vidger/data/df.deseq.RData: load().. ok [1 object(s)]; updateObject(DESeqDataSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File vidger/data/df.edger.RData: load().. ok [1 object(s)]; updateObject(DGEList, check=FALSE).. no match, no-op; nothing to update ==> 0
File ViSEAGO/data/myGOs.RData: load().. ok [1 object(s)]; updateObject(GO_SS, check=FALSE).. no match, no-op; nothing to update ==> 0
File vissE/data/hgsc.rda: load().. ok [1 object(s)]; updateObject(GeneSetCollection, check=FALSE).. no match, no-op; nothing to update ==> 0
File vissE/R/sysdata.rda: load().. ok [2 object(s)]; updateObject(list, check=FALSE).. no match, no-op; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File VplotR/data/ABF1_sacCer3.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File VplotR/data/ATAC_ce11_Serizay2020.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File VplotR/data/bam_test.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File VplotR/data/ce11_all_REs.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File VplotR/data/ce11_proms.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File VplotR/data/CTCF_hg38.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File VplotR/data/MNase_sacCer3_Henikoff2011_subset.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File VplotR/data/MNase_sacCer3_Henikoff2011.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File VplotR/data/REB1_sacCer3.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. no match, no-op; nothing to update ==> 0
File vsn/data/kidney.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File vsn/data/lymphoma.RData: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File vtpnet/data/cancerMap.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File vtpnet/data/maurGWAS.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File vtpnet/data/pax4_75.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File vtpnet/data/pax4_85.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File vtpnet/data/pax4.rda: load().. ok [1 object(s)]; updateObject(GRanges, check=FALSE).. MATCH, object updated; won't save file (dry run) ==> 1
File wateRmelon/data/age_coefficients.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File wateRmelon/data/coef.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File wateRmelon/data/epic.controls.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File wateRmelon/data/hannumCoef.rda: load().. ok [1 object(s)]; updateObject(numeric, check=FALSE).. no match, no-op; nothing to update ==> 0
File wateRmelon/data/iDMR.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File wateRmelon/data/melon.rda: load().. ok [1 object(s)]; updateObject(MethyLumiSet, check=FALSE).. returned an error ==> -1
File wateRmelon/data/sexCoef.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File wavClusteR/data/model.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File weitrix/data/simwei.rda: load().. ok [1 object(s)]; updateObject(SummarizedExperiment, check=FALSE).. no match, no-op; nothing to update ==> 0
File wiggleplotr/data/ncoa7_cdss.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File wiggleplotr/data/ncoa7_exons.rda: load().. ok [1 object(s)]; updateObject(CompressedGRangesList, check=FALSE).. no match, no-op; nothing to update ==> 0
File wiggleplotr/data/ncoa7_metadata.rda: load().. ok [1 object(s)]; updateObject(tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File wpm/data/data_test.rda: load().. ok [1 object(s)]; updateObject(spec_tbl_df, check=FALSE).. no match, no-op; nothing to update ==> 0
File xcms/data/faahko_sub.RData: load().. ok [1 object(s)]; updateObject(XCMSnExp, check=FALSE).. returned an error ==> -1
File xcms/data/xdata.RData: load().. ok [1 object(s)]; updateObject(XCMSnExp, check=FALSE).. returned an error ==> -1
File XDE/data/expressionSetList.RData: load().. ok [1 object(s)]; updateObject(ExpressionSetList, check=FALSE).. no match, no-op; nothing to update ==> 0
File XDE/data/xmcmc.RData: load().. ok [1 object(s)]; updateObject(XdeMcmc, check=FALSE).. no match, no-op; nothing to update ==> 0
File XDE/inst/logFiles/BES.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File XDE/inst/logFiles/postAvg.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
File Xeva/inst/extdata/batch_list.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File Xeva/inst/extdata/rnaseq.rds: readRDS().. ok; updateObject(ExpressionSet, check=FALSE).. no match, no-op ==> 0
File Xeva/data/brca.rda: load().. ok [1 object(s)]; updateObject(XevaSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File Xeva/data/PDXMI.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File Xeva/data/repdx.rda: load().. ok [1 object(s)]; updateObject(XevaSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File XINA/data/gene_info.RData: load().. ok [2 object(s)]; updateObject(character, check=FALSE).. no match, no-op; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File XINA/data/HPRD.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File XINA/data/string_example.RData: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File XINA/data/xina_example.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File XINA/data/xina_result_example.RData: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File xmapbridge/data/xmapbridge.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File XNAString/data/complementary_bases.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File XNAString/data/xna_dictionary.rda: load().. ok [1 object(s)]; updateObject(data.table, check=FALSE).. no match, no-op; nothing to update ==> 0
File yamss/data/cmsRawExample.rda: load().. ok [1 object(s)]; updateObject(CMSraw, check=FALSE).. no match, no-op; nothing to update ==> 0
File yamss/inst/scripts/digests.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/build/vignette.rds: readRDS().. ok; updateObject(data.frame, check=FALSE).. no match, no-op ==> 0
File YAPSA/data/AlexCosmicValid_sig_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/cutoffs_pcawg.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/cutoffs.rda: load().. ok [8 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/exchange_colour_vector.rda: load().. ok [1 object(s)]; updateObject(character, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/GenomeOfNl_MutCat.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/GenomeOfNl_raw.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/lymphoma_cohort_LCD_results.rda: load().. ok [4 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/lymphoma_Nature2013_raw.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/lymphoma_PID.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/lymphoma_test.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/lymphomaNature2013_mutCat_df.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/sigs_pcawg.rda: load().. ok [6 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/sigs.rda: load().. ok [8 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/smallCellLungCancerMutCat_NatureGenetics2012.rda: load().. ok [1 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/data/targetCapture_cor_factors.rda: load().. ok [1 object(s)]; updateObject(list, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/inst/YAPSA_datasets/cutoffs_pcawg.rda: load().. ok [3 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/inst/YAPSA_datasets/cutoffs.rda: load().. ok [8 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/inst/YAPSA_datasets/sigs_pcawg.rda: load().. ok [6 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File YAPSA/inst/YAPSA_datasets/sigs.rda: load().. ok [8 object(s)]; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; updateObject(data.frame, check=FALSE).. no match, no-op; nothing to update ==> 0
File yarn/data/bladder.rdata: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File yarn/data/skin.rdata: load().. ok [1 object(s)]; updateObject(ExpressionSet, check=FALSE).. no match, no-op; nothing to update ==> 0
File zFPKM/vignettes/gse94802.rds: readRDS().. ok; updateObject(list, check=FALSE).. no match, no-op ==> 0
File zinbwave/data/toydata.rda: load().. ok [1 object(s)]; updateObject(matrix, check=FALSE).. no match, no-op; nothing to update ==> 0
    user   system  elapsed 
1449.227   55.514 1516.612 
Warning message:
'studiesTable' dataset is defunct; see 'getStudies()' 
R Under development (unstable) (2022-01-05 r81451)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
LAPACK: /home/biocbuild/bbs-3.15-bioc/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
 [3] LC_TIME=en_GB                 LC_COLLATE=en_US.UTF-8       
 [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8      
 [7] LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8          
 [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8     
[11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

attached base packages:
 [1] parallel  grid      stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
  [1] yamss_1.21.1                       Xeva_1.11.0                       
  [3] XDE_2.41.0                         ViSEAGO_1.9.0                     
  [5] VariantFiltering_1.31.0            VanillaICE_1.57.2                 
  [7] universalmotif_1.13.6              UMI4Cats_1.5.0                    
  [9] TSRchitect_1.21.1                  tRanslatome_1.33.0                
 [11] transite_1.13.1                    transcriptR_1.23.1                
 [13] slingshot_2.3.0                    trackViewer_1.31.2                
 [15] ToxicoGx_1.5.0                     topGO_2.47.0                      
 [17] topdownr_1.17.1                    tilingArray_1.73.0                
 [19] pixmap_0.4-12                      tigre_1.49.0                      
 [21] GenomicFiles_1.31.0                ontoProc_1.17.0                   
 [23] TCseq_1.19.0                       maftools_2.11.0                   
 [25] TarSeqQC_1.25.1                    TargetSearch_1.51.0               
 [27] mzID_1.33.0                        TAPseq_1.7.0                      
 [29] synapter_2.19.0                    supersigs_1.3.1                   
 [31] SummarizedBenchmark_2.13.1         tibble_3.1.6                      
 [33] crayon_1.4.2                       sessioninfo_1.2.2                 
 [35] digest_0.6.29                      dplyr_1.0.7                       
 [37] stringr_1.4.0                      rlang_0.4.12                      
 [39] UpSetR_1.4.0                       tidyr_1.1.4                       
 [41] struct_1.7.0                       Structstrings_1.11.0              
 [43] staRank_1.37.0                     ssrch_1.11.0                      
 [45] srnadiff_1.15.0                    SplicingGraphs_1.35.0             
 [47] spkTools_1.51.0                    spicyR_1.7.2                      
 [49] Spectra_1.5.5                      sparrow_1.1.3                     
 [51] SomaticSignatures_2.31.1           soGGi_1.27.1                      
 [53] SMITE_1.23.1                       SIAMCAT_1.15.0                    
 [55] SeqSQC_1.17.0                      SeqGSEA_1.35.0                    
 [57] segmentSeq_2.29.1                  segmenter_1.1.0                   
 [59] scClassify_1.7.1                   zinbwave_1.17.0                   
 [61] scanMiR_1.1.0                      sangerseqR_1.31.1                 
 [63] sangeranalyseR_1.5.1               snpStats_1.45.0                   
 [65] PWMEnrich_4.31.0                   Rtreemix_1.57.0                   
 [67] RTN_2.19.0                         RTCGAToolbox_2.25.1               
 [69] Rqc_1.29.0                         ShortRead_1.53.1                  
 [71] Rsamtools_2.11.0                   BiocParallel_1.29.10              
 [73] rprimer_0.99.9                     RNASeqR_1.13.0                    
 [75] RNAmodR.RiboMethSeq_1.9.0          RNAmodR.AlkAnilineSeq_1.9.0       
 [77] RNAmodR_1.9.1                      RNAinteract_1.43.0                
 [79] RLSeq_1.1.0                        Ringo_1.59.0                      
 [81] rGREAT_1.27.0                      rexposome_1.17.1                  
 [83] Rcade_1.37.0                       randPack_1.41.0                   
 [85] RadioGx_1.5.0                      R453Plus1Toolbox_1.45.0           
 [87] r3Cseq_1.41.0                      R3CPET_1.27.0                     
 [89] puma_3.37.0                        pulsedSilac_1.9.1                 
 [91] psygenet2r_1.27.0                  ProteomicsAnnotationHubData_1.25.2
 [93] AnnotationHub_3.3.7                BiocFileCache_2.3.3               
 [95] dbplyr_2.1.1                       ProteoDisco_1.1.3                 
 [97] pRoloc_1.35.0                      procoil_2.23.0                    
 [99] proActiv_1.5.0                     PrecisionTrialDrawer_1.11.0       
[101] pqsfinder_2.11.2                   esATAC_1.17.0                     
[103] PhosR_1.5.1                        phenoTest_1.43.0                  
[105] PharmacoGx_2.7.0                   perturbatr_1.15.0                 
[107] PDATK_1.3.1                        PathoStat_1.21.0                  
[109] PANR_1.41.0                        cn.mops_1.41.1                    
[111] pandaR_1.27.0                      OSAT_1.43.0                       
[113] openPrimeR_1.17.0                  openCyto_2.7.0                    
[115] NxtIRFcore_1.1.1                   ReadqPCR_1.41.0                   
[117] HTqPCR_1.49.0                      NOISeq_2.39.0                     
[119] ngsReports_1.11.0                  netresponse_1.55.0                
[121] reshape2_1.4.4                     mclust_5.4.9                      
[123] minet_3.53.0                       rmarkdown_2.11                    
[125] Rgraphviz_2.39.0                   BiocStyle_2.23.1                  
[127] netprioR_1.21.0                    NBSplice_1.13.0                   
[129] NanoStringQCPro_1.27.0             biomaRt_2.51.2                    
[131] MutationalPatterns_3.5.1           musicatk_1.5.0                    
[133] biosigner_1.23.0                   ropls_1.27.4                      
[135] multiHiCcompare_1.13.0             MultiDataSet_1.23.0               
[137] MSstatsConvert_1.5.0               QFeatures_1.5.2                   
[139] msPurity_1.21.0                    MSnID_1.29.0                      
[141] mpra_1.17.1                        MotifDb_1.37.0                    
[143] MMDiff2_1.23.1                     ensemblVEP_1.37.0                 
[145] MMAPPR2_1.9.0                      mitoClone2_1.1.0                  
[147] miRNApath_1.55.0                   MinimumDistance_1.39.0            
[149] hgu133a.db_3.13.0                  org.Hs.eg.db_3.14.0               
[151] MineICA_1.35.0                     mina_1.3.0                        
[153] MIGSA_1.19.0                       midasHLA_1.3.0                    
[155] MicrobiotaProcess_1.7.5            microbiomeMarker_1.1.1            
[157] TreeSummarizedExperiment_2.3.0     mgsa_1.43.0                       
[159] methylPipe_1.29.2                  minfi_1.41.1                      
[161] MethylAid_1.29.0                   methrix_1.9.0                     
[163] methylKit_1.21.0                   MSnbase_2.21.4                    
[165] metaMS_1.31.0                      metahdep_1.53.0                   
[167] metagenomeSeq_1.37.0               MAST_1.21.3                       
[169] MassArray_1.47.0                   marray_1.73.0                     
[171] MAIT_1.29.0                        maigesPack_1.59.0                 
[173] MAGAR_1.3.0                        MADSEQ_1.21.1                     
[175] MACSQuantifyR_1.9.0                lumi_2.47.0                       
[177] LowMACA_1.25.0                     loci2path_1.15.1                  
[179] LOBSTAHS_1.21.0                    CAMERA_1.51.0                     
[181] lipidr_2.9.0                       AnnotationDbi_1.57.1              
[183] IWTomics_1.19.1                    isomiRs_1.23.1                    
[185] IsoformSwitchAnalyzeR_1.17.04      IRISFGM_1.3.0                     
[187] inveRsion_1.43.0                   INSPEcT_1.25.0                    
[189] infercnv_1.11.1                    immunoClust_1.27.1                
[191] ImmuneSpaceR_1.23.0                idiogram_1.71.0                   
[193] plotrix_3.8-2                      iCOBRA_1.23.2                     
[195] hmdbQuery_1.15.2                   HiTC_1.39.0                       
[197] HiLDA_1.9.0                        InteractionSet_1.23.1             
[199] hermes_0.99.4                      heatmaps_1.19.1                   
[201] fabia_2.41.0                       GWASTools_1.41.0                  
[203] GreyListChIP_1.27.0                edgeR_3.37.0                      
[205] gespeR_1.27.0                      ggplot2_3.3.5                     
[207] GeomxTools_2.1.0                   GenomicSuperSignature_1.3.1       
[209] genomeIntervals_1.51.0             geNetClassifier_1.35.0            
[211] GeneRegionScan_1.51.0              GARS_1.15.0                       
[213] VariantAnnotation_1.41.3           FoldGO_1.13.0                     
[215] flowClust_3.33.0                   flowStats_4.7.0                   
[217] flowBin_1.31.0                     flowBeads_1.33.0                  
[219] FELLA_1.15.0                       fcoex_1.9.0                       
[221] exomePeak2_1.7.1                   SGSeq_1.29.0                      
[223] TFBSTools_1.33.0                   enhancerHomologSearch_1.1.0       
[225] DSS_2.43.2                         DriverNet_1.35.0                  
[227] dpeak_1.7.0                        GOSemSim_2.21.1                   
[229] Doscheda_1.17.0                    DIAlignR_2.3.1                    
[231] DESeq2_1.35.0                      deltaGseg_1.35.0                  
[233] deepSNV_1.41.0                     deco_1.11.1                       
[235] ddCt_1.51.0                        cytomapper_1.7.1                  
[237] cummeRbund_2.37.0                  CTDquerier_2.3.1                  
[239] CSSP_1.33.0                        oligoClasses_1.57.0               
[241] CrispRVariants_1.23.0              crisprBase_0.99.8                 
[243] CoreGx_1.7.0                       coRdon_1.13.0                     
[245] contiBAIT_1.23.1                   cola_2.1.0                        
[247] CoGAPS_3.15.1                      codelink_1.63.0                   
[249] CNVrd2_1.33.0                      CNEr_1.31.1                       
[251] Gviz_1.39.2                        CNAnorm_1.41.0                    
[253] cmapR_1.7.0                        clusterExperiment_2.15.1          
[255] bigmemory_4.5.36                   cliqueMS_1.9.0                    
[257] cleanUpdTSeq_1.33.0                chromVAR_1.17.1                   
[259] ChromHeatMap_1.49.0                ChIPQC_1.31.1                     
[261] ChIPexoQual_1.19.1                 ChIPanalyser_1.17.1               
[263] Chicago_1.23.0                     CGHbase_1.55.0                    
[265] CeTF_1.7.0                         CEMiTool_1.19.1                   
[267] CellNOptR_1.41.0                   cellmigRation_1.3.0               
[269] cellHTS2_2.59.0                    CellBarcode_1.1.0                 
[271] CellaRepertorium_1.5.0             celda_1.11.0                      
[273] categoryCompare_1.39.0             flowCore_2.7.0                    
[275] casper_2.29.1                      CancerInSilico_2.15.0             
[277] xcms_3.17.3                        CAGEr_2.1.3                       
[279] bsseq_1.31.1                       bnbc_1.17.1                       
[281] BiSeq_1.35.0                       GenomeInfoDb_1.31.1               
[283] pogos_1.15.1                       restfulSE_1.17.0                  
[285] DelayedArray_0.21.2                IRanges_2.29.1                    
[287] MatrixGenerics_1.7.0               matrixStats_0.61.0                
[289] limma_3.51.2                       ChemmineR_3.47.0                  
[291] BindingSiteFinder_1.1.3            methylumi_2.41.1                  
[293] phyloseq_1.39.1                    beadarraySNP_1.61.0               
[295] BCRANK_1.57.0                      baySeq_2.29.0                     
[297] BASiCS_2.7.2                       BaseSpaceR_1.39.0                 
[299] rstan_2.21.3                       BANDITS_1.11.0                    
[301] Biostrings_2.63.1                  ballgown_2.27.1                   
[303] Autotuner_1.9.1                    ASICS_2.11.0                      
[305] graph_1.73.0                       AnVILBilling_1.5.0                
[307] AnnotationHubData_1.25.4           futile.logger_1.4.3               
[309] annotate_1.73.0                    amplican_1.17.1                   
[311] altcdfenvs_2.57.0                  GenomicAlignments_1.31.2          
[313] GenomicRanges_1.47.6               AllelicImbalance_1.33.1           
[315] SeuratObject_4.0.4                 Seurat_4.0.6                      
[317] GSEABase_1.57.0                    affy_1.73.0                       
[319] SummarizedExperiment_1.25.3        MultiAssayExperiment_1.21.5       
[321] SingleCellExperiment_1.17.2        Matrix_1.4-0                      
[323] ACME_2.51.0                        QDNAseq_1.31.0                    
[325] Biobase_2.55.0                     updateObject_0.2.2                
[327] S4Vectors_0.33.10                  BiocGenerics_0.41.2               

loaded via a namespace (and not attached):
  [1] caret_6.0-90                             
  [2] GWASExactHW_1.01                         
  [3] graphite_1.41.0                          
  [4] LaplacesDemon_16.1.6                     
  [5] coin_1.4-2                               
  [6] kernlab_0.9-29                           
  [7] hexbin_1.28.2                            
  [8] vipor_0.4.5                              
  [9] crlmm_1.53.0                             
 [10] rncl_0.8.4                               
 [11] RSpectra_0.16-0                          
 [12] loo_2.4.1                                
 [13] shinyBS_0.61                             
 [14] ggstar_1.0.3                             
 [15] wordcloud_2.6                            
 [16] polyclip_1.10-0                          
 [17] scran_1.23.1                             
 [18] anota_1.43.0                             
 [19] combi_1.7.2                              
 [20] forcats_0.5.1                            
 [21] pathwayPCA_1.11.0                        
 [22] quadprog_1.5-8                           
 [23] DRIMSeq_1.23.0                           
 [24] generics_0.1.1                           
 [25] babelgene_21.4                           
 [26] OrganismDbi_1.37.1                       
 [27] biodb_1.3.1                              
 [28] sass_0.4.0                               
 [29] pkgbuild_1.3.1                           
 [30] MSQC_1.0.2                               
 [31] ellipse_0.4.2                            
 [32] mixOmics_6.19.1                          
 [33] changepoint_2.2.2                        
 [34] pkgconfig_2.0.3                          
 [35] drc_3.0-1                                
 [36] PRROC_1.3.1                              
 [37] Hmisc_4.6-0                              
 [38] GlobalOptions_0.1.2                      
 [39] beanplot_1.2                             
 [40] tidygraph_1.2.0                          
 [41] fastmatch_1.1-3                          
 [42] ggpointdensity_0.1.0                     
 [43] sctransform_0.3.3                        
 [44] psych_2.1.9                              
 [45] deltaCaptureC_1.9.1                      
 [46] sets_1.0-20                              
 [47] circlize_0.4.13                          
 [48] tximeta_1.13.5                           
 [49] distr_2.8.0                              
 [50] hwriter_1.3.2                            
 [51] magic_1.5-9                              
 [52] DEoptimR_1.0-10                          
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 [54] clValid_0.7                              
 [55] ggiraph_0.8.1                            
 [56] shinyTree_0.2.7                          
 [57] multipanelfigure_2.1.2                   
 [58] rtracklayer_1.55.3                       
 [59] lsa_0.73.2                               
 [60] motifmatchr_1.17.0                       
 [61] relations_0.6-10                         
 [62] pkgmaker_0.32.2                          
 [63] yaml_2.2.1                               
 [64] base64_2.0                               
 [65] prodlim_2019.11.13                       
 [66] nnls_1.4                                 
 [67] flowFP_1.53.0                            
 [68] ncdfFlow_2.41.0                          
 [69] ade4_1.7-18                              
 [70] NISTunits_1.0.1                          
 [71] GenomicTools_0.2.9.7                     
 [72] seqinr_4.2-8                             
 [73] cowplot_1.1.1                            
 [74] carData_3.0-5                            
 [75] rappdirs_0.3.3                           
 [76] DEXSeq_1.41.0                            
 [77] lsr_0.5.2                                
 [78] fastmap_1.1.0                            
 [79] FSelector_0.33                           
 [80] scuttle_1.5.0                            
 [81] extrafont_0.17                           
 [82] boot_1.3-28                              
 [83] tzdb_0.2.0                               
 [84] shiny_1.7.1                              
 [85] evaluate_0.14                            
 [86] shape_1.4.6                              
 [87] inum_1.0-4                               
 [88] assertthat_0.2.1                         
 [89] goseq_1.47.0                             
 [90] dtw_1.22-3                               
 [91] randomForest_4.6-14                      
 [92] irlba_2.3.5                              
 [93] rJava_1.0-6                              
 [94] mapproj_1.2.8                            
 [95] deldir_1.0-6                             
 [96] IRdisplay_1.1                            
 [97] RnBeads.hg19_1.27.1                      
 [98] base64url_1.4                            
 [99] gower_0.2.2                              
[100] truncnorm_1.0-8                          
[101] mixsqp_0.3-43                            
[102] tools_4.2.0                              
[103] BumpyMatrix_1.3.0                        
[104] BB_2019.10-1                             
[105] rvest_1.0.2                              
[106] Rhtslib_1.27.1                           
[107] Ckmeans.1d.dp_4.3.3                      
[108] ptw_1.9-15                               
[109] BH_1.78.0-0                              
[110] BBmisc_1.11                              
[111] xts_0.12.1                               
[112] ggforce_0.3.3                            
[113] DiffBind_3.5.3                           
[114] ggthemes_4.2.4                           
[115] RNeXML_2.4.5                             
[116] quantmod_0.4.18                          
[117] egg_0.4.5                                
[118] howmany_0.3-1                            
[119] rafalib_1.0.0                            
[120] jquerylib_0.1.4                          
[121] intergraph_2.0-2                         
[122] minqa_1.2.4                              
[123] bumphunter_1.37.1                        
[124] lubridate_1.8.0                          
[125] gtable_0.3.0                             
[126] RedeR_1.43.0                             
[127] mitools_2.4                              
[128] matrixTests_0.1.9.1                      
[129] abind_1.4-5                              
[130] shinythemes_1.2.0                        
[131] caretEnsemble_2.0.1                      
[132] parallelMap_1.5.1                        
[133] fBasics_3042.89.1                        
[134] betareg_3.1-4                            
[135] gsubfn_0.7                               
[136] multiSight_1.3.0                         
[137] Cubist_0.3.0                             
[138] maxLik_1.5-2                             
[139] FlowSOM_2.3.0                            
[140] mgcv_1.8-38                              
[141] MassSpecWavelet_1.61.0                   
[142] sandwich_3.0-1                           
[143] webshot_0.5.2                            
[144] microbiome_1.17.1                        
[145] pwr_1.3-0                                
[146] biglm_0.9-2.1                            
[147] miscTools_0.6-26                         
[148] DT_0.20                                  
[149] aricode_1.0.0                            
[150] ggtreeExtra_1.5.2                        
[151] aggregation_1.0.1                        
[152] km.ci_0.5-2                              
[153] RWeka_0.4-44                             
[154] cytolib_2.7.1                            
[155] logging_0.10-108                         
[156] survMisc_0.5.5                           
[157] skmeans_0.2-14                           
[158] MSstatsSampleSize_1.9.0                  
[159] BSgenome.Hsapiens.UCSC.hg19_1.4.3        
[160] Formula_1.2-4                            
[161] ggplotify_0.1.0                          
[162] DiagrammeR_1.0.6.1                       
[163] formattable_0.2.1                        
[164] Pigengene_1.21.36                        
[165] uchardet_1.1.0                           
[166] labeling_0.4.2                           
[167] gistr_0.9.0                              
[168] biomformat_1.23.0                        
[169] ellipsis_0.3.2                           
[170] caTools_1.18.2                           
[171] log4r_0.4.2                              
[172] easyPubMed_2.13                          
[173] made4_1.69.0                             
[174] ggcyto_1.23.0                            
[175] rainbow_3.6                              
[176] future.apply_1.8.1                       
[177] EDASeq_2.29.0                            
[178] globals_0.14.0                           
[179] AnnotationForge_1.37.0                   
[180] RaggedExperiment_1.19.0                  
[181] nleqslv_3.3.2                            
[182] GEOquery_2.63.3                          
[183] diagram_1.6.5                            
[184] cluster_2.1.2                            
[185] ggpp_0.4.3                               
[186] raster_3.5-11                            
[187] dotCall64_1.0-1                          
[188] class_7.3-20                             
[189] tseries_0.10-49                          
[190] pbdZMQ_0.3-6                             
[191] timeSeries_3062.100                      
[192] DBI_1.1.2                                
[193] chipseq_1.45.1                           
[194] ggpubr_0.4.0                             
[195] rbokeh_0.5.2                             
[196] bigstatsr_1.5.5                          
[197] googleVis_0.6.11                         
[198] splines_4.2.0                            
[199] mlr_2.19.0                               
[200] pscl_1.5.5                               
[201] survivalROC_1.0.3                        
[202] qlcMatrix_0.9.7                          
[203] JADE_2.0-3                               
[204] diffusr_0.1.4                            
[205] partykit_1.2-15                          
[206] splitstackshape_1.4.8                    
[207] rootSolve_1.8.2.3                        
[208] ontologyIndex_2.7                        
[209] ontologyPlot_1.6                         
[210] SPEM_1.35.0                              
[211] HardyWeinberg_1.7.4                      
[212] snow_0.4-4                               
[213] leiden_0.3.9                             
[214] apcluster_1.4.8                          
[215] e1071_1.7-9                              
[216] bigassertr_0.1.5                         
[217] scam_1.2-12                              
[218] kebabs_1.29.0                            
[219] hopach_2.55.0                            
[220] nor1mix_1.3-0                            
[221] gMWT_1.1.1                               
[222] statnet.common_4.5.0                     
[223] aroma.light_3.25.0                       
[224] cleaver_1.33.0                           
[225] labelled_2.9.0                           
[226] assertive.base_0.0-9                     
[227] prettydoc_0.4.1                          
[228] rhdf5client_1.17.0                       
[229] aplot_0.1.2                              
[230] base64enc_0.1-3                          
[231] KEGGgraph_1.55.0                         
[232] ape_5.6-1                                
[233] htmlTable_2.4.0                          
[234] doRNG_1.8.2                              
[235] lambda.r_1.2.4                           
[236] rhdf5_2.39.2                             
[237] farver_2.1.0                             
[238] beeswarm_0.4.0                           
[239] GOstats_2.61.0                           
[240] openxlsx_4.2.5                           
[241] phylobase_0.8.10                         
[242] gridGraphics_0.5-1                       
[243] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
[244] argparse_2.1.3                           
[245] kknn_1.3.1                               
[246] systemPipeR_2.1.11                       
[247] survey_4.1-1                             
[248] magicaxis_2.2.1                          
[249] prettyunits_1.1.1                        
[250] BiocVersion_3.15.0                       
[251] multtest_2.51.0                          
[252] LowMACAAnnotation_0.99.3                 
[253] cachem_1.0.6                             
[254] rjson_0.2.21                             
[255] assertive.numbers_0.0-2                  
[256] pipeFrame_1.11.0                         
[257] bigmemory.sri_0.1.3                      
[258] microbenchmark_1.4.9                     
[259] latticeExtra_0.6-29                      
[260] networkD3_0.4                            
[261] compiler_4.2.0                           
[262] seqLogo_1.61.1                           
[263] withr_2.4.3                              
[264] omicade4_1.35.0                          
[265] sSeq_1.33.0                              
[266] formatR_1.11                             
[267] msigdbr_7.4.1                            
[268] gmodels_2.18.1                           
[269] gplots_3.1.1                             
[270] klaR_0.6-15                              
[271] roxygen2_7.1.2                           
[272] SnowballC_0.7.0                          
[273] httpuv_1.6.5                             
[274] rentrez_1.2.3                            
[275] rstatix_0.7.0                            
[276] outliers_0.14                            
[277] arm_1.12-2                               
[278] remotes_2.4.2                            
[279] ICSNP_1.1-1                              
[280] org.Mm.eg.db_3.14.0                      
[281] factoextra_1.0.7                         
[282] GenomicFeatures_1.47.5                   
[283] knitr_1.37                               
[284] seriation_1.3.1                          
[285] convert_1.71.0                           
[286] sigPathway_1.63.0                        
[287] sparseMatrixStats_1.7.0                  
[288] tmvtnorm_1.4-10                          
[289] metap_1.7                                
[290] plotly_4.10.0                            
[291] celestial_1.4.6                          
[292] RMSNumpress_1.0.1                        
[293] doSNOW_1.0.19                            
[294] pcaPP_1.9-74                             
[295] blob_1.2.2                               
[296] ChIPseeker_1.31.3                        
[297] libcoin_1.0-9                            
[298] glmnet_4.1-3                             
[299] Rdpack_2.1.3                             
[300] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2     
[301] scrime_1.3.5                             
[302] chron_2.3-56                             
[303] fda_5.5.1                                
[304] EBImage_4.37.0                           
[305] systemPipeRdata_1.23.0                   
[306] fastICA_1.2-3                            
[307] pryr_0.1.5                               
[308] golem_0.3.1                              
[309] scatterplot3d_0.3-41                     
[310] DEGreport_1.31.1                         
[311] agricolae_1.3-5                          
[312] statmod_1.4.36                           
[313] biocViews_1.63.2                         
[314] spatstat.data_2.1-2                      
[315] amap_0.8-18                              
[316] qqman_0.1.8                              
[317] ParamHelpers_1.14                        
[318] bootstrap_2019.6                         
[319] fds_1.8                                  
[320] fansi_1.0.0                              
[321] HiCcompare_1.17.1                        
[322] Rbowtie2_2.1.0                           
[323] poweRlaw_0.70.6                          
[324] R.methodsS3_1.8.1                        
[325] R6_2.5.1                                 
[326] robustbase_0.93-9                        
[327] isva_1.9                                 
[328] nloptr_1.2.2.3                           
[329] clinfun_1.0.15                           
[330] excelR_0.4.0                             
[331] rprojroot_2.0.2                          
[332] rWikiPathways_1.15.0                     
[333] ggalluvial_0.12.3                        
[334] evd_2.3-3                                
[335] jpeg_0.1-9                               
[336] highr_0.9                                
[337] R.oo_1.24.0                              
[338] interactiveDisplayBase_1.33.0            
[339] EnvStats_2.4.0                           
[340] locfdr_1.1-8                             
[341] DaMiRseq_2.7.1                           
[342] segmented_1.3-4                          
[343] brglm_0.7.2                              
[344] vcfR_1.12.0                              
[345] RUnit_0.4.32                             
[346] biganalytics_1.1.21                      
[347] BiocCheck_1.31.24                        
[348] rsample_0.1.1                            
[349] config_0.3.1                             
[350] lifecycle_1.0.1                          
[351] plotROC_2.2.1                            
[352] wavethresh_4.6.8                         
[353] recipes_0.1.17                           
[354] KernSmooth_2.23-20                       
[355] Rmpfr_0.8-7                              
[356] flowViz_1.59.0                           
[357] R2jags_0.7-1                             
[358] anocva_0.1.1                             
[359] leaps_3.1                                
[360] genefilter_1.77.0                        
[361] plgem_1.67.0                             
[362] PMA_1.2.1                                
[363] rgl_0.108.3                              
[364] omicRexposome_1.17.1                     
[365] quantsmooth_1.61.0                       
[366] downloader_0.4                           
[367] gamlss.data_6.0-2                        
[368] assertive.files_0.0-2                    
[369] dockerfiler_0.1.4                        
[370] graphlayouts_0.8.0                       
[371] norm_1.0-9.5                             
[372] V8_4.0.0                                 
[373] shinyWidgets_0.6.3                       
[374] MLSeq_2.13.0                             
[375] bit_4.0.4                                
[376] mzR_2.29.1                               
[377] Rtsne_0.15                               
[378] flexmix_2.3-17                           
[379] XML_3.99-0.8                             
[380] PerformanceAnalytics_2.0.4               
[381] OmicsLonDA_1.11.1                        
[382] BiocSingular_1.11.0                      
[383] gamlss.dist_6.0-1                        
[384] Rlabkey_2.8.2                            
[385] survminer_0.4.9                          
[386] broom_0.7.11                             
[387] motifStack_1.39.0                        
[388] AlgDesign_1.2.0                          
[389] EnsDb.Hsapiens.v86_2.99.0                
[390] MuMIn_1.43.17                            
[391] RnBeads_2.13.2                           
[392] RcppRoll_0.3.0                           
[393] MatrixModels_0.5-0                       
[394] expm_0.999-6                             
[395] vegan_2.5-7                              
[396] xfun_0.29                                
[397] processx_3.5.2                           
[398] BiasedUrn_1.07                           
[399] clue_0.3-60                              
[400] ismev_1.42                               
[401] combinat_0.0-8                           
[402] futile.options_1.0.1                     
[403] ggraph_2.0.5                             
[404] locfit_1.5-9.4                           
[405] flashClust_1.01-2                        
[406] spatstat.utils_2.3-0                     
[407] fields_13.3                              
[408] zip_2.2.0                                
[409] ggbeeswarm_0.6.0                         
[410] rrcov_1.6-0                              
[411] codetools_0.2-18                         
[412] emdbook_1.3.12                           
[413] tximport_1.23.2                          
[414] goftest_1.2-3                            
[415] genefu_2.27.0                            
[416] profileModel_0.6.1                       
[417] pvclust_2.2-0                            
[418] aws.s3_0.3.21                            
[419] readr_2.1.1                              
[420] mnormt_2.0.2                             
[421] pcaMethods_1.87.0                        
[422] AnnotationFilter_1.19.0                  
[423] metagene_2.27.1                          
[424] spatstat.geom_2.3-1                      
[425] quantreg_5.86                            
[426] startupmsg_0.9.6                         
[427] beachmat_2.11.0                          
[428] SuppDists_1.1-9.7                        
[429] bbmle_1.0.24                             
[430] reactable_0.2.3                          
[431] dichromat_2.0-0                          
[432] MCL_1.0                                  
[433] ICS_1.3-1                                
[434] svgPanZoom_0.3.4                         
[435] dendextend_1.15.2                        
[436] chromhmmData_0.99.2                      
[437] filelock_1.0.2                           
[438] assertive.properties_0.0-4               
[439] affyio_1.65.0                            
[440] mathjaxr_1.4-0                           
[441] RCircos_1.2.2                            
[442] slam_0.1-50                              
[443] StanHeaders_2.21.0-7                     
[444] fgsea_1.21.0                             
[445] TSP_1.1-11                               
[446] htmltools_0.5.2                          
[447] spam_2.8-0                               
[448] igraph_1.2.11                            
[449] promises_1.2.0.1                         
[450] GenomeInfoDbData_1.2.7                   
[451] BSgenome.Drerio.UCSC.danRer7_1.4.0       
[452] lokern_1.1-9                             
[453] concaveman_1.1.0                         
[454] bit64_4.0.5                              
[455] PepsNMR_1.13.0                           
[456] tidyselect_1.1.1                         
[457] alabama_2015.3-1                         
[458] bdsmatrix_1.3-4                          
[459] gdata_2.18.0                             
[460] doParallel_1.0.16                        
[461] TTR_0.24.3                               
[462] genalg_0.2.0                             
[463] glue_1.6.0                               
[464] bnlearn_4.7                              
[465] docopt_0.7.1                             
[466] phangorn_2.8.1                           
[467] timeDate_3043.102                        
[468] cellranger_1.1.0                         
[469] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2  
[470] car_3.0-12                               
[471] Nozzle.R1_1.1-1                          
[472] zoo_1.8-9                                
[473] shadowtext_0.1.1                         
[474] permute_0.9-5                            
[475] AdaptGauss_1.5.6                         
[476] SpatialTools_1.0.4                       
[477] gaga_2.41.0                              
[478] minpack.lm_1.2-1                         
[479] reactome.db_1.77.0                       
[480] uwot_0.1.11                              
[481] yulab.utils_0.0.4                        
[482] operator.tools_1.6.3                     
[483] TrajectoryUtils_1.3.0                    
[484] MASS_7.3-55                              
[485] oligo_1.59.0                             
[486] gdsfmt_1.31.0                            
[487] eulerr_6.1.1                             
[488] GGally_2.1.2                             
[489] flexclust_1.4-0                          
[490] readxl_1.3.1                             
[491] scales_1.1.1                             
[492] mutoss_0.1-12                            
[493] vioplot_0.3.7                            
[494] intrinsicDimension_1.2.0                 
[495] httr_1.4.2                               
[496] BiocSet_1.9.1                            
[497] rsvd_1.0.5                               
[498] rsvg_2.1.2                               
[499] SparseM_1.81                             
[500] nlme_3.1-155                             
[501] JASPAR2018_1.1.1                         
[502] Modstrings_1.11.1                        
[503] scater_1.23.2                            
[504] bamsignals_1.27.1                        
[505] pROC_1.18.0                              
[506] VennDiagram_1.7.1                        
[507] parallelDist_0.2.4                       
[508] tensor_1.5                               
[509] fst_0.9.4                                
[510] geneLenDataBase_1.31.0                   
[511] TxDb.Hsapiens.UCSC.hg38.knownGene_3.14.0 
[512] purrr_0.3.4                              
[513] fastseg_1.41.0                           
[514] MCMCprecision_0.4.0                      
[515] VariantTools_1.37.1                      
[516] RProtoBufLib_2.7.0                       
[517] RANN_2.6.1                               
[518] clusterRepro_0.9                         
[519] bslib_0.3.1                              
[520] ggtree_3.3.1                             
[521] affxparser_1.67.0                        
[522] utf8_1.2.2                               
[523] vsn_3.63.0                               
[524] mppa_1.0                                 
[525] CircStats_0.2-6                          
[526] geneClassifiers_1.19.0                   
[527] bitops_1.0-7                             
[528] illuminaio_0.37.0                        
[529] lme4_1.1-27.1                            
[530] flock_0.7                                
[531] RankProd_3.21.0                          
[532] callr_3.7.0                              
[533] ipred_0.9-12                             
[534] flowWorkspace_4.7.0                      
[535] DNAcopy_1.69.0                           
[536] preprocessCore_1.57.0                    
[537] FCBF_2.3.1                               
[538] viridis_0.6.2                            
[539] pkgload_1.2.4                            
[540] rARPACK_0.11-0                           
[541] tweenr_1.0.2                             
[542] ggExtra_0.9                              
[543] ConsensusClusterPlus_1.59.0              
[544] stringi_1.7.6                            
[545] scatterpie_0.1.7                         
[546] Heatplus_3.3.0                           
[547] IDPmisc_1.1.20                           
[548] gargle_1.2.0                             
[549] randomcoloR_1.1.0.1                      
[550] modeltools_0.2-23                        
[551] assertive.sets_0.0-3                     
[552] ruv_0.9.7.1                              
[553] TeachingDemos_2.12                       
[554] rjags_4-12                               
[555] plsVarSel_0.9.7                          
[556] BiocNeighbors_1.13.0                     
[557] ncdf4_1.19                               
[558] LiblineaR_2.10-12                        
[559] WGCNA_1.70-3                             
[560] mice_3.14.0                              
[561] MLInterfaces_1.75.0                      
[562] RcppAnnoy_0.0.19                         
[563] scattermore_0.7                          
[564] anyLib_1.0.5                             
[565] xgboost_1.5.0.2                          
[566] bluster_1.5.0                            
[567] chk_0.7.0                                
[568] aws.signature_0.6.0                      
[569] ppcor_1.1                                
[570] DiscriMiner_0.1-29                       
[571] sfsmisc_1.1-12                           
[572] extrafontdb_1.0                          
[573] svglite_2.0.0                            
[574] treeio_1.19.1                            
[575] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
[576] pipeComp_1.5.0                           
[577] regioneR_1.27.1                          
[578] waffle_0.7.0                             
[579] biovizBase_1.43.1                        
[580] invgamma_1.1                             
[581] ggnewscale_0.4.5                         
[582] hdrcde_3.4                               
[583] curl_4.3.2                               
[584] data.table_1.14.2                        
[585] gmapR_1.37.0                             
[586] multcomp_1.4-18                          
[587] sparsesvd_0.2                            
[588] desc_1.4.0                               
[589] clusterProfiler_4.3.2                    
[590] verification_1.42                        
[591] restfulr_0.0.13                          
[592] DrImpute_1.0                             
[593] ScaledMatrix_1.3.0                       
[594] infotheo_1.2.0                           
[595] bigrquery_1.4.0                          
[596] calibrate_1.7.7                          
[597] NxtIRFdata_1.1.0                         
[598] bioDist_1.67.0                           
[599] hypergraph_1.67.0                        
[600] BiocIO_1.5.0                             
[601] RJSONIO_1.3-1.6                          
[602] GetoptLong_1.0.5                         
[603] brew_1.0-6                               
[604] ProtGenerics_1.27.2                      
[605] plsgenomics_1.5-2                        
[606] DelayedMatrixStats_1.17.0                
[607] ggbio_1.43.0                             
[608] SOMNiBUS_1.3.0                           
[609] mixtools_1.2.0                           
[610] devtools_2.4.3                           
[611] pbapply_1.5-0                            
[612] ggdendro_0.1.22                          
[613] terra_1.5-12                             
[614] enrichplot_1.15.2                        
[615] cli_3.1.0                                
[616] GenomicTools.fileHandler_0.1.5.9         
[617] Rcpp_1.0.7                               
[618] fftwtools_0.9-11                         
[619] rhdf5filters_1.7.0                       
[620] ff_4.0.5                                 
[621] reshape_0.8.8                            
[622] splots_1.61.0                            
[623] progress_1.2.2                           
[624] fs_1.5.2                                 
[625] CATALYST_1.19.0                          
[626] logger_0.2.2                             
[627] lpSolve_5.6.15                           
[628] RBGL_1.71.0                              
[629] gmm_1.6-6                                
[630] corrplot_0.92                            
[631] proxyC_0.2.4                             
[632] gmp_0.6-2.1                              
[633] ggseqlogo_0.1                            
[634] MSstats_4.3.0                            
[635] xtable_1.8-4                             
[636] C50_0.1.5                                
[637] RCy3_2.15.1                              
[638] KMsurv_0.1-5                             
[639] gtools_3.9.2                             
[640] sna_2.6                                  
[641] pinfsc50_1.2.0                           
[642] bigparallelr_0.3.2                       
[643] TFMPvalue_0.0.8                          
[644] mvtnorm_1.1-3                            
[645] grImport_0.9-5                           
[646] DO.db_2.9                                
[647] HDF5Array_1.23.2                         
[648] taRifx_1.0.6.2                           
[649] MsFeatures_1.3.0                         
[650] RcppParallel_5.1.5                       
[651] muStat_1.7.0                             
[652] stringdist_0.9.8                         
[653] hash_2.2.6.1                             
[654] usethis_2.1.5                            
[655] ggfortify_0.4.14                         
[656] visNetwork_2.1.0                         
[657] DECIPHER_2.23.0                          
[658] ensembldb_2.19.7                         
[659] listenv_0.8.0                            
[660] ExperimentHub_2.3.4                      
[661] RLHub_1.1.0                              
[662] apeglm_1.17.0                            
[663] jsonlite_1.7.2                           
[664] BSgenome_1.63.3                          
[665] gridExtra_2.3                            
[666] ggsignif_0.6.3                           
[667] checkmate_2.0.0                          
[668] strucchange_1.5-2                        
[669] NanoStringNCTools_1.3.0                  
[670] som_0.3-5.1                              
[671] RcppEigen_0.3.3.9.1                      
[672] heatmaply_1.3.0                          
[673] enrichR_3.0                              
[674] princurve_2.1.6                          
[675] formula.tools_1.7.1                      
[676] Wrench_1.13.0                            
[677] cqn_1.41.0                               
[678] proto_1.0.0                              
[679] KEGGREST_1.35.0                          
[680] mime_0.12                                
[681] viridisLite_0.4.0                        
[682] GenomicScores_2.7.1                      
[683] future_1.23.0                            
[684] tmvnsim_1.0-2                            
[685] RhpcBLASctl_0.21-247.1                   
[686] ks_1.13.3                                
[687] parallelly_1.30.0                        
[688] lattice_0.20-45                          
[689] RWekajars_3.9.3-2                        
[690] corrgram_1.14                            
[691] globaltest_5.49.1                        
[692] foreign_0.8-82                           
[693] praznik_10.0.0                           
[694] furrr_0.2.3                              
[695] EBarrays_2.59.0                          
[696] sparseMVN_0.2.2                          
[697] shinydashboard_0.7.2                     
[698] mirTarRnaSeq_1.3.0                       
[699] RSNNS_0.4-14                             
[700] backports_1.4.1                          
[701] pheatmap_1.0.12                          
[702] plyr_1.8.6                               
[703] impute_1.69.0                            
[704] MALDIquant_1.21                          
[705] RSQLite_2.2.9                            
[706] TMixClust_1.17.0                         
[707] phyclust_0.1-30                          
[708] colorRamps_2.3                           
[709] gss_2.2-3                                
[710] qdapTools_1.3.5                          
[711] ggpmisc_0.4.5                            
[712] Rhdf5lib_1.17.0                          
[713] rbibutils_2.2.7                          
[714] testthat_3.1.1                           
[715] sampling_2.9                             
[716] RCurl_1.98-1.5                           
[717] lasso2_1.2-22                            
[718] ineq_0.2-13                              
[719] maps_3.4.0                               
[720] pkgdown_2.0.2                            
[721] cgdsr_1.3.0                              
[722] DOSE_3.21.2                              
[723] deSolve_1.30                             
[724] htmlwidgets_1.5.4                        
[725] tiff_0.1-10                              
[726] lars_1.2                                 
[727] survcomp_1.45.1                          
[728] intervals_0.15.2                         
[729] Cepo_1.1.1                               
[730] foreach_1.5.1                            
[731] viper_1.29.0                             
[732] proxy_0.4-26                             
[733] FactoMineR_2.4                           
[734] SmartSVA_0.1.3                           
[735] entropy_1.3.1                            
[736] shinyjs_2.1.0                            
[737] TFisher_0.2.0                            
[738] ANCOMBC_1.5.0                            
[739] spatstat.core_2.3-2                      
[740] R2HTML_2.3.2                             
[741] miniUI_0.1.1.1                           
[742] lpSolveAPI_5.5.2.0-17.7                  
[743] sva_3.43.0                               
[744] conquer_1.2.1                            
[745] questionr_0.7.6                          
[746] Category_2.61.0                          
[747] ps_1.6.0                                 
[748] BioNet_1.55.0                            
[749] sqldf_0.4-11                             
[750] makecdfenv_1.71.0                        
[751] shinycssloaders_1.0.0                    
[752] ggrepel_0.9.1                            
[753] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0
[754] metapod_1.3.0                            
[755] ggfun_0.0.4                              
[756] logistf_1.24                             
[757] GO.db_3.14.0                             
[758] gamlss_5.3-4                             
[759] FME_1.3.6.2                              
[760] systemfonts_1.0.3                        
[761] dqrng_0.3.0                              
[762] ggridges_0.5.3                           
[763] haven_2.4.3                              
[764] lava_1.6.10                              
[765] R.utils_2.11.0                           
[766] rmeta_3.0                                
[767] lgr_0.4.3                                
[768] qvalue_2.27.0                            
[769] munsell_0.5.0                            
[770] Rsolnp_1.16                              
[771] NMF_0.23.0                               
[772] later_1.3.0                              
[773] switchBox_1.31.0                         
[774] GeneMeta_1.67.0                          
[775] paintmap_1.0                             
[776] RColorBrewer_1.1-2                       
[777] gridBase_0.4-7                           
[778] dynamicTreeCut_1.63-1                    
[779] cobs_1.3-4                               
[780] patchwork_1.1.1                          
[781] imputeLCMD_2.0                           
[782] FNN_1.1.3                                
[783] fitdistrplus_1.1-6                       
[784] shinytoastr_2.1.1                        
[785] spatial_7.3-15                           
[786] TH.data_1.1-0                            
[787] reportROC_3.5                            
[788] softImpute_1.4-1                         
[789] Rttf2pt1_1.3.9                           
[790] pillar_1.6.4                             
[791] lmerTest_3.1-3                           
[792] ComplexHeatmap_2.11.0                    
[793] sm_2.2-5.7                               
[794] coda_0.19-4                              
[795] DEsingle_1.15.0                          
[796] hypeR_1.11.0                             
[797] sn_2.0.1                                 
[798] R2WinBUGS_2.1-21                         
[799] sp_1.4-6                                 
[800] yaImpute_1.0-32                          
[801] vctrs_0.3.8                              
[802] network_1.17.1                           
[803] exomeCopy_1.41.1                         
[804] corpcor_1.6.10                           
[805] assertive.types_0.0-3                    
[806] lazyeval_0.2.2                           
[807] org.Sc.sgd.db_3.14.0                     
[808] uuid_1.0-3                               
[809] spatstat.sparse_2.1-0                    
[810] ROCR_1.0-11                              
[811] ModelMetrics_1.2.2.2                     
[812] colorspace_2.0-2                         
[813] magick_2.7.3                             
[814] rpart_4.1-15                             
[815] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[816] CytoML_2.7.0                             
[817] zlibbioc_1.41.0                          
[818] crul_1.2.0                               
[819] httpcode_0.3.0                           
[820] SNPRelate_1.29.0                         
[821] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
[822] ashr_2.2-47                              
[823] pracma_2.3.6                             
[824] spBayes_0.4-5                            
[825] piano_2.11.0                             
[826] Delaporte_8.0.1                          
[827] nnet_7.3-17                              
[828] IRkernel_1.3                             
[829] repr_1.1.4                               
[830] CGHcall_2.57.0                           
[831] rngtools_1.5.2                           
[832] tidytree_0.3.7                           
[833] kableExtra_1.3.4                         
[834] Polychrome_1.3.1                         
[835] markdown_1.1                             
[836] DirichletMultinomial_1.37.0              
[837] siggenes_1.69.0                          
[838] rstudioapi_0.13                          
[839] R.cache_0.15.0                           
[840] MsCoreUtils_1.7.1                        
[841] geneplotter_1.73.0                       
[842] dmt_0.8.20                               
[843] pls_2.8-0                                
[844] fastcluster_1.2.3                        
[845] askpass_1.1                              
[846] VGAM_1.1-5                               
[847] hms_1.1.1                                
[848] iterators_1.0.13                         
[849] XVector_0.35.0                           
[850] ReactomePA_1.39.0                        
[851] valr_0.6.4                               
[852] BiocManager_1.30.16                      
[853] inline_0.3.19                            
[854] SQUAREM_2021.1                           
[855] xml2_1.3.3                               
[856] numDeriv_2016.8-1.1                      
[857] pander_0.6.4                             
[858] lmtest_0.9-39                            
[859] reticulate_1.22                          
[860] ggnetwork_0.5.10                         
[861] survival_3.2-13                          
[862] png_0.1-7                                
[863] magrittr_2.0.1                           
[864] attempt_0.3.1                            
[865] pathview_1.35.0                          
[866] registry_0.5-1                           
[867] memoise_2.0.1                            
[868] openssl_1.4.6                            
            used   (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells  71317941 3808.8  107656388 5749.5 102768440 5488.5
Vcells 141775592 1081.7  373562516 2850.1 373562134 2850.1
codes
  -3   -2   -1    0    1    2    3    4    5    7 
  12   14   55 1979    7    2    1    4    1    1 
[1] 16
[1] 0.007707129
DONE.
