RnBeads.Rcheck/tests_i386/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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> BiocGenerics:::testPackage("RnBeads")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
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Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
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Attaching package: 'bit'
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Attaching package ff
- getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp61CG7a/ff"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==37570478.08 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==1878523904 -- consider a different value for tuning your system
Attaching package: 'ff'
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Spam version 2.6-0 (2020-12-14) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
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suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
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See https://github.com/NCAR/Fields for
an extensive vignette, other supplements and source code
Attaching package: 'gplots'
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Attaching package: 'limma'
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Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
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colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Attaching package: 'Biostrings'
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locfit 1.5-9.4 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'plyr'
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2021-05-06 06:32:21 0.4 STATUS STARTED Unit testing: differential
2021-05-06 06:32:21 0.4 STATUS STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2021-05-06 06:32:21 0.4 STATUS COMPLETED Testing function: rowWelchP
2021-05-06 06:32:21 0.4 STATUS STARTED Testing function: limmaP
2021-05-06 06:32:22 0.4 STATUS COMPLETED Testing function: limmaP
2021-05-06 06:32:22 0.4 STATUS STARTED Testing function: computeDiffTab.extended.site
2021-05-06 06:32:22 0.4 INFO Conducting differential analysis using limma
2021-05-06 06:32:22 0.4 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2021-05-06 06:32:22 0.4 STATUS STARTED Testing function: computeDiffTab.default.region
2021-05-06 06:32:22 0.4 INFO Conducting differential analysis using limma
2021-05-06 06:32:33 0.6 STATUS COMPLETED Testing function: computeDiffTab.default.region
2021-05-06 06:32:33 0.6 STATUS STARTED Testing function: combineTestPvalsMeth
2021-05-06 06:32:33 0.6 STATUS COMPLETED Testing function: combineTestPvalsMeth
2021-05-06 06:32:33 0.6 STATUS STARTED Testing function: get.adjustment.variables
2021-05-06 06:32:33 0.6 STATUS COMPLETED Testing function: get.adjustment.variables
2021-05-06 06:32:33 0.6 STATUS STARTED Testing function: get.comparison.info
2021-05-06 06:32:33 0.7 STATUS COMPLETED Testing function: get.comparison.info
2021-05-06 06:32:33 0.7 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2021-05-06 06:32:34 0.7 STATUS STARTED Retrieving comparison info
2021-05-06 06:32:34 0.7 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:32:34 0.7 STATUS STARTED Computing differential methylation tables
2021-05-06 06:32:34 0.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:32:34 0.7 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:32:34 0.7 INFO Conducting differential analysis using limma
2021-05-06 06:32:34 0.7 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:32:34 0.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:32:34 0.7 STATUS Computed table for tiling
2021-05-06 06:32:35 0.7 STATUS Computed table for genes
2021-05-06 06:32:35 0.8 STATUS Computed table for promoters
2021-05-06 06:32:36 0.8 STATUS Computed table for cpgislands
2021-05-06 06:32:36 0.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:32:36 0.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:32:37 0.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:32:37 0.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:32:37 0.8 INFO Conducting differential analysis using limma
2021-05-06 06:32:37 0.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:32:37 0.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:32:38 0.8 STATUS Computed table for tiling
2021-05-06 06:32:38 0.8 STATUS Computed table for genes
2021-05-06 06:32:38 0.8 STATUS Computed table for promoters
2021-05-06 06:32:39 0.8 STATUS Computed table for cpgislands
2021-05-06 06:32:39 0.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:32:39 0.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:32:39 0.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:32:39 0.8 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2021-05-06 06:32:39 0.8 STATUS STARTED Testing function: diffVar
2021-05-06 06:32:39 0.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:33:53 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:33:54 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:33:54 2.8 WARNING Could not compute p-values with diffVar, returning NA
2021-05-06 06:33:54 2.8 INFO diffVar from missMethyl package not properly running
2021-05-06 06:33:54 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:33:54 2.8 STATUS STARTED Testing function: apply.iEVORA
2021-05-06 06:33:54 2.8 STATUS STARTED iEVORA method
2021-05-06 06:33:55 2.8 INFO No DVCs detected. All p-values set to 1.
2021-05-06 06:33:55 2.8 STATUS COMPLETED iEVORA method
2021-05-06 06:33:55 2.8 STATUS STARTED Testing function: rnb.execute.diffVar
2021-05-06 06:33:56 2.8 STATUS STARTED Differential Variability
2021-05-06 06:33:56 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:33:56 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:33:56 2.9 INFO No imputation method selected, 'knn' method used.
2021-05-06 06:33:56 2.9 STATUS STARTED Imputation procedure knn
2021-05-06 06:33:56 2.9 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:33:56 2.9 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:33:56 2.9 INFO Conducting differential variability using diffVar
2021-05-06 06:33:56 2.9 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:33:56 2.9 STATUS COMPLETED diffVar method
2021-05-06 06:33:57 2.9 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:33:58 2.9 STATUS Computed table for tiling
2021-05-06 06:33:58 3.0 STATUS Computed table for genes
2021-05-06 06:33:59 3.0 STATUS Computed table for promoters
2021-05-06 06:33:59 3.0 STATUS Computed table for cpgislands
2021-05-06 06:33:59 3.0 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:34:00 3.0 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:00 3.0 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:00 3.0 INFO Conducting differential variability using diffVar
2021-05-06 06:34:00 3.0 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:34:00 3.0 STATUS COMPLETED diffVar method
2021-05-06 06:34:00 3.1 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:34:02 2.8 STATUS Computed table for tiling
2021-05-06 06:34:02 2.8 STATUS Computed table for genes
2021-05-06 06:34:02 2.8 STATUS Computed table for promoters
2021-05-06 06:34:03 2.8 STATUS Computed table for cpgislands
2021-05-06 06:34:03 2.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:34:03 2.8 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:03 2.8 STATUS COMPLETED Differential Variability
2021-05-06 06:34:03 2.8 STATUS COMPLETED Testing function: rnb.execute.diffVar
2021-05-06 06:34:03 2.8 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 06:34:03 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:03 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:04 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:04 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:04 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:04 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:04 2.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:34:04 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:34:04 2.8 INFO Conducting differential variability using diffVar
2021-05-06 06:34:04 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:34:04 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:34:05 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:05 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:06 2.8 STATUS Computed table for tiling
2021-05-06 06:34:06 2.8 STATUS Computed table for genes
2021-05-06 06:34:07 2.8 STATUS Computed table for promoters
2021-05-06 06:34:08 2.8 STATUS Computed table for cpgislands
2021-05-06 06:34:08 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:08 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:08 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:08 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:08 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:08 2.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:34:08 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:34:08 2.8 INFO Conducting differential variability using diffVar
2021-05-06 06:34:09 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:34:09 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:34:09 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:09 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:10 2.8 STATUS Computed table for tiling
2021-05-06 06:34:10 2.8 STATUS Computed table for genes
2021-05-06 06:34:11 2.8 STATUS Computed table for promoters
2021-05-06 06:34:12 2.8 STATUS Computed table for cpgislands
2021-05-06 06:34:12 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:12 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:12 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:13 2.8 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 06:34:13 2.8 STATUS STARTED Testing class: RnBDiffMeth
2021-05-06 06:34:13 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:13 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:13 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:13 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:13 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:13 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:13 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:14 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:14 2.8 STATUS Computed table for tiling
2021-05-06 06:34:14 2.8 STATUS Computed table for genes
2021-05-06 06:34:15 2.8 STATUS Computed table for promoters
2021-05-06 06:34:15 2.8 STATUS Computed table for cpgislands
2021-05-06 06:34:15 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:15 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:15 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:16 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:16 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:16 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:16 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:16 2.8 STATUS Computed table for tiling
2021-05-06 06:34:17 2.8 STATUS Computed table for genes
2021-05-06 06:34:18 2.8 STATUS Computed table for promoters
2021-05-06 06:34:18 2.8 STATUS Computed table for cpgislands
2021-05-06 06:34:18 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:18 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:18 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:18 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:19 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:19 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:19 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:19 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:19 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:19 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:19 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:20 2.8 STATUS Computed table for genes
2021-05-06 06:34:20 2.8 STATUS Computed table for tiling
2021-05-06 06:34:20 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:20 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:20 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:20 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:20 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:21 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:21 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:21 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:21 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:21 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:21 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:21 2.8 STATUS Computed table for genes
2021-05-06 06:34:22 2.8 STATUS Computed table for tiling
2021-05-06 06:34:22 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:22 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:22 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:22 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:22 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:22 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:22 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:22 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:23 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:23 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:23 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:24 2.8 STATUS Computed table for promoters
2021-05-06 06:34:24 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:24 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:24 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:24 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:24 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:24 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:24 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:25 2.8 STATUS Computed table for promoters
2021-05-06 06:34:25 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:25 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:25 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:25 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:25 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:25 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:25 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:25 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:26 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:26 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:26 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:26 2.8 STATUS Computed table for genes
2021-05-06 06:34:27 2.8 STATUS Computed table for tiling
2021-05-06 06:34:27 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:27 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:27 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:27 2.8 STATUS STARTED Testing function: get.region.types
2021-05-06 06:34:27 2.8 STATUS COMPLETED Testing function: get.region.types
2021-05-06 06:34:27 2.8 STATUS STARTED Testing function: get.comparisons
2021-05-06 06:34:27 2.8 STATUS COMPLETED Testing function: get.comparisons
2021-05-06 06:34:27 2.8 STATUS STARTED Testing function: get.comparison.grouplabels
2021-05-06 06:34:27 2.8 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-05-06 06:34:27 2.8 STATUS STARTED Testing function: get.site.test.method
2021-05-06 06:34:28 2.8 STATUS COMPLETED Testing function: get.site.test.method
2021-05-06 06:34:28 2.8 STATUS STARTED Testing function: get.table
2021-05-06 06:34:28 2.8 STATUS COMPLETED Testing function: get.table
2021-05-06 06:34:28 2.8 STATUS STARTED Testing function: addDiffMethTable
2021-05-06 06:34:28 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:28 2.8 STATUS COMPLETED Testing function: addDiffMethTable
2021-05-06 06:34:28 2.8 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-05-06 06:34:29 2.8 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-05-06 06:34:29 2.8 STATUS STARTED Destructor
2021-05-06 06:34:29 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:29 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:29 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:29 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:29 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:29 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:29 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:29 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:29 2.8 STATUS COMPLETED Destructor
2021-05-06 06:34:30 2.8 STATUS COMPLETED Testing class: RnBDiffMeth
2021-05-06 06:34:30 2.8 STATUS COMPLETED Testing function: apply.iEVORA
2021-05-06 06:34:30 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:30 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:30 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:30 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:30 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:30 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:30 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:30 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:32 2.8 STATUS Computed table for tiling
2021-05-06 06:34:32 2.8 STATUS Computed table for genes
2021-05-06 06:34:32 2.8 STATUS Computed table for promoters
2021-05-06 06:34:32 2.8 STATUS Computed table for cpgislands
2021-05-06 06:34:32 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:33 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:33 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:33 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:33 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:33 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:33 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:34 2.8 STATUS Computed table for tiling
2021-05-06 06:34:34 2.8 STATUS Computed table for genes
2021-05-06 06:34:34 2.8 STATUS Computed table for promoters
2021-05-06 06:34:34 2.8 STATUS Computed table for cpgislands
2021-05-06 06:34:35 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:35 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:35 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:35 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:35 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:35 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:35 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:35 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:35 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:35 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:35 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:36 2.8 STATUS Computed table for genes
2021-05-06 06:34:37 2.8 STATUS Computed table for tiling
2021-05-06 06:34:37 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:37 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:37 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:37 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:37 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:37 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:38 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:38 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:38 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:38 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:38 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:38 2.8 STATUS Computed table for genes
2021-05-06 06:34:39 2.8 STATUS Computed table for tiling
2021-05-06 06:34:39 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:39 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:39 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:39 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:39 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:39 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:39 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:39 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:40 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:40 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:40 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:40 2.8 STATUS Computed table for promoters
2021-05-06 06:34:40 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:40 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:40 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:40 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:41 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:41 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:41 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:41 2.8 STATUS Computed table for promoters
2021-05-06 06:34:42 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:42 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:42 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:42 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:42 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:42 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:42 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:42 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:42 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:42 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:43 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:44 2.8 STATUS Computed table for genes
2021-05-06 06:34:44 2.8 STATUS Computed table for tiling
2021-05-06 06:34:44 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:45 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:45 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:34:45 2.8 STATUS STARTED Testing function: get.region.types
2021-05-06 06:34:45 2.8 STATUS COMPLETED Testing function: get.region.types
2021-05-06 06:34:45 2.8 STATUS STARTED Testing function: get.comparisons
2021-05-06 06:34:45 2.8 STATUS COMPLETED Testing function: get.comparisons
2021-05-06 06:34:45 2.8 STATUS STARTED Testing function: get.comparison.grouplabels
2021-05-06 06:34:45 2.8 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-05-06 06:34:46 2.8 STATUS STARTED Testing function: get.site.test.method
2021-05-06 06:34:46 2.8 STATUS COMPLETED Testing function: get.site.test.method
2021-05-06 06:34:46 2.8 STATUS STARTED Testing function: get.table
2021-05-06 06:34:46 2.8 STATUS COMPLETED Testing function: get.table
2021-05-06 06:34:46 2.8 STATUS STARTED Testing function: addDiffMethTable
2021-05-06 06:34:46 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:46 2.8 STATUS COMPLETED Testing function: addDiffMethTable
2021-05-06 06:34:47 2.8 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-05-06 06:34:47 2.8 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-05-06 06:34:47 2.8 STATUS STARTED Destructor
2021-05-06 06:34:47 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:47 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:47 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:47 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:47 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:47 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:48 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:48 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:34:48 2.8 STATUS COMPLETED Destructor
2021-05-06 06:34:48 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:48 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:49 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:34:49 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:34:49 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:34:49 2.8 WARNING Could not compute p-values with diffVar, returning NA
2021-05-06 06:34:49 2.8 INFO diffVar from missMethyl package not properly running
2021-05-06 06:34:50 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:34:50 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:34:50 2.8 STATUS STARTED Unit testing: differential
2021-05-06 06:34:50 2.8 STATUS STARTED Testing function: rowWelchP
2021-05-06 06:34:50 2.8 STATUS COMPLETED Testing function: rowWelchP
2021-05-06 06:34:50 2.8 STATUS STARTED Testing function: limmaP
2021-05-06 06:34:51 2.9 STATUS COMPLETED Testing function: limmaP
2021-05-06 06:34:51 2.9 STATUS STARTED Testing function: computeDiffTab.extended.site
2021-05-06 06:34:51 2.9 INFO Conducting differential analysis using limma
2021-05-06 06:34:51 2.9 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2021-05-06 06:34:51 2.9 STATUS STARTED Testing function: computeDiffTab.default.region
2021-05-06 06:34:51 2.9 INFO Conducting differential analysis using limma
2021-05-06 06:34:52 2.9 STATUS COMPLETED Testing function: computeDiffTab.default.region
2021-05-06 06:34:52 2.9 STATUS STARTED Testing function: combineTestPvalsMeth
2021-05-06 06:34:52 2.9 STATUS COMPLETED Testing function: combineTestPvalsMeth
2021-05-06 06:34:52 2.9 STATUS STARTED Testing function: get.adjustment.variables
2021-05-06 06:34:52 2.9 STATUS COMPLETED Testing function: get.adjustment.variables
2021-05-06 06:34:52 2.9 STATUS STARTED Testing function: get.comparison.info
2021-05-06 06:34:53 2.9 STATUS COMPLETED Testing function: get.comparison.info
2021-05-06 06:34:53 2.9 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2021-05-06 06:34:53 2.9 STATUS STARTED Retrieving comparison info
2021-05-06 06:34:53 2.9 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:34:53 2.9 STATUS STARTED Computing differential methylation tables
2021-05-06 06:34:53 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:53 2.9 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:53 2.9 INFO Conducting differential analysis using limma
2021-05-06 06:34:54 2.9 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:54 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:54 2.9 STATUS Computed table for tiling
2021-05-06 06:34:55 2.9 STATUS Computed table for genes
2021-05-06 06:34:56 2.8 STATUS Computed table for promoters
2021-05-06 06:34:56 2.8 STATUS Computed table for cpgislands
2021-05-06 06:34:56 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:57 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:34:57 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:57 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:34:57 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:34:57 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:34:57 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:58 2.8 STATUS Computed table for tiling
2021-05-06 06:34:58 2.8 STATUS Computed table for genes
2021-05-06 06:34:59 2.8 STATUS Computed table for promoters
2021-05-06 06:34:59 2.8 STATUS Computed table for cpgislands
2021-05-06 06:34:59 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:34:59 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:34:59 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:35:00 2.8 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2021-05-06 06:35:00 2.8 STATUS STARTED Testing function: diffVar
2021-05-06 06:35:00 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:35:00 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:35:00 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:35:00 2.8 WARNING Could not compute p-values with diffVar, returning NA
2021-05-06 06:35:00 2.8 INFO diffVar from missMethyl package not properly running
2021-05-06 06:35:01 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:35:01 2.8 STATUS STARTED Testing function: apply.iEVORA
2021-05-06 06:35:01 2.8 STATUS STARTED iEVORA method
2021-05-06 06:35:02 2.8 INFO No DVCs detected. All p-values set to 1.
2021-05-06 06:35:02 2.8 STATUS COMPLETED iEVORA method
2021-05-06 06:35:02 2.8 STATUS STARTED Testing function: rnb.execute.diffVar
2021-05-06 06:35:03 2.8 STATUS STARTED Differential Variability
2021-05-06 06:35:03 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:35:03 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:35:03 2.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:35:03 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:35:03 2.8 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:03 2.8 INFO Conducting differential variability using diffVar
2021-05-06 06:35:03 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:35:04 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:35:04 2.8 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:35:04 2.8 STATUS Computed table for tiling
2021-05-06 06:35:04 2.8 STATUS Computed table for genes
2021-05-06 06:35:05 2.8 STATUS Computed table for promoters
2021-05-06 06:35:05 2.8 STATUS Computed table for cpgislands
2021-05-06 06:35:05 2.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:35:05 2.8 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:05 2.8 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:05 2.8 INFO Conducting differential variability using diffVar
2021-05-06 06:35:06 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:35:06 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:35:06 2.8 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:35:06 2.8 STATUS Computed table for tiling
2021-05-06 06:35:07 2.9 STATUS Computed table for genes
2021-05-06 06:35:10 2.8 STATUS Computed table for promoters
2021-05-06 06:35:10 2.8 STATUS Computed table for cpgislands
2021-05-06 06:35:11 2.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:35:11 2.8 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:11 2.8 STATUS COMPLETED Differential Variability
2021-05-06 06:35:11 2.8 STATUS COMPLETED Testing function: rnb.execute.diffVar
2021-05-06 06:35:11 2.8 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 06:35:11 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:35:11 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:35:11 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:35:11 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:12 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:12 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:12 2.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:35:12 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:35:12 2.8 INFO Conducting differential variability using diffVar
2021-05-06 06:35:12 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:35:12 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:35:12 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:12 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:13 2.8 STATUS Computed table for tiling
2021-05-06 06:35:14 2.8 STATUS Computed table for genes
2021-05-06 06:35:14 2.8 STATUS Computed table for promoters
2021-05-06 06:35:15 2.8 STATUS Computed table for cpgislands
2021-05-06 06:35:15 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:16 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:16 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:16 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:16 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:16 2.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:35:16 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:35:16 2.8 INFO Conducting differential variability using diffVar
2021-05-06 06:35:16 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:35:17 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:35:17 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:17 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:18 2.8 STATUS Computed table for tiling
2021-05-06 06:35:18 2.8 STATUS Computed table for genes
2021-05-06 06:35:18 2.8 STATUS Computed table for promoters
2021-05-06 06:35:19 2.8 STATUS Computed table for cpgislands
2021-05-06 06:35:19 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:19 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:19 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:35:19 2.8 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 06:35:19 2.8 STATUS STARTED Testing class: RnBDiffMeth
2021-05-06 06:35:19 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:35:20 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:35:20 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:35:20 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:20 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:20 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:20 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:20 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:22 2.8 STATUS Computed table for tiling
2021-05-06 06:35:22 2.8 STATUS Computed table for genes
2021-05-06 06:35:23 2.8 STATUS Computed table for promoters
2021-05-06 06:35:23 2.8 STATUS Computed table for cpgislands
2021-05-06 06:35:23 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:23 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:24 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:24 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:24 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:24 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:24 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:25 2.8 STATUS Computed table for tiling
2021-05-06 06:35:25 2.8 STATUS Computed table for genes
2021-05-06 06:35:25 2.8 STATUS Computed table for promoters
2021-05-06 06:35:26 2.8 STATUS Computed table for cpgislands
2021-05-06 06:35:27 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:27 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:27 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:35:27 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:35:27 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:35:27 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:35:27 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:27 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:27 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:28 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:28 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:28 2.8 STATUS Computed table for genes
2021-05-06 06:35:28 2.8 STATUS Computed table for tiling
2021-05-06 06:35:29 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:29 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:29 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:35:29 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:35:29 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:35:29 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:35:29 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:29 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:29 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:29 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:30 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:30 2.8 STATUS Computed table for genes
2021-05-06 06:35:30 2.8 STATUS Computed table for tiling
2021-05-06 06:35:30 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:31 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:31 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:35:31 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:35:31 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:35:31 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:35:31 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:31 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:31 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:31 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:31 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:32 2.8 STATUS Computed table for promoters
2021-05-06 06:35:32 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:32 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:32 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:32 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:32 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:32 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:32 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:33 2.8 STATUS Computed table for promoters
2021-05-06 06:35:33 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:33 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:33 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:35:33 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:35:33 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:35:33 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:35:33 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:34 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:34 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:34 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:34 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:35 2.8 STATUS Computed table for genes
2021-05-06 06:35:36 2.8 STATUS Computed table for tiling
2021-05-06 06:35:36 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:36 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:36 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:35:37 2.8 STATUS STARTED Testing function: get.region.types
2021-05-06 06:35:37 2.8 STATUS COMPLETED Testing function: get.region.types
2021-05-06 06:35:37 2.8 STATUS STARTED Testing function: get.comparisons
2021-05-06 06:35:37 2.8 STATUS COMPLETED Testing function: get.comparisons
2021-05-06 06:35:37 2.8 STATUS STARTED Testing function: get.comparison.grouplabels
2021-05-06 06:35:37 2.8 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-05-06 06:35:37 2.8 STATUS STARTED Testing function: get.site.test.method
2021-05-06 06:35:37 2.8 STATUS COMPLETED Testing function: get.site.test.method
2021-05-06 06:35:37 2.8 STATUS STARTED Testing function: get.table
2021-05-06 06:35:37 2.8 STATUS COMPLETED Testing function: get.table
2021-05-06 06:35:38 2.8 STATUS STARTED Testing function: addDiffMethTable
2021-05-06 06:35:38 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:38 2.8 STATUS COMPLETED Testing function: addDiffMethTable
2021-05-06 06:35:38 2.8 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-05-06 06:35:38 2.8 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-05-06 06:35:38 2.8 STATUS STARTED Destructor
2021-05-06 06:35:39 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:35:39 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:35:39 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:35:39 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:35:39 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:35:39 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:35:39 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:35:39 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:35:39 2.8 STATUS COMPLETED Destructor
2021-05-06 06:35:40 2.8 STATUS COMPLETED Testing class: RnBDiffMeth
2021-05-06 06:35:40 2.8 STATUS COMPLETED Testing function: apply.iEVORA
2021-05-06 06:35:40 2.8 STATUS STARTED iEVORA method
2021-05-06 06:35:41 2.8 INFO No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2
2021-05-06 06:35:42 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:35:42 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:35:42 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:35:42 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:42 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:42 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:42 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:42 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:44 2.8 STATUS Computed table for tiling
2021-05-06 06:35:44 2.8 STATUS Computed table for genes
2021-05-06 06:35:45 2.8 STATUS Computed table for promoters
2021-05-06 06:35:45 2.8 STATUS Computed table for cpgislands
2021-05-06 06:35:45 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:45 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:45 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:46 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:46 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:46 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:46 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:46 2.8 STATUS Computed table for tiling
2021-05-06 06:35:47 2.8 STATUS Computed table for genes
2021-05-06 06:35:47 2.8 STATUS Computed table for promoters
2021-05-06 06:35:48 2.8 STATUS Computed table for cpgislands
2021-05-06 06:35:48 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:48 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:48 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:35:48 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:35:48 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:35:48 2.8 STATUS STARTED Computing differential methylation tables
2021-05-06 06:35:48 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:49 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:49 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:49 2.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:35:49 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:35:49 2.8 INFO Conducting differential variability using diffVar
2021-05-06 06:35:49 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:35:49 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:35:50 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:50 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:51 2.8 STATUS Computed table for tiling
2021-05-06 06:35:52 2.8 STATUS Computed table for genes
2021-05-06 06:35:52 2.8 STATUS Computed table for promoters
2021-05-06 06:35:52 2.8 STATUS Computed table for cpgislands
2021-05-06 06:35:53 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:53 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:35:53 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:53 2.8 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:35:53 2.8 INFO Conducting differential analysis using limma
2021-05-06 06:35:53 2.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:35:53 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:35:53 2.8 INFO Conducting differential variability using diffVar
2021-05-06 06:35:53 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:35:53 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:35:54 2.8 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:35:54 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:57 2.8 STATUS Computed table for tiling
2021-05-06 06:35:57 2.8 STATUS Computed table for genes
2021-05-06 06:35:58 2.8 STATUS Computed table for promoters
2021-05-06 06:35:58 2.8 STATUS Computed table for cpgislands
2021-05-06 06:35:59 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:35:59 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:35:59 2.8 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:35:59 2.8 STATUS STARTED Differential Variability
2021-05-06 06:35:59 2.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:35:59 2.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:35:59 2.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:36:00 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:36:00 2.8 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:36:00 2.8 INFO Conducting differential variability using diffVar
2021-05-06 06:36:00 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:36:00 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:36:00 2.8 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:36:01 2.8 STATUS Computed table for tiling
2021-05-06 06:36:03 2.8 STATUS Computed table for genes
2021-05-06 06:36:03 2.8 STATUS Computed table for promoters
2021-05-06 06:36:04 2.8 STATUS Computed table for cpgislands
2021-05-06 06:36:04 2.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:36:04 2.8 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:36:04 2.8 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:36:04 2.8 INFO Conducting differential variability using diffVar
2021-05-06 06:36:04 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:36:04 2.8 STATUS COMPLETED diffVar method
2021-05-06 06:36:05 2.8 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:36:05 2.8 STATUS Computed table for tiling
2021-05-06 06:36:06 2.8 STATUS Computed table for genes
2021-05-06 06:36:06 2.8 STATUS Computed table for promoters
2021-05-06 06:36:06 2.8 STATUS Computed table for cpgislands
2021-05-06 06:36:06 2.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:36:07 2.8 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:36:07 2.8 STATUS COMPLETED Differential Variability
2021-05-06 06:36:07 2.8 STATUS STARTED Analysis
2021-05-06 06:36:07 2.8 INFO Loaded information from data.RData
2021-05-06 06:36:07 2.8 STATUS STARTED Processing Detection P-values
2021-05-06 06:36:07 2.8 INFO Removed 3979 probes that overlap with SNPs
2021-05-06 06:36:08 2.8 INFO Completed Greedycut on 510 samples
2021-05-06 06:36:08 2.8 STATUS COMPLETED Processing Detection P-values
2021-05-06 06:36:08 2.8 WARNING File not found: data2.RData
2021-05-06 06:36:08 2.8 STATUS COMPLETED Analysis
2021-05-06 06:36:08 2.8 STATUS STARTED Testing imputation
2021-05-06 06:36:08 2.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:36:10 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:36:10 2.8 STATUS STARTED Imputation procedure mean.samples
2021-05-06 06:36:11 2.8 STATUS COMPLETED Imputation procedure mean.samples
2021-05-06 06:36:11 2.8 STATUS STARTED Imputation procedure mean.cpgs
2021-05-06 06:36:12 2.8 STATUS COMPLETED Imputation procedure mean.cpgs
2021-05-06 06:36:12 2.8 STATUS STARTED Imputation procedure random
2021-05-06 06:36:12 2.8 STATUS COMPLETED Imputation procedure random
2021-05-06 06:36:13 2.8 STATUS COMPLETED Testing imputation
2021-05-06 06:36:13 2.8 STATUS STARTED Testing age prediction
2021-05-06 06:36:13 2.8 STATUS STARTED Performing Age Prediction
2021-05-06 06:36:17 3.0 STATUS COMPLETED Performing Age Prediction
2021-05-06 06:36:17 3.0 STATUS COMPLETED Testing age prediction
2021-05-06 06:36:17 3.0 STATUS STARTED Performing Age Prediction
2021-05-06 06:36:21 3.2 STATUS COMPLETED Performing Age Prediction
2021-05-06 06:36:21 3.2 STATUS STARTED Imputation procedure knn
2021-05-06 06:36:22 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:36:23 2.8 STATUS STARTED Imputation procedure mean.samples
2021-05-06 06:36:23 2.8 STATUS COMPLETED Imputation procedure mean.samples
2021-05-06 06:36:23 2.8 STATUS STARTED Imputation procedure mean.cpgs
2021-05-06 06:36:24 2.9 STATUS COMPLETED Imputation procedure mean.cpgs
2021-05-06 06:36:24 2.9 STATUS STARTED Imputation procedure random
2021-05-06 06:36:24 2.9 STATUS COMPLETED Imputation procedure random
2021-05-06 06:36:24 2.9 STATUS STARTED Testing imputation
2021-05-06 06:36:25 2.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:36:26 2.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:36:26 2.8 STATUS STARTED Imputation procedure mean.samples
2021-05-06 06:36:26 2.9 STATUS COMPLETED Imputation procedure mean.samples
2021-05-06 06:36:27 2.9 STATUS STARTED Imputation procedure mean.cpgs
2021-05-06 06:36:27 2.9 STATUS COMPLETED Imputation procedure mean.cpgs
2021-05-06 06:36:27 2.9 STATUS STARTED Imputation procedure random
2021-05-06 06:36:29 2.8 STATUS COMPLETED Imputation procedure random
2021-05-06 06:36:29 2.8 STATUS COMPLETED Testing imputation
2021-05-06 06:36:29 2.8 STATUS STARTED Testing age prediction
2021-05-06 06:36:29 2.8 STATUS STARTED Performing Age Prediction
2021-05-06 06:36:31 3.0 STATUS COMPLETED Performing Age Prediction
2021-05-06 06:36:31 3.0 STATUS COMPLETED Testing age prediction
RUNIT TEST PROTOCOL -- Thu May 06 06:36:59 2021
***********************************************
Number of test functions: 24
Number of errors: 0
Number of failures: 0
1 Test Suite :
RnBeads RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24
Number of errors: 0
Number of failures: 0
There were 25 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
249.73 19.81 298.51
|
RnBeads.Rcheck/tests_x64/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("RnBeads")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'bit'
The following object is masked from 'package:base':
xor
Attaching package ff
- getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpI3cKAq/ff"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==685831618.56 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==34291580928 -- consider a different value for tuning your system
Attaching package: 'ff'
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
Spam version 2.6-0 (2020-12-14) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following object is masked from 'package:stats4':
mle
The following objects are masked from 'package:base':
backsolve, forwardsolve
See https://github.com/NCAR/Fields for
an extensive vignette, other supplements and source code
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Attaching package: 'gridExtra'
The following object is masked from 'package:BiocGenerics':
combine
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:MASS':
select
Attaching package: 'MatrixGenerics'
The following object is masked from 'package:Biobase':
rowMedians
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Attaching package: 'Biostrings'
The following objects are masked from 'package:ff':
mismatch, pattern
The following object is masked from 'package:base':
strsplit
locfit 1.5-9.4 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:matrixStats':
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The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
2021-05-06 06:37:25 0.7 STATUS STARTED Unit testing: differential
2021-05-06 06:37:25 0.7 STATUS STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2021-05-06 06:37:25 0.7 STATUS COMPLETED Testing function: rowWelchP
2021-05-06 06:37:26 0.7 STATUS STARTED Testing function: limmaP
2021-05-06 06:37:26 0.7 STATUS COMPLETED Testing function: limmaP
2021-05-06 06:37:26 0.7 STATUS STARTED Testing function: computeDiffTab.extended.site
2021-05-06 06:37:26 0.7 INFO Conducting differential analysis using limma
2021-05-06 06:37:26 0.7 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2021-05-06 06:37:26 0.7 STATUS STARTED Testing function: computeDiffTab.default.region
2021-05-06 06:37:26 0.7 INFO Conducting differential analysis using limma
2021-05-06 06:37:34 0.9 STATUS COMPLETED Testing function: computeDiffTab.default.region
2021-05-06 06:37:34 0.9 STATUS STARTED Testing function: combineTestPvalsMeth
2021-05-06 06:37:34 0.9 STATUS COMPLETED Testing function: combineTestPvalsMeth
2021-05-06 06:37:34 0.9 STATUS STARTED Testing function: get.adjustment.variables
2021-05-06 06:37:35 0.9 STATUS COMPLETED Testing function: get.adjustment.variables
2021-05-06 06:37:35 0.9 STATUS STARTED Testing function: get.comparison.info
2021-05-06 06:37:35 0.9 STATUS COMPLETED Testing function: get.comparison.info
2021-05-06 06:37:35 0.9 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2021-05-06 06:37:35 1.0 STATUS STARTED Retrieving comparison info
2021-05-06 06:37:35 1.0 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:37:35 1.0 STATUS STARTED Computing differential methylation tables
2021-05-06 06:37:35 1.0 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:37:35 1.0 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:37:35 1.0 INFO Conducting differential analysis using limma
2021-05-06 06:37:35 1.0 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:37:35 1.0 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:37:36 1.0 STATUS Computed table for tiling
2021-05-06 06:37:36 1.0 STATUS Computed table for genes
2021-05-06 06:37:36 1.1 STATUS Computed table for promoters
2021-05-06 06:37:38 1.0 STATUS Computed table for cpgislands
2021-05-06 06:37:38 1.0 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:37:39 1.0 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:37:39 1.0 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:37:39 1.0 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:37:39 1.0 INFO Conducting differential analysis using limma
2021-05-06 06:37:39 1.0 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:37:39 1.0 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:37:40 1.0 STATUS Computed table for tiling
2021-05-06 06:37:40 1.0 STATUS Computed table for genes
2021-05-06 06:37:40 1.1 STATUS Computed table for promoters
2021-05-06 06:37:41 1.1 STATUS Computed table for cpgislands
2021-05-06 06:37:41 1.1 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:37:41 1.1 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:37:41 1.1 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:37:41 1.1 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2021-05-06 06:37:41 1.1 STATUS STARTED Testing function: diffVar
2021-05-06 06:37:41 1.1 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:39:03 3.7 STATUS COMPLETED diffVar method
2021-05-06 06:39:03 3.7 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:39:03 3.7 WARNING Could not compute p-values with diffVar, returning NA
2021-05-06 06:39:03 3.7 INFO diffVar from missMethyl package not properly running
2021-05-06 06:39:03 3.7 STATUS COMPLETED diffVar method
2021-05-06 06:39:03 3.7 STATUS STARTED Testing function: apply.iEVORA
2021-05-06 06:39:03 3.7 STATUS STARTED iEVORA method
2021-05-06 06:39:04 3.8 INFO No DVCs detected. All p-values set to 1.
2021-05-06 06:39:04 3.8 STATUS COMPLETED iEVORA method
2021-05-06 06:39:04 3.8 STATUS STARTED Testing function: rnb.execute.diffVar
2021-05-06 06:39:05 3.8 STATUS STARTED Differential Variability
2021-05-06 06:39:05 3.8 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:05 3.8 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:05 3.8 INFO No imputation method selected, 'knn' method used.
2021-05-06 06:39:05 3.8 STATUS STARTED Imputation procedure knn
2021-05-06 06:39:05 3.8 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:39:05 3.8 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:05 3.8 INFO Conducting differential variability using diffVar
2021-05-06 06:39:05 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:39:05 3.8 STATUS COMPLETED diffVar method
2021-05-06 06:39:05 3.8 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:39:08 3.6 STATUS Computed table for tiling
2021-05-06 06:39:08 3.6 STATUS Computed table for genes
2021-05-06 06:39:08 3.6 STATUS Computed table for promoters
2021-05-06 06:39:09 3.6 STATUS Computed table for cpgislands
2021-05-06 06:39:09 3.6 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:39:09 3.6 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:09 3.6 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:09 3.6 INFO Conducting differential variability using diffVar
2021-05-06 06:39:09 3.6 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:39:09 3.6 STATUS COMPLETED diffVar method
2021-05-06 06:39:09 3.6 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:39:10 3.6 STATUS Computed table for tiling
2021-05-06 06:39:10 3.6 STATUS Computed table for genes
2021-05-06 06:39:14 3.4 STATUS Computed table for promoters
2021-05-06 06:39:14 3.4 STATUS Computed table for cpgislands
2021-05-06 06:39:14 3.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:39:14 3.4 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:14 3.4 STATUS COMPLETED Differential Variability
2021-05-06 06:39:14 3.4 STATUS COMPLETED Testing function: rnb.execute.diffVar
2021-05-06 06:39:14 3.4 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 06:39:15 3.5 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:15 3.5 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:15 3.5 STATUS STARTED Computing differential methylation tables
2021-05-06 06:39:15 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:15 3.5 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:15 3.5 INFO Conducting differential analysis using limma
2021-05-06 06:39:15 3.5 STATUS STARTED Imputation procedure knn
2021-05-06 06:39:15 3.5 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:39:15 3.5 INFO Conducting differential variability using diffVar
2021-05-06 06:39:15 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:39:15 3.5 STATUS COMPLETED diffVar method
2021-05-06 06:39:15 3.5 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:15 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:17 3.6 STATUS Computed table for tiling
2021-05-06 06:39:23 2.9 STATUS Computed table for genes
2021-05-06 06:39:23 2.9 STATUS Computed table for promoters
2021-05-06 06:39:24 2.9 STATUS Computed table for cpgislands
2021-05-06 06:39:24 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:24 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:24 2.9 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:24 2.9 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:24 2.9 INFO Conducting differential analysis using limma
2021-05-06 06:39:24 2.9 STATUS STARTED Imputation procedure knn
2021-05-06 06:39:24 2.9 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:39:24 2.9 INFO Conducting differential variability using diffVar
2021-05-06 06:39:25 2.9 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:39:25 3.0 STATUS COMPLETED diffVar method
2021-05-06 06:39:25 3.0 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:25 3.0 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:26 3.1 STATUS Computed table for tiling
2021-05-06 06:39:27 3.2 STATUS Computed table for genes
2021-05-06 06:39:28 3.3 STATUS Computed table for promoters
2021-05-06 06:39:29 3.3 STATUS Computed table for cpgislands
2021-05-06 06:39:29 3.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:29 3.3 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:30 3.3 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:39:30 3.3 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 06:39:30 3.3 STATUS STARTED Testing class: RnBDiffMeth
2021-05-06 06:39:30 3.3 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:30 3.3 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:30 3.3 STATUS STARTED Computing differential methylation tables
2021-05-06 06:39:30 3.3 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:30 3.3 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:30 3.3 INFO Conducting differential analysis using limma
2021-05-06 06:39:30 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:30 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:31 3.4 STATUS Computed table for tiling
2021-05-06 06:39:32 3.4 STATUS Computed table for genes
2021-05-06 06:39:32 3.4 STATUS Computed table for promoters
2021-05-06 06:39:32 3.4 STATUS Computed table for cpgislands
2021-05-06 06:39:32 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:33 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:33 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:33 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:33 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:33 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:33 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:34 3.4 STATUS Computed table for tiling
2021-05-06 06:39:34 3.4 STATUS Computed table for genes
2021-05-06 06:39:34 3.4 STATUS Computed table for promoters
2021-05-06 06:39:35 3.4 STATUS Computed table for cpgislands
2021-05-06 06:39:35 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:35 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:35 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:39:35 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:35 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:35 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:39:35 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:35 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:36 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:36 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:36 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:36 3.4 STATUS Computed table for genes
2021-05-06 06:39:38 3.4 STATUS Computed table for tiling
2021-05-06 06:39:38 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:38 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:38 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:39:38 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:39 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:39 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:39:39 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:39 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:39 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:39 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:39 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:39 3.4 STATUS Computed table for genes
2021-05-06 06:39:40 3.4 STATUS Computed table for tiling
2021-05-06 06:39:40 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:40 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:40 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:39:40 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:40 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:40 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:39:41 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:41 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:41 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:41 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:41 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:41 3.4 STATUS Computed table for promoters
2021-05-06 06:39:41 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:41 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:41 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:42 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:42 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:42 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:42 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:42 3.4 STATUS Computed table for promoters
2021-05-06 06:39:42 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:42 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:42 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:39:42 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:43 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:43 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:39:43 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:43 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:43 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:43 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:43 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:43 3.4 STATUS Computed table for genes
2021-05-06 06:39:44 3.4 STATUS Computed table for tiling
2021-05-06 06:39:44 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:44 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:44 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:39:44 3.4 STATUS STARTED Testing function: get.region.types
2021-05-06 06:39:45 3.4 STATUS COMPLETED Testing function: get.region.types
2021-05-06 06:39:45 3.4 STATUS STARTED Testing function: get.comparisons
2021-05-06 06:39:45 3.4 STATUS COMPLETED Testing function: get.comparisons
2021-05-06 06:39:45 3.4 STATUS STARTED Testing function: get.comparison.grouplabels
2021-05-06 06:39:45 3.4 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-05-06 06:39:45 3.4 STATUS STARTED Testing function: get.site.test.method
2021-05-06 06:39:45 3.4 STATUS COMPLETED Testing function: get.site.test.method
2021-05-06 06:39:45 3.4 STATUS STARTED Testing function: get.table
2021-05-06 06:39:45 3.4 STATUS COMPLETED Testing function: get.table
2021-05-06 06:39:45 3.4 STATUS STARTED Testing function: addDiffMethTable
2021-05-06 06:39:45 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:46 3.4 STATUS COMPLETED Testing function: addDiffMethTable
2021-05-06 06:39:46 3.4 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-05-06 06:39:46 3.4 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-05-06 06:39:46 3.4 STATUS STARTED Destructor
2021-05-06 06:39:46 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:39:46 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:39:46 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:39:47 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:39:47 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:39:47 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:39:47 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:39:47 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:39:47 3.4 STATUS COMPLETED Destructor
2021-05-06 06:39:47 3.4 STATUS COMPLETED Testing class: RnBDiffMeth
2021-05-06 06:39:47 3.4 STATUS COMPLETED Testing function: apply.iEVORA
2021-05-06 06:39:49 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:49 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:49 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:39:49 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:49 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:49 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:49 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:49 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:50 3.4 STATUS Computed table for tiling
2021-05-06 06:39:50 3.4 STATUS Computed table for genes
2021-05-06 06:39:51 3.4 STATUS Computed table for promoters
2021-05-06 06:39:51 3.4 STATUS Computed table for cpgislands
2021-05-06 06:39:51 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:51 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:51 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:51 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:51 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:52 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:52 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:52 3.4 STATUS Computed table for tiling
2021-05-06 06:39:53 3.4 STATUS Computed table for genes
2021-05-06 06:39:53 3.4 STATUS Computed table for promoters
2021-05-06 06:39:54 3.4 STATUS Computed table for cpgislands
2021-05-06 06:39:54 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:54 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:39:54 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:39:54 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:54 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:54 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:39:54 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:54 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:54 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:55 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:55 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:55 3.4 STATUS Computed table for genes
2021-05-06 06:39:57 3.4 STATUS Computed table for tiling
2021-05-06 06:39:57 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:57 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:57 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:39:57 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:57 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:57 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:39:58 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:58 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:58 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:39:58 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:39:58 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:58 3.4 STATUS Computed table for genes
2021-05-06 06:39:59 3.4 STATUS Computed table for tiling
2021-05-06 06:39:59 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:39:59 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:59 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:39:59 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:39:59 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:39:59 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:39:59 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:39:59 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:39:59 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:00 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:00 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:00 3.4 STATUS Computed table for promoters
2021-05-06 06:40:00 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:00 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:00 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:00 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:00 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:00 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:01 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:01 3.4 STATUS Computed table for promoters
2021-05-06 06:40:01 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:01 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:01 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:40:01 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:02 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:02 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:40:02 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:02 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:02 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:02 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:02 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:02 3.4 STATUS Computed table for genes
2021-05-06 06:40:03 3.4 STATUS Computed table for tiling
2021-05-06 06:40:03 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:03 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:03 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:40:03 3.4 STATUS STARTED Testing function: get.region.types
2021-05-06 06:40:03 3.4 STATUS COMPLETED Testing function: get.region.types
2021-05-06 06:40:04 3.4 STATUS STARTED Testing function: get.comparisons
2021-05-06 06:40:04 3.4 STATUS COMPLETED Testing function: get.comparisons
2021-05-06 06:40:04 3.4 STATUS STARTED Testing function: get.comparison.grouplabels
2021-05-06 06:40:04 3.4 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-05-06 06:40:04 3.4 STATUS STARTED Testing function: get.site.test.method
2021-05-06 06:40:04 3.4 STATUS COMPLETED Testing function: get.site.test.method
2021-05-06 06:40:04 3.4 STATUS STARTED Testing function: get.table
2021-05-06 06:40:04 3.4 STATUS COMPLETED Testing function: get.table
2021-05-06 06:40:04 3.4 STATUS STARTED Testing function: addDiffMethTable
2021-05-06 06:40:04 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:05 3.4 STATUS COMPLETED Testing function: addDiffMethTable
2021-05-06 06:40:05 3.4 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-05-06 06:40:05 3.4 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-05-06 06:40:05 3.4 STATUS STARTED Destructor
2021-05-06 06:40:05 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:05 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:05 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:05 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:05 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:05 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:06 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:06 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:06 3.4 STATUS COMPLETED Destructor
2021-05-06 06:40:06 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:07 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:08 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:40:08 3.4 STATUS COMPLETED diffVar method
2021-05-06 06:40:08 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:40:08 3.4 WARNING Could not compute p-values with diffVar, returning NA
2021-05-06 06:40:08 3.4 INFO diffVar from missMethyl package not properly running
2021-05-06 06:40:08 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:40:08 3.4 STATUS COMPLETED diffVar method
2021-05-06 06:40:08 3.4 STATUS STARTED Unit testing: differential
2021-05-06 06:40:08 3.4 STATUS STARTED Testing function: rowWelchP
2021-05-06 06:40:09 3.4 STATUS COMPLETED Testing function: rowWelchP
2021-05-06 06:40:09 3.4 STATUS STARTED Testing function: limmaP
2021-05-06 06:40:09 3.4 STATUS COMPLETED Testing function: limmaP
2021-05-06 06:40:09 3.4 STATUS STARTED Testing function: computeDiffTab.extended.site
2021-05-06 06:40:09 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:09 3.4 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2021-05-06 06:40:09 3.4 STATUS STARTED Testing function: computeDiffTab.default.region
2021-05-06 06:40:09 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:10 3.4 STATUS COMPLETED Testing function: computeDiffTab.default.region
2021-05-06 06:40:10 3.4 STATUS STARTED Testing function: combineTestPvalsMeth
2021-05-06 06:40:10 3.4 STATUS COMPLETED Testing function: combineTestPvalsMeth
2021-05-06 06:40:10 3.4 STATUS STARTED Testing function: get.adjustment.variables
2021-05-06 06:40:10 3.4 STATUS COMPLETED Testing function: get.adjustment.variables
2021-05-06 06:40:10 3.4 STATUS STARTED Testing function: get.comparison.info
2021-05-06 06:40:10 3.4 STATUS COMPLETED Testing function: get.comparison.info
2021-05-06 06:40:10 3.4 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2021-05-06 06:40:11 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:11 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:11 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:40:11 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:11 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:11 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:11 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:11 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:12 3.4 STATUS Computed table for tiling
2021-05-06 06:40:12 3.4 STATUS Computed table for genes
2021-05-06 06:40:12 3.4 STATUS Computed table for promoters
2021-05-06 06:40:13 3.4 STATUS Computed table for cpgislands
2021-05-06 06:40:13 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:13 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:13 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:13 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:13 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:13 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:13 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:14 3.4 STATUS Computed table for tiling
2021-05-06 06:40:14 3.5 STATUS Computed table for genes
2021-05-06 06:40:15 3.5 STATUS Computed table for promoters
2021-05-06 06:40:15 3.5 STATUS Computed table for cpgislands
2021-05-06 06:40:15 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:15 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:15 3.5 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:40:16 3.5 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2021-05-06 06:40:16 3.5 STATUS STARTED Testing function: diffVar
2021-05-06 06:40:16 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:40:16 3.5 STATUS COMPLETED diffVar method
2021-05-06 06:40:16 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:40:16 3.5 WARNING Could not compute p-values with diffVar, returning NA
2021-05-06 06:40:16 3.5 INFO diffVar from missMethyl package not properly running
2021-05-06 06:40:16 3.5 STATUS COMPLETED diffVar method
2021-05-06 06:40:16 3.5 STATUS STARTED Testing function: apply.iEVORA
2021-05-06 06:40:16 3.5 STATUS STARTED iEVORA method
2021-05-06 06:40:19 3.4 INFO No DVCs detected. All p-values set to 1.
2021-05-06 06:40:19 3.4 STATUS COMPLETED iEVORA method
2021-05-06 06:40:19 3.4 STATUS STARTED Testing function: rnb.execute.diffVar
2021-05-06 06:40:19 3.4 STATUS STARTED Differential Variability
2021-05-06 06:40:19 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:19 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:20 3.4 STATUS STARTED Imputation procedure knn
2021-05-06 06:40:20 3.4 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:40:20 3.4 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:20 3.4 INFO Conducting differential variability using diffVar
2021-05-06 06:40:20 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:40:20 3.4 STATUS COMPLETED diffVar method
2021-05-06 06:40:20 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:40:21 3.4 STATUS Computed table for tiling
2021-05-06 06:40:21 3.4 STATUS Computed table for genes
2021-05-06 06:40:22 3.4 STATUS Computed table for promoters
2021-05-06 06:40:22 3.4 STATUS Computed table for cpgislands
2021-05-06 06:40:22 3.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:40:22 3.4 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:22 3.4 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:22 3.4 INFO Conducting differential variability using diffVar
2021-05-06 06:40:22 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:40:22 3.4 STATUS COMPLETED diffVar method
2021-05-06 06:40:23 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:40:23 3.4 STATUS Computed table for tiling
2021-05-06 06:40:24 3.4 STATUS Computed table for genes
2021-05-06 06:40:24 3.4 STATUS Computed table for promoters
2021-05-06 06:40:24 3.4 STATUS Computed table for cpgislands
2021-05-06 06:40:24 3.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:40:24 3.4 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:24 3.4 STATUS COMPLETED Differential Variability
2021-05-06 06:40:24 3.4 STATUS COMPLETED Testing function: rnb.execute.diffVar
2021-05-06 06:40:25 3.4 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 06:40:25 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:25 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:25 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:40:25 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:25 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:25 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:25 3.4 STATUS STARTED Imputation procedure knn
2021-05-06 06:40:25 3.4 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:40:25 3.4 INFO Conducting differential variability using diffVar
2021-05-06 06:40:25 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:40:27 3.4 STATUS COMPLETED diffVar method
2021-05-06 06:40:27 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:27 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:28 3.4 STATUS Computed table for tiling
2021-05-06 06:40:29 3.4 STATUS Computed table for genes
2021-05-06 06:40:30 3.4 STATUS Computed table for promoters
2021-05-06 06:40:30 3.4 STATUS Computed table for cpgislands
2021-05-06 06:40:30 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:30 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:30 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:30 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:30 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:31 3.4 STATUS STARTED Imputation procedure knn
2021-05-06 06:40:31 3.4 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:40:31 3.4 INFO Conducting differential variability using diffVar
2021-05-06 06:40:31 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:40:31 3.4 STATUS COMPLETED diffVar method
2021-05-06 06:40:31 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:31 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:32 3.4 STATUS Computed table for tiling
2021-05-06 06:40:33 3.4 STATUS Computed table for genes
2021-05-06 06:40:33 3.4 STATUS Computed table for promoters
2021-05-06 06:40:34 3.4 STATUS Computed table for cpgislands
2021-05-06 06:40:34 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:34 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:34 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:40:34 3.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 06:40:34 3.4 STATUS STARTED Testing class: RnBDiffMeth
2021-05-06 06:40:34 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:34 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:34 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:40:34 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:34 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:34 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:34 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:34 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:35 3.4 STATUS Computed table for tiling
2021-05-06 06:40:35 3.4 STATUS Computed table for genes
2021-05-06 06:40:36 3.4 STATUS Computed table for promoters
2021-05-06 06:40:36 3.4 STATUS Computed table for cpgislands
2021-05-06 06:40:36 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:36 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:36 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:36 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:36 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:36 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:36 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:37 3.4 STATUS Computed table for tiling
2021-05-06 06:40:38 3.4 STATUS Computed table for genes
2021-05-06 06:40:38 3.4 STATUS Computed table for promoters
2021-05-06 06:40:38 3.4 STATUS Computed table for cpgislands
2021-05-06 06:40:39 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:39 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:39 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:40:39 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:39 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:39 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:40:39 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:39 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:39 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:39 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:39 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:40 3.4 STATUS Computed table for genes
2021-05-06 06:40:40 3.4 STATUS Computed table for tiling
2021-05-06 06:40:40 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:40 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:40 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:40:40 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:41 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:41 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:40:41 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:41 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:41 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:41 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:41 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:41 3.4 STATUS Computed table for genes
2021-05-06 06:40:42 3.4 STATUS Computed table for tiling
2021-05-06 06:40:42 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:42 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:42 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:40:42 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:42 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:42 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:40:42 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:42 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:42 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:42 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:43 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:43 3.4 STATUS Computed table for promoters
2021-05-06 06:40:43 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:43 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:43 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:43 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:43 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:43 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:43 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:44 3.4 STATUS Computed table for promoters
2021-05-06 06:40:44 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:44 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:44 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:40:44 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:44 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:44 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:40:44 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:44 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:44 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:44 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:44 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:45 3.5 STATUS Computed table for genes
2021-05-06 06:40:46 3.4 STATUS Computed table for tiling
2021-05-06 06:40:46 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:46 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:46 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:40:46 3.4 STATUS STARTED Testing function: get.region.types
2021-05-06 06:40:46 3.4 STATUS COMPLETED Testing function: get.region.types
2021-05-06 06:40:46 3.4 STATUS STARTED Testing function: get.comparisons
2021-05-06 06:40:46 3.4 STATUS COMPLETED Testing function: get.comparisons
2021-05-06 06:40:46 3.4 STATUS STARTED Testing function: get.comparison.grouplabels
2021-05-06 06:40:46 3.4 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-05-06 06:40:47 3.4 STATUS STARTED Testing function: get.site.test.method
2021-05-06 06:40:47 3.4 STATUS COMPLETED Testing function: get.site.test.method
2021-05-06 06:40:47 3.4 STATUS STARTED Testing function: get.table
2021-05-06 06:40:47 3.4 STATUS COMPLETED Testing function: get.table
2021-05-06 06:40:47 3.4 STATUS STARTED Testing function: addDiffMethTable
2021-05-06 06:40:47 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:47 3.4 STATUS COMPLETED Testing function: addDiffMethTable
2021-05-06 06:40:47 3.4 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-05-06 06:40:47 3.4 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-05-06 06:40:48 3.4 STATUS STARTED Destructor
2021-05-06 06:40:48 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:48 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:48 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:48 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:48 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:48 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:48 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:48 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 06:40:48 3.4 STATUS COMPLETED Destructor
2021-05-06 06:40:48 3.4 STATUS COMPLETED Testing class: RnBDiffMeth
2021-05-06 06:40:48 3.4 STATUS COMPLETED Testing function: apply.iEVORA
2021-05-06 06:40:49 3.4 STATUS STARTED iEVORA method
2021-05-06 06:40:50 3.4 INFO No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2
2021-05-06 06:40:50 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:50 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:50 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:40:50 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:50 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:50 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:50 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:51 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:51 3.4 STATUS Computed table for tiling
2021-05-06 06:40:52 3.4 STATUS Computed table for genes
2021-05-06 06:40:52 3.4 STATUS Computed table for promoters
2021-05-06 06:40:52 3.4 STATUS Computed table for cpgislands
2021-05-06 06:40:53 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:53 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:53 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:53 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:53 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:53 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:53 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:54 3.4 STATUS Computed table for tiling
2021-05-06 06:40:55 3.4 STATUS Computed table for genes
2021-05-06 06:40:55 3.4 STATUS Computed table for promoters
2021-05-06 06:40:56 3.4 STATUS Computed table for cpgislands
2021-05-06 06:40:56 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:56 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:40:56 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:40:56 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:40:56 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:40:56 3.4 STATUS STARTED Computing differential methylation tables
2021-05-06 06:40:56 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:40:56 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:40:56 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:40:56 3.4 STATUS STARTED Imputation procedure knn
2021-05-06 06:40:56 3.4 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:40:56 3.4 INFO Conducting differential variability using diffVar
2021-05-06 06:40:57 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:40:57 3.4 STATUS COMPLETED diffVar method
2021-05-06 06:40:57 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:40:57 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:40:58 3.4 STATUS Computed table for tiling
2021-05-06 06:40:59 3.4 STATUS Computed table for genes
2021-05-06 06:40:59 3.4 STATUS Computed table for promoters
2021-05-06 06:41:01 3.4 STATUS Computed table for cpgislands
2021-05-06 06:41:01 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:41:01 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:41:01 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:41:01 3.4 STATUS STARTED Computing Differential Methylation Table
2021-05-06 06:41:01 3.4 INFO Conducting differential analysis using limma
2021-05-06 06:41:01 3.4 STATUS STARTED Imputation procedure knn
2021-05-06 06:41:01 3.4 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:41:01 3.4 INFO Conducting differential variability using diffVar
2021-05-06 06:41:01 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:41:01 3.4 STATUS COMPLETED diffVar method
2021-05-06 06:41:02 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-05-06 06:41:02 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:41:02 3.4 STATUS Computed table for tiling
2021-05-06 06:41:03 3.4 STATUS Computed table for genes
2021-05-06 06:41:04 3.4 STATUS Computed table for promoters
2021-05-06 06:41:04 3.4 STATUS Computed table for cpgislands
2021-05-06 06:41:04 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 06:41:04 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 06:41:04 3.4 STATUS COMPLETED Computing differential methylation tables
2021-05-06 06:41:05 3.4 STATUS STARTED Differential Variability
2021-05-06 06:41:05 3.4 STATUS STARTED Retrieving comparison info
2021-05-06 06:41:05 3.4 STATUS COMPLETED Retrieving comparison info
2021-05-06 06:41:05 3.4 STATUS STARTED Imputation procedure knn
2021-05-06 06:41:05 3.4 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:41:05 3.4 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:41:05 3.4 INFO Conducting differential variability using diffVar
2021-05-06 06:41:05 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:41:05 3.4 STATUS COMPLETED diffVar method
2021-05-06 06:41:05 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:41:06 3.4 STATUS Computed table for tiling
2021-05-06 06:41:06 3.5 STATUS Computed table for genes
2021-05-06 06:41:08 2.9 STATUS Computed table for promoters
2021-05-06 06:41:09 2.9 STATUS Computed table for cpgislands
2021-05-06 06:41:09 2.9 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:41:09 2.9 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-05-06 06:41:09 2.9 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:41:09 2.9 INFO Conducting differential variability using diffVar
2021-05-06 06:41:09 2.9 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 06:41:09 2.9 STATUS COMPLETED diffVar method
2021-05-06 06:41:09 2.9 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 06:41:10 2.9 STATUS Computed table for tiling
2021-05-06 06:41:10 2.9 STATUS Computed table for genes
2021-05-06 06:41:10 2.9 STATUS Computed table for promoters
2021-05-06 06:41:11 3.0 STATUS Computed table for cpgislands
2021-05-06 06:41:11 3.0 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 06:41:11 3.0 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-05-06 06:41:11 3.0 STATUS COMPLETED Differential Variability
2021-05-06 06:41:11 3.0 STATUS STARTED Analysis
2021-05-06 06:41:11 3.0 INFO Loaded information from data.RData
2021-05-06 06:41:11 3.0 STATUS STARTED Processing Detection P-values
2021-05-06 06:41:11 3.0 INFO Removed 3979 probes that overlap with SNPs
2021-05-06 06:41:11 3.0 INFO Completed Greedycut on 510 samples
2021-05-06 06:41:11 3.0 STATUS COMPLETED Processing Detection P-values
2021-05-06 06:41:11 3.0 WARNING File not found: data2.RData
2021-05-06 06:41:11 3.0 STATUS COMPLETED Analysis
2021-05-06 06:41:11 3.0 STATUS STARTED Testing imputation
2021-05-06 06:41:12 3.0 STATUS STARTED Imputation procedure knn
2021-05-06 06:41:13 3.2 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:41:13 3.2 STATUS STARTED Imputation procedure mean.samples
2021-05-06 06:41:13 3.4 STATUS COMPLETED Imputation procedure mean.samples
2021-05-06 06:41:14 3.4 STATUS STARTED Imputation procedure mean.cpgs
2021-05-06 06:41:16 3.4 STATUS COMPLETED Imputation procedure mean.cpgs
2021-05-06 06:41:16 3.4 STATUS STARTED Imputation procedure random
2021-05-06 06:41:16 3.4 STATUS COMPLETED Imputation procedure random
2021-05-06 06:41:16 3.4 STATUS COMPLETED Testing imputation
2021-05-06 06:41:16 3.4 STATUS STARTED Testing age prediction
2021-05-06 06:41:16 3.4 STATUS STARTED Performing Age Prediction
2021-05-06 06:41:19 3.6 STATUS COMPLETED Performing Age Prediction
2021-05-06 06:41:19 3.6 STATUS COMPLETED Testing age prediction
2021-05-06 06:41:19 3.6 STATUS STARTED Performing Age Prediction
2021-05-06 06:41:23 3.5 STATUS COMPLETED Performing Age Prediction
2021-05-06 06:41:23 3.5 STATUS STARTED Imputation procedure knn
2021-05-06 06:41:24 3.5 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:41:24 3.5 STATUS STARTED Imputation procedure mean.samples
2021-05-06 06:41:24 3.5 STATUS COMPLETED Imputation procedure mean.samples
2021-05-06 06:41:24 3.5 STATUS STARTED Imputation procedure mean.cpgs
2021-05-06 06:41:25 3.5 STATUS COMPLETED Imputation procedure mean.cpgs
2021-05-06 06:41:25 3.5 STATUS STARTED Imputation procedure random
2021-05-06 06:41:26 3.5 STATUS COMPLETED Imputation procedure random
2021-05-06 06:41:26 3.5 STATUS STARTED Testing imputation
2021-05-06 06:41:26 3.5 STATUS STARTED Imputation procedure knn
2021-05-06 06:41:27 3.5 STATUS COMPLETED Imputation procedure knn
2021-05-06 06:41:27 3.5 STATUS STARTED Imputation procedure mean.samples
2021-05-06 06:41:28 3.5 STATUS COMPLETED Imputation procedure mean.samples
2021-05-06 06:41:28 3.5 STATUS STARTED Imputation procedure mean.cpgs
2021-05-06 06:41:28 3.5 STATUS COMPLETED Imputation procedure mean.cpgs
2021-05-06 06:41:29 3.5 STATUS STARTED Imputation procedure random
2021-05-06 06:41:29 3.5 STATUS COMPLETED Imputation procedure random
2021-05-06 06:41:29 3.5 STATUS COMPLETED Testing imputation
2021-05-06 06:41:29 3.5 STATUS STARTED Testing age prediction
2021-05-06 06:41:29 3.5 STATUS STARTED Performing Age Prediction
2021-05-06 06:41:32 3.5 STATUS COMPLETED Performing Age Prediction
2021-05-06 06:41:32 3.5 STATUS COMPLETED Testing age prediction
RUNIT TEST PROTOCOL -- Thu May 06 06:41:52 2021
***********************************************
Number of test functions: 24
Number of errors: 0
Number of failures: 0
1 Test Suite :
RnBeads RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24
Number of errors: 0
Number of failures: 0
There were 25 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
266.23 6.70 292.00
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