Multiple platform build/check report for BioC 3.12 - CHECK report for metaseqR on tokay1

Package: metaseqR

Version: 1.30.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings metaseqR_1.30.0.tar.gz

StartedAt: 2021-05-06 04:27:06 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 04:38:49 -0400 (Thu, 06 May 2021)

EllapsedTime: 703.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: metaseqR.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaseqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings metaseqR_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/metaseqR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metaseqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaseqR' version '1.30.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'metaseqR' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  Warning: Package 'metaseqR' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/metaseqR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'BSgenome' 'BiocManager' 'GenomicRanges' 'RMySQL' 'RSQLite'
  'Rsamtools' 'TCC' 'VennDiagram' 'parallel' 'rtracklayer' 'survcomp'
  'zoo'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
biasPlotToJSON: no visible binding for global variable 'nams'
cddat: no visible global function definition for 'assayData'
cddat: no visible global function definition for 'ks.test'
cddat: no visible global function definition for 'p.adjust'
cdplot: no visible global function definition for 'lines'
correct.transcripts: no visible global function definition for
  'makeGRangesFromDataFrame'
correct.transcripts: no visible global function definition for 'flank'
correct.transcripts: no visible global function definition for 'resize'
correct.transcripts: no visible global function definition for 'start'
correct.transcripts: no visible global function definition for 'end'
countsBioToJSON: no visible binding for global variable 'nams'
diagplot.avg.ftd : <anonymous>: no visible binding for global variable
  'sd'
diagplot.avg.ftd: no visible global function definition for 'par'
diagplot.avg.ftd: no visible global function definition for 'plot.new'
diagplot.avg.ftd: no visible global function definition for
  'plot.window'
diagplot.avg.ftd: no visible global function definition for 'axis'
diagplot.avg.ftd: no visible global function definition for 'lines'
diagplot.avg.ftd: no visible global function definition for 'grid'
diagplot.avg.ftd: no visible global function definition for 'title'
diagplot.cor: no visible global function definition for 'cor'
diagplot.cor: no visible global function definition for
  'colorRampPalette'
diagplot.edaseq: no visible global function definition for
  'AnnotatedDataFrame'
diagplot.edaseq: no visible global function definition for 'grid'
diagplot.filtered: no visible global function definition for 'par'
diagplot.filtered: no visible global function definition for 'plot.new'
diagplot.filtered: no visible global function definition for
  'plot.window'
diagplot.filtered: no visible global function definition for 'axis'
diagplot.filtered: no visible global function definition for 'text'
diagplot.filtered: no visible global function definition for 'title'
diagplot.filtered: no visible global function definition for 'mtext'
diagplot.filtered: no visible global function definition for 'grid'
diagplot.ftd: no visible global function definition for 'par'
diagplot.ftd: no visible global function definition for 'plot.new'
diagplot.ftd: no visible global function definition for 'plot.window'
diagplot.ftd: no visible global function definition for 'axis'
diagplot.ftd: no visible global function definition for 'lines'
diagplot.ftd: no visible global function definition for 'grid'
diagplot.ftd: no visible global function definition for 'title'
diagplot.mds: no visible global function definition for 'as.dist'
diagplot.mds: no visible global function definition for 'cor'
diagplot.mds: no visible global function definition for 'cmdscale'
diagplot.mds: no visible global function definition for 'text'
diagplot.mds: no visible global function definition for 'grid'
diagplot.noiseq: no visible global function definition for 'grid'
diagplot.noiseq: no visible global function definition for 'new'
diagplot.noiseq : <anonymous>: no visible global function definition
  for 'quantile'
diagplot.noiseq.saturation: no visible global function definition for
  'par'
diagplot.noiseq.saturation: no visible global function definition for
  'plot.new'
diagplot.noiseq.saturation: no visible global function definition for
  'plot.window'
diagplot.noiseq.saturation: no visible global function definition for
  'axis'
diagplot.noiseq.saturation: no visible global function definition for
  'title'
diagplot.noiseq.saturation: no visible global function definition for
  'lines'
diagplot.noiseq.saturation: no visible global function definition for
  'points'
diagplot.noiseq.saturation: no visible global function definition for
  'grid'
diagplot.noiseq.saturation: no visible global function definition for
  'mtext'
diagplot.pairs: no visible global function definition for 'par'
diagplot.pairs: no visible global function definition for 'text'
diagplot.pairs: no visible global function definition for 'arrows'
diagplot.pairs: no visible global function definition for 'lines'
diagplot.pairs: no visible global function definition for 'cor'
diagplot.roc: no visible global function definition for 'par'
diagplot.roc: no visible global function definition for 'plot.new'
diagplot.roc: no visible global function definition for 'plot.window'
diagplot.roc: no visible global function definition for 'axis'
diagplot.roc: no visible global function definition for 'lines'
diagplot.roc: no visible global function definition for 'grid'
diagplot.roc: no visible global function definition for 'title'
diagplot.venn: no visible global function definition for 'runif'
diagplot.venn: no visible global function definition for
  'draw.pairwise.venn'
diagplot.venn: no visible global function definition for
  'draw.triple.venn'
diagplot.venn: no visible global function definition for
  'draw.quad.venn'
diagplot.venn: no visible global function definition for
  'draw.quintuple.venn'
diagplot.volcano: no visible global function definition for 'runif'
diagplot.volcano: no visible global function definition for 'par'
diagplot.volcano: no visible global function definition for 'plot.new'
diagplot.volcano: no visible global function definition for
  'plot.window'
diagplot.volcano: no visible global function definition for 'axis'
diagplot.volcano: no visible global function definition for 'title'
diagplot.volcano: no visible global function definition for 'points'
diagplot.volcano: no visible global function definition for 'abline'
diagplot.volcano: no visible global function definition for 'grid'
estimate.aufc.weights: no visible global function definition for
  'runif'
estimate.aufc.weights : <anonymous>: no visible global function
  definition for 'rollmean'
estimate.sim.params : <anonymous>: no visible global function
  definition for 'var'
estimate.sim.params : <anonymous>: no visible global function
  definition for 'optimize'
estimate.sim.params: no visible global function definition for
  'dev.new'
estimate.sim.params: no visible global function definition for 'title'
estimate.sim.params: no visible global function definition for 'grid'
filter.genes: no visible binding for global variable 'quantile'
filter.genes: no visible global function definition for 'median'
filter.genes: no visible global function definition for 'quantile'
fisher.method: no visible global function definition for 'pchisq'
fisher.method: no visible global function definition for 'p.adjust'
fisher.method.perm : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for 'na.exclude'
fisher.method.perm: no visible global function definition for
  'p.adjust'
get.defaults: no visible binding for global variable 'median'
get.gc.content: no visible global function definition for 'GRanges'
get.gc.content: no visible global function definition for 'Rle'
get.gc.content: no visible global function definition for 'IRanges'
get.gc.content: no visible global function definition for
  'makeGRangesFromDataFrame'
get.gc.content: no visible global function definition for 'getSeq'
get.gc.content: no visible global function definition for
  'alphabetFrequency'
get.ucsc.annotation: no visible global function definition for
  'dbDriver'
get.ucsc.annotation: no visible global function definition for
  'dbConnect'
get.ucsc.annotation: no visible global function definition for
  'dbGetQuery'
get.ucsc.annotation: no visible global function definition for
  'dbDisconnect'
get.ucsc.annotation : <anonymous>: no visible global function
  definition for 'makeGRangesFromDataFrame'
get.ucsc.annotation: no visible global function definition for
  'seqnames'
get.ucsc.annotation: no visible global function definition for 'start'
get.ucsc.annotation: no visible global function definition for 'end'
get.ucsc.annotation: no visible global function definition for 'strand'
get.ucsc.dbl: no visible global function definition for 'dbDriver'
get.ucsc.dbl: no visible global function definition for 'dbConnect'
get.ucsc.dbl: no visible global function definition for 'dbWriteTable'
get.ucsc.dbl: no visible global function definition for 'dbDisconnect'
graphics.close: no visible global function definition for 'dev.off'
graphics.open: no visible global function definition for 'dev.new'
graphics.open: no visible global function definition for 'pdf'
graphics.open: no visible global function definition for 'postscript'
graphics.open: no visible global function definition for 'png'
graphics.open: no visible global function definition for 'jpeg'
graphics.open: no visible global function definition for 'bmp'
graphics.open: no visible global function definition for 'tiff'
load.bs.genome: no visible global function definition for
  'installed.genomes'
load.bs.genome: no visible global function definition for 'getBSgenome'
make.sim.data.sd: no visible global function definition for 'runif'
make.sim.data.sd: no visible global function definition for 'rnbinom'
make.sim.data.sd: no visible global function definition for 'rexp'
make.sim.data.tcc: no visible global function definition for 'runif'
make.stat : <anonymous>: no visible global function definition for
  'median'
make.stat : <anonymous>: no visible global function definition for 'sd'
make.stat : <anonymous>: no visible global function definition for
  'mad'
meta.perm : <anonymous>: no visible global function definition for
  'runif'
meta.perm: no visible global function definition for 'mclapply'
meta.test : <anonymous>: no visible binding for global variable
  'combine.test'
metaseqr: no visible binding for global variable 'p.adjust.methods'
metaseqr : <anonymous>: no visible binding for global variable
  'p.adjust'
metaseqr : <anonymous>: no visible global function definition for
  'p.adjust'
normalize.edaseq: no visible global function definition for
  'AnnotatedDataFrame'
normalize.noiseq: no visible global function definition for 'assayData'
read2count: no visible global function definition for 'GRanges'
read2count: no visible global function definition for 'Rle'
read2count: no visible global function definition for 'IRanges'
read2count: no visible global function definition for
  'makeGRangesFromDataFrame'
read2count: no visible global function definition for 'seqnames'
read2count: no visible global function definition for 'start'
read2count: no visible global function definition for 'end'
read2count: no visible global function definition for 'strand'
read2count: no visible global function definition for 'promoters'
read2count: no visible global function definition for 'resize'
read2count : <anonymous>: no visible global function definition for
  'import.bed'
read2count : <anonymous>: no visible global function definition for
  'as'
read2count : <anonymous>: no visible global function definition for
  'seqnames'
read2count : <anonymous>: no visible global function definition for
  'seqlevels'
read2count : <anonymous>: no visible global function definition for
  'countOverlaps'
read2count: no visible global function definition for 'asBam'
read2count : <anonymous>: no visible global function definition for
  'readGAlignments'
read2count : <anonymous>: no visible global function definition for
  'BamFile'
read2count : <anonymous>: no visible global function definition for
  'countBam'
read2count : <anonymous>: no visible global function definition for
  'ScanBamParam'
read2count : <anonymous>: no visible global function definition for
  'scanBamFlag'
read2count : <anonymous>: no visible global function definition for
  'strand<-'
read2count : <anonymous>: no visible global function definition for
  'strand'
read2count : <anonymous>: no visible global function definition for
  'summarizeOverlaps'
read2count : <anonymous>: no visible global function definition for
  'assays'
reduce.exons : <anonymous>: no visible global function definition for
  'reduce'
reduce.exons : <anonymous>: no visible global function definition for
  'DataFrame'
reduce.exons : <anonymous>: no visible global function definition for
  'mcols<-'
reduce.transcripts.utr : <anonymous>: no visible global function
  definition for 'reduce'
reduce.transcripts.utr : <anonymous>: no visible global function
  definition for 'DataFrame'
reduce.transcripts.utr : <anonymous>: no visible global function
  definition for 'mcols<-'
reduce.transcripts.utr.transcript : <anonymous>: no visible global
  function definition for 'reduce'
reduce.transcripts.utr.transcript : <anonymous>: no visible global
  function definition for 'DataFrame'
reduce.transcripts.utr.transcript : <anonymous>: no visible global
  function definition for 'mcols<-'
stat.bayseq: no visible global function definition for 'new'
stat.deseq: no visible global function definition for 'is'
stat.deseq: no visible global function definition for 'sizeFactors<-'
stat.edger: no visible global function definition for 'model.matrix'
stat.limma: no visible global function definition for 'model.matrix'
stat.nbpseq: no visible global function definition for 'is'
stat.nbpseq: no visible global function definition for 'sizeFactors<-'
stat.noiseq: no visible global function definition for 'assayData'
stat.noiseq: no visible global function definition for 'sizeFactors<-'
wapply: no visible global function definition for 'mclapply'
wp.adjust: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  AnnotatedDataFrame BamFile DataFrame GRanges IRanges Rle ScanBamParam
  abline alphabetFrequency arrows as as.dist asBam assayData assays
  axis bmp cmdscale colorRampPalette combine.test cor countBam
  countOverlaps dbConnect dbDisconnect dbDriver dbGetQuery dbWriteTable
  dev.new dev.off draw.pairwise.venn draw.quad.venn draw.quintuple.venn
  draw.triple.venn end flank getBSgenome getSeq grid import.bed
  installed.genomes is jpeg ks.test lines mad makeGRangesFromDataFrame
  mclapply mcols<- median model.matrix mtext na.exclude nams new
  optimize p.adjust p.adjust.methods par pchisq pdf plot.new
  plot.window png points postscript promoters quantile readGAlignments
  reduce resize rexp rnbinom rollmean runif scanBamFlag sd seqlevels
  seqnames sizeFactors<- start strand strand<- summarizeOverlaps text
  tiff title var
Consider adding
  importFrom("grDevices", "bmp", "colorRampPalette", "dev.new",
             "dev.off", "jpeg", "pdf", "png", "postscript", "tiff")
  importFrom("graphics", "abline", "arrows", "axis", "grid", "lines",
             "mtext", "par", "plot.new", "plot.window", "points", "text",
             "title")
  importFrom("methods", "as", "is", "new")
  importFrom("stats", "as.dist", "cmdscale", "cor", "end", "ks.test",
             "mad", "median", "model.matrix", "na.exclude", "optimize",
             "p.adjust", "p.adjust.methods", "pchisq", "quantile",
             "rexp", "rnbinom", "runif", "sd", "start", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
diagplot.de.heatmap 10.38   0.48   10.86
diagplot.pairs       8.43   0.09    8.51
diagplot.volcano     7.08   0.14    7.26
diagplot.filtered    3.36   0.01    6.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
diagplot.pairs      8.14   0.22    8.35
diagplot.de.heatmap 7.59   0.13    7.71
diagplot.volcano    5.91   0.06    5.97
diagplot.filtered   3.01   0.06    6.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/metaseqR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/metaseqR_1.30.0.tar.gz && rm -rf metaseqR.buildbin-libdir && mkdir metaseqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaseqR.buildbin-libdir metaseqR_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL metaseqR_1.30.0.zip && rm metaseqR_1.30.0.tar.gz metaseqR_1.30.0.zip
###
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install for i386

* installing *source* package 'metaseqR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2 
** help
*** installing help indices
  converting help for package 'metaseqR'
    finding HTML links ... done
    as.class.vector                         html  
    build.export                            html  
    calc.f1score                            html  
    calc.otr                                html  
    cddat                                   html  
    cdplot                                  html  
    check.contrast.format                   html  
    check.file.args                         html  
    check.graphics.file                     html  
    check.graphics.type                     html  
    check.libsize                           html  
    check.main.args                         html  
    check.num.args                          html  
    check.packages                          html  
    check.parallel                          html  
    check.text.args                         html  
    combine.bonferroni                      html  
    combine.maxp                            html  
    combine.minp                            html  
    combine.simes                           html  
    combine.weight                          html  
    construct.gene.model                    html  
    construct.utr.model                     html  
    diagplot.avg.ftd                        html  
    diagplot.boxplot                        html  
    diagplot.cor                            html  
    diagplot.de.heatmap                     html  
    diagplot.edaseq                         html  
    diagplot.filtered                       html  
    diagplot.ftd                            html  
    diagplot.mds                            html  
    diagplot.metaseqr                       html  
    diagplot.noiseq                         html  
    diagplot.noiseq.saturation              html  
    diagplot.pairs                          html  
    diagplot.roc                            html  
    diagplot.venn                           html  
    diagplot.volcano                        html  
    disp                                    html  
    downsample.counts                       html  
    estimate.aufc.weights                   html  
    estimate.sim.params                     html  
    filter.exons                            html  
    filter.genes                            html  
    filter.high                             html  
    filter.low                              html  
    fisher.method                           html  
    fisher.method.perm                      html  
    fisher.sum                              html  
    get.annotation                          html  
    get.arg                                 html  
    get.biotypes                            html  
    get.bs.organism                         html  
    get.dataset                             html  
    get.defaults                            html  
    get.ensembl.annotation                  html  
    get.exon.attributes                     html  
    get.gc.content                          html  
    get.gene.attributes                     html  
    get.host                                html  
    get.preset.opts                         html  
    get.strict.biofilter                    html  
    get.transcript.utr.attributes           html  
    get.ucsc.annotation                     html  
    get.ucsc.credentials                    html  
    get.ucsc.dbl                            html  
    get.ucsc.organism                       html  
    get.ucsc.query                          html  
    get.ucsc.tabledef                       html  
    get.ucsc.tbl.tpl                        html  
    get.valid.chrs                          html  
    get.weights                             html  
    graphics.close                          html  
    graphics.open                           html  
    hg19.exon.counts                        html  
    libsize.list.hg19                       html  
    libsize.list.mm9                        html  
    load.bs.genome                          html  
    log2disp                                html  
    make.avg.expression                     html  
    make.contrast.list                      html  
    make.export.list                        html  
    make.fold.change                        html  
    make.grid                               html  
    make.highcharts.points                  html  
    make.html.body                          html  
    make.html.cells                         html  
    make.html.header                        html  
    make.html.rows                          html  
    make.html.table                         html  
    make.matrix                             html  
    make.path.struct                        html  
    make.permutation                        html  
    make.project.path                       html  
    make.report.messages                    html  
    make.sample.list                        html  
    make.sim.data.sd                        html  
    make.sim.data.tcc                       html  
    make.stat                               html  
    make.transformation                     html  
    make.venn.areas                         html  
    make.venn.colorscheme                   html  
    make.venn.counts                        html  
    make.venn.pairs                         html  
    meta.perm                               html  
    meta.test                               html  
    meta.worker                             html  
    metaseqR-package                        html  
    metaseqr                                html  
    mlfo                                    html  
    mm9.gene.counts                         html  
    nat2log                                 html  
    normalize.deseq                         html  
    normalize.edaseq                        html  
    normalize.edger                         html  
    normalize.nbpseq                        html  
    normalize.noiseq                        html  
    read.targets                            html  
    read2count                              html  
    reduce.exons                            html  
    reduce.gene.data                        html  
    sample.list.hg19                        html  
    sample.list.mm9                         html  
    set.arg                                 html  
    stat.bayseq                             html  
    stat.deseq                              html  
    stat.edger                              html  
    stat.limma                              html  
    stat.nbpseq                             html  
    stat.noiseq                             html  
    validate.alg.args                       html  
    validate.list.args                      html  
    wapply                                  html  
    wp.adjust                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
Warning: Package 'metaseqR' is deprecated and will be removed from Bioconductor
  version 3.13. Package functionality moved to Bioconductor package
  metaseqR2.
** testing if installed package can be loaded from final location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
Warning: Package 'metaseqR' is deprecated and will be removed from Bioconductor
  version 3.13. Package functionality moved to Bioconductor package
  metaseqR2.
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'metaseqR' ...
** testing if installed package can be loaded
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
  version 3.13. Please use DESeq2
Warning: Package 'metaseqR' is deprecated and will be removed from Bioconductor
  version 3.13. Package functionality moved to Bioconductor package
  metaseqR2.
* MD5 sums
packaged installation of 'metaseqR' as metaseqR_1.30.0.zip
* DONE (metaseqR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'metaseqR' successfully unpacked and MD5 sums checked


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)

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("metaseqR")

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


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: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

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

The following object is masked from 'package:Biobase':

    rowMedians

locfit 1.5-9.4 	 2020-03-24

Attaching package: 'locfit'

The following objects are masked from 'package:ShortRead':

    left, right


Attaching package: 'limma'

The following object is masked from 'package:DESeq':

    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:Rsamtools':

    index, index<-

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


2021-05-06 04:37:51: Data processing started...

Read counts file: imported custom data frame
Conditions: G1, G2
Samples to include: G1_rep1, G1_rep2, G1_rep3, G2_rep1, G2_rep2, G2_rep3
Samples to exclude: none
Requested contrasts: G1_vs_G2
Annotation: embedded
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: all.basic
Transcriptional level: gene
Exon filters: none applied
Gene filters: none applied
Filter application: postnorm
Normalization algorithm: edaseq
Normalization arguments: 
  within.which: loess
  between.which: full
Statistical algorithm: edger, limma
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
  limma: none
Meta-analysis method: simes
Multiple testing correction: BH
Logarithmic transformation offset: 1
Analysis preset: all.basic
Quality control plots: 
Figure format: png
Output directory: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpuk3B22
Output data: annotation, p.value, adj.p.value, meta.p.value, adj.meta.p.value, fold.change
Output scale(s): natural, log2
Output values: normalized
Saving gene model to C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpuk3B22/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edaseq
Running statistical tests with: edger
  Contrast: G1_vs_G2
Running statistical tests with: limma
  Contrast: G1_vs_G2
Performing meta-analysis with simes
Building output files...
  Contrast: G1_vs_G2
    Adding non-filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...

2021-05-06 04:37:51: Data processing finished!


Total processing time: 00 seconds


Estimating AUFC weights... Please wait...
Processing edger
Processing limma

Retrieving edger
Retrieving limma

2021-05-06 04:37:52: Data processing started...

Read counts file: imported custom data frame
Conditions: e14.5, adult_8_weeks
Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2
Samples to exclude: none
Requested contrasts: e14.5_vs_adult_8_weeks
Library sizes: 
  e14.5_1: 3102907
  e14.5_2: 2067905
  a8w_1: 3742059
  a8w_2: 4403954
Annotation: download
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: medium.basic
Transcriptional level: gene
Exon filters: min.active.exons
  min.active.exons: 
    exons.per.gene: 5
    min.exons: 2
    frac: 0.2
Gene filters: length, avg.reads, expression, biotype
  length: 
    length: 500
  avg.reads: 
    average.per.bp: 100
    quantile: 0.25
  expression: 
    median: TRUE
    mean: FALSE
    quantile: NA
    known: NA
    custom: NA
  biotype: 
    pseudogene: FALSE
    snRNA: FALSE
    protein_coding: FALSE
    antisense: FALSE
    miRNA: FALSE
    lincRNA: FALSE
    snoRNA: FALSE
    processed_transcript: FALSE
    misc_RNA: FALSE
    rRNA: TRUE
    sense_overlapping: FALSE
    sense_intronic: FALSE
    polymorphic_pseudogene: FALSE
    non_coding: FALSE
    three_prime_overlapping_ncrna: FALSE
    IG_C_gene: FALSE
    IG_J_gene: FALSE
    IG_D_gene: FALSE
    IG_V_gene: FALSE
    ncrna_host: FALSE
Filter application: postnorm
Normalization algorithm: edger
Normalization arguments: 
  method: TMM
  logratioTrim: 0.3
  sumTrim: 0.05
  doWeighting: TRUE
  Acutoff: -1e+10
  p: 0.75
Statistical algorithm: edger, limma
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
  limma: none
Meta-analysis method: simes
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Analysis preset: medium.basic
Quality control plots: mds
Figure format: png
Output directory: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpuk3B22
Output data: annotation, p.value, adj.p.value, meta.p.value, adj.meta.p.value, fold.change
Output scale(s): natural, log2
Output values: normalized
Downloading gene annotation for mm9...
Saving gene model to C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpuk3B22/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edger
Applying gene filter length...
  Threshold below which ignored: 500
Applying gene filter avg.reads...
  Threshold below which ignored: 0.0659670745106788
Applying gene filter expression...
  Threshold below which ignored: 68
Applying gene filter biotype...
  Biotypes ignored: rRNA
2106 genes filtered out
1681 genes remain after filtering
Running statistical tests with: edger
  Contrast: e14.5_vs_adult_8_weeks
  Contrast e14.5_vs_adult_8_weeks: found 906 genes
Running statistical tests with: limma
  Contrast: e14.5_vs_adult_8_weeks
  Contrast e14.5_vs_adult_8_weeks: found 911 genes
Performing meta-analysis with simes
Building output files...
  Contrast: e14.5_vs_adult_8_weeks
    Adding non-filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...
    Adding filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...
Creating quality control graphs...
Plotting in png format...
  Plotting mds...
Creating HTML report...
Compressing figures...  adding: Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpuk3B22/plots/qc/mds.png (deflated 62%)


2021-05-06 04:38:00: Data processing finished!


Total processing time: 08 seconds



RUNIT TEST PROTOCOL -- Thu May 06 04:38:00 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metaseqR RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  28.71    2.31   38.53


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("metaseqR")

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


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: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

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

The following object is masked from 'package:Biobase':

    rowMedians

locfit 1.5-9.4 	 2020-03-24

Attaching package: 'locfit'

The following objects are masked from 'package:ShortRead':

    left, right


Attaching package: 'limma'

The following object is masked from 'package:DESeq':

    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:Rsamtools':

    index, index<-

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


2021-05-06 04:38:28: Data processing started...

Read counts file: imported custom data frame
Conditions: G1, G2
Samples to include: G1_rep1, G1_rep2, G1_rep3, G2_rep1, G2_rep2, G2_rep3
Samples to exclude: none
Requested contrasts: G1_vs_G2
Annotation: embedded
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: all.basic
Transcriptional level: gene
Exon filters: none applied
Gene filters: none applied
Filter application: postnorm
Normalization algorithm: edaseq
Normalization arguments: 
  within.which: loess
  between.which: full
Statistical algorithm: edger, limma
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
  limma: none
Meta-analysis method: simes
Multiple testing correction: BH
Logarithmic transformation offset: 1
Analysis preset: all.basic
Quality control plots: 
Figure format: png
Output directory: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpqojxh0
Output data: annotation, p.value, adj.p.value, meta.p.value, adj.meta.p.value, fold.change
Output scale(s): natural, log2
Output values: normalized
Saving gene model to C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpqojxh0/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edaseq
Running statistical tests with: edger
  Contrast: G1_vs_G2
Running statistical tests with: limma
  Contrast: G1_vs_G2
Performing meta-analysis with simes
Building output files...
  Contrast: G1_vs_G2
    Adding non-filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...

2021-05-06 04:38:28: Data processing finished!


Total processing time: 00 seconds


Estimating AUFC weights... Please wait...
Processing edger
Processing limma

Retrieving edger
Retrieving limma

2021-05-06 04:38:29: Data processing started...

Read counts file: imported custom data frame
Conditions: e14.5, adult_8_weeks
Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2
Samples to exclude: none
Requested contrasts: e14.5_vs_adult_8_weeks
Library sizes: 
  e14.5_1: 3102907
  e14.5_2: 2067905
  a8w_1: 3742059
  a8w_2: 4403954
Annotation: download
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: medium.basic
Transcriptional level: gene
Exon filters: min.active.exons
  min.active.exons: 
    exons.per.gene: 5
    min.exons: 2
    frac: 0.2
Gene filters: length, avg.reads, expression, biotype
  length: 
    length: 500
  avg.reads: 
    average.per.bp: 100
    quantile: 0.25
  expression: 
    median: TRUE
    mean: FALSE
    quantile: NA
    known: NA
    custom: NA
  biotype: 
    pseudogene: FALSE
    snRNA: FALSE
    protein_coding: FALSE
    antisense: FALSE
    miRNA: FALSE
    lincRNA: FALSE
    snoRNA: FALSE
    processed_transcript: FALSE
    misc_RNA: FALSE
    rRNA: TRUE
    sense_overlapping: FALSE
    sense_intronic: FALSE
    polymorphic_pseudogene: FALSE
    non_coding: FALSE
    three_prime_overlapping_ncrna: FALSE
    IG_C_gene: FALSE
    IG_J_gene: FALSE
    IG_D_gene: FALSE
    IG_V_gene: FALSE
    ncrna_host: FALSE
Filter application: postnorm
Normalization algorithm: edger
Normalization arguments: 
  method: TMM
  logratioTrim: 0.3
  sumTrim: 0.05
  doWeighting: TRUE
  Acutoff: -1e+10
  p: 0.75
Statistical algorithm: edger, limma
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
  limma: none
Meta-analysis method: simes
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Analysis preset: medium.basic
Quality control plots: mds
Figure format: png
Output directory: C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpqojxh0
Output data: annotation, p.value, adj.p.value, meta.p.value, adj.meta.p.value, fold.change
Output scale(s): natural, log2
Output values: normalized
Downloading gene annotation for mm9...
Saving gene model to C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpqojxh0/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edger
Applying gene filter length...
  Threshold below which ignored: 500
Applying gene filter avg.reads...
  Threshold below which ignored: 0.0659670745106788
Applying gene filter expression...
  Threshold below which ignored: 68
Applying gene filter biotype...
  Biotypes ignored: rRNA
2106 genes filtered out
1681 genes remain after filtering
Running statistical tests with: edger
  Contrast: e14.5_vs_adult_8_weeks
  Contrast e14.5_vs_adult_8_weeks: found 906 genes
Running statistical tests with: limma
  Contrast: e14.5_vs_adult_8_weeks
  Contrast e14.5_vs_adult_8_weeks: found 911 genes
Performing meta-analysis with simes
Building output files...
  Contrast: e14.5_vs_adult_8_weeks
    Adding non-filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...
    Adding filtered data...
      binding annotation...
      binding p-values...
      binding FDRs...
      binding meta p-values...
      binding adjusted meta p-values...
      binding natural normalized fold changes...
      binding log2 normalized fold changes...
    Writing output...
Creating quality control graphs...
Plotting in png format...
  Plotting mds...
Creating HTML report...
Compressing figures...  adding: Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpqojxh0/plots/qc/mds.png (deflated 62%)


2021-05-06 04:38:35: Data processing finished!


Total processing time: 06 seconds



RUNIT TEST PROTOCOL -- Thu May 06 04:38:35 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
metaseqR RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  26.65    1.04   34.92

name	user	system	elapsed
as.class.vector	0	0	0
build.export	0	0	0
calc.f1score	0.01	0.00	0.02
calc.otr	0	0	0
check.contrast.format	0	0	0
check.file.args	0	0	0
check.libsize	0	0	0
check.num.args	0.02	0.00	0.01
check.packages	0.18	0.03	0.22
check.parallel	0	0	0
check.text.args	0	0	0
combine.bonferroni	0	0	0
combine.maxp	0	0	0
combine.minp	0	0	0
combine.simes	0	0	0
combine.weight	0	0	0
construct.gene.model	0	0	0
construct.utr.model	0	0	0
diagplot.avg.ftd	0.18	0.01	0.19
diagplot.boxplot	2.73	0.21	2.93
diagplot.cor	1.28	0.00	1.28
diagplot.de.heatmap	10.38	0.48	10.86
diagplot.edaseq	2.11	0.30	2.41
diagplot.filtered	3.36	0.01	6.75
diagplot.ftd	0.01	0.03	0.05
diagplot.mds	2.02	0.22	2.23
diagplot.metaseqr	1.01	0.06	1.08
diagplot.noiseq	1.67	0.10	1.80
diagplot.pairs	8.43	0.09	8.51
diagplot.roc	0.03	0.03	0.06
diagplot.venn	0.35	0.10	0.81
diagplot.volcano	7.08	0.14	7.26
disp	0	0	0
downsample.counts	0.00	0.02	0.02
estimate.aufc.weights	0	0	0
estimate.sim.params	0	0	0
filter.exons	0	0	0
filter.genes	0	0	0
filter.high	0.04	0.00	0.08
filter.low	0.00	0.01	0.01
fisher.method	0.02	0.00	0.05
fisher.method.perm	0.06	0.00	0.08
fisher.sum	0	0	0
get.annotation	0	0	0
get.arg	0	0	0
get.biotypes	0	0	0
get.bs.organism	0	0	0
get.dataset	0	0	0
get.defaults	0	0	0
get.ensembl.annotation	0	0	0
get.exon.attributes	0	0	0
get.gc.content	0	0	0
get.gene.attributes	0	0	0
get.host	0	0	0
get.preset.opts	0	0	0
get.strict.biofilter	0	0	0
get.transcript.utr.attributes	0	0	0
get.ucsc.annotation	0	0	0
get.ucsc.credentials	0	0	0
get.ucsc.dbl	0	0	0
get.ucsc.organism	0	0	0
get.ucsc.query	0	0	0
get.ucsc.tabledef	0	0	0
get.ucsc.tbl.tpl	0	0	0
get.valid.chrs	0	0	0
get.weights	0	0	0
graphics.close	0	0	0
graphics.open	0	0	0
load.bs.genome	0	0	0
make.avg.expression	0	0	0
make.contrast.list	0	0	0
make.fold.change	0	0	0
make.grid	0	0	0
make.html.body	0	0	0
make.html.cells	0	0	0
make.html.header	0	0	0
make.html.rows	0	0	0
make.html.table	0	0	0
make.matrix	0	0	0
make.permutation	0	0	0
make.sample.list	0.01	0.00	0.01
make.sim.data.sd	0	0	0
make.sim.data.tcc	0	0	0
make.stat	0	0	0
make.transformation	0	0	0
make.venn.areas	0	0	0
make.venn.colorscheme	0	0	0
make.venn.counts	0	0	0
make.venn.pairs	0	0	0
meta.perm	0	0	0
meta.test	0	0	0
meta.worker	0	0	0
metaseqr	0.02	0.00	0.02
mlfo	0	0	0
normalize.deseq	0	0	0
normalize.edaseq	0	0	0
normalize.edger	0	0	0
normalize.nbpseq	0	0	0
normalize.noiseq	0	0	0
read.targets	0	0	0
read2count	0	0	0
reduce.exons	0	0	0
reduce.gene.data	0	0	0
set.arg	0	0	0
stat.bayseq	0	0	0
stat.deseq	0	0	0
stat.edger	0	0	0
stat.limma	0	0	0
stat.nbpseq	0	0	0
stat.noiseq	0	0	0
validate.alg.args	0	0	0
validate.list.args	0	0	0
wapply	0	0	0

name	user	system	elapsed
as.class.vector	0	0	0
build.export	0	0	0
calc.f1score	0.02	0.00	0.02
calc.otr	0	0	0
check.contrast.format	0	0	0
check.file.args	0	0	0
check.libsize	0	0	0
check.num.args	0	0	0
check.packages	0.12	0.04	0.17
check.parallel	0	0	0
check.text.args	0	0	0
combine.bonferroni	0	0	0
combine.maxp	0	0	0
combine.minp	0	0	0
combine.simes	0	0	0
combine.weight	0	0	0
construct.gene.model	0	0	0
construct.utr.model	0	0	0
diagplot.avg.ftd	0.13	0.00	0.19
diagplot.boxplot	1.83	0.06	1.89
diagplot.cor	1.75	0.08	1.83
diagplot.de.heatmap	7.59	0.13	7.71
diagplot.edaseq	1.35	0.08	1.43
diagplot.filtered	3.01	0.06	6.03
diagplot.ftd	0.02	0.05	0.06
diagplot.mds	1.17	0.01	1.19
diagplot.metaseqr	1.28	0.11	1.39
diagplot.noiseq	2.09	0.09	2.19
diagplot.pairs	8.14	0.22	8.35
diagplot.roc	0.05	0.00	0.05
diagplot.venn	0.20	0.05	0.25
diagplot.volcano	5.91	0.06	5.97
disp	0	0	0
downsample.counts	0	0	0
estimate.aufc.weights	0	0	0
estimate.sim.params	0	0	0
filter.exons	0	0	0
filter.genes	0	0	0
filter.high	0.02	0.00	0.02
filter.low	0.01	0.00	0.01
fisher.method	0.02	0.00	0.02
fisher.method.perm	0.04	0.00	0.04
fisher.sum	0	0	0
get.annotation	0	0	0
get.arg	0	0	0
get.biotypes	0	0	0
get.bs.organism	0	0	0
get.dataset	0	0	0
get.defaults	0	0	0
get.ensembl.annotation	0	0	0
get.exon.attributes	0	0	0
get.gc.content	0	0	0
get.gene.attributes	0	0	0
get.host	0	0	0
get.preset.opts	0	0	0
get.strict.biofilter	0	0	0
get.transcript.utr.attributes	0	0	0
get.ucsc.annotation	0	0	0
get.ucsc.credentials	0	0	0
get.ucsc.dbl	0	0	0
get.ucsc.organism	0	0	0
get.ucsc.query	0	0	0
get.ucsc.tabledef	0	0	0
get.ucsc.tbl.tpl	0	0	0
get.valid.chrs	0	0	0
get.weights	0	0	0
graphics.close	0	0	0
graphics.open	0	0	0
load.bs.genome	0	0	0
make.avg.expression	0	0	0
make.contrast.list	0	0	0
make.fold.change	0	0	0
make.grid	0	0	0
make.html.body	0	0	0
make.html.cells	0	0	0
make.html.header	0	0	0
make.html.rows	0	0	0
make.html.table	0	0	0
make.matrix	0	0	0
make.permutation	0	0	0
make.sample.list	0	0	0
make.sim.data.sd	0	0	0
make.sim.data.tcc	0	0	0
make.stat	0	0	0
make.transformation	0	0	0
make.venn.areas	0	0	0
make.venn.colorscheme	0	0	0
make.venn.counts	0	0	0
make.venn.pairs	0	0	0
meta.perm	0	0	0
meta.test	0	0	0
meta.worker	0	0	0
metaseqr	0	0	0
mlfo	0	0	0
normalize.deseq	0	0	0
normalize.edaseq	0	0	0
normalize.edger	0	0	0
normalize.nbpseq	0	0	0
normalize.noiseq	0	0	0
read.targets	0	0	0
read2count	0	0	0
reduce.exons	0	0	0
reduce.gene.data	0	0	0
set.arg	0	0	0
stat.bayseq	0	0	0
stat.deseq	0	0	0
stat.edger	0	0	0
stat.limma	0	0	0
stat.nbpseq	0	0	0
stat.noiseq	0	0	0
validate.alg.args	0	0	0
validate.list.args	0	0	0
wapply	0	0	0

CHECK report for metaseqR on tokay1

Summary

Command output

Installation output

Tests output

Example timings