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CHECK report for SeqGSEA on malbec1

This page was generated on 2021-05-06 12:29:04 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the SeqGSEA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1681/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqGSEA 1.30.0  (landing page)
Xi Wang
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SeqGSEA
Branch: RELEASE_3_12
Last Commit: 8c89028
Last Changed Date: 2020-10-27 10:50:11 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SeqGSEA
Version: 1.30.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings SeqGSEA_1.30.0.tar.gz
StartedAt: 2021-05-06 05:56:50 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:01:49 -0400 (Thu, 06 May 2021)
EllapsedTime: 299.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SeqGSEA.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings SeqGSEA_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/SeqGSEA.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.30.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SeqGSEA’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-bioc/meat/SeqGSEA.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘estiExonProbVar’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DENBStatPermut4GSEA: no visible global function definition for
  ‘%dopar%’
DENBStatPermut4GSEA: no visible global function definition for
  ‘foreach’
DENBStatPermut4GSEA: no visible binding for global variable ‘i’
DENBTest: no visible global function definition for ‘p.adjust’
DEpermutePval: no visible global function definition for ‘p.adjust’
DSpermute4GSEA: no visible global function definition for ‘%dopar%’
DSpermute4GSEA: no visible global function definition for ‘foreach’
DSpermute4GSEA : <anonymous>: no visible binding for global variable
  ‘i’
DSpermutePval: no visible global function definition for ‘p.adjust’
calES.perm: no visible global function definition for ‘%dopar%’
calES.perm: no visible global function definition for ‘foreach’
calES.perm: no visible binding for global variable ‘i’
calES.perm: no visible global function definition for ‘%do%’
calES.perm: no visible binding for global variable ‘j’
loadExonCountData : <anonymous>: no visible global function definition
  for ‘read.table’
plotES : <anonymous>: no visible global function definition for
  ‘density’
plotES: no visible global function definition for ‘density’
plotES : <anonymous>: no visible global function definition for
  ‘points’
plotES: no visible global function definition for ‘points’
plotES: no visible global function definition for ‘colors’
plotES: no visible global function definition for ‘lines’
plotES: no visible global function definition for ‘legend’
plotES: no visible global function definition for ‘dev.off’
plotGeneScore: no visible global function definition for ‘lines’
plotGeneScore: no visible global function definition for ‘colors’
plotGeneScore: no visible global function definition for ‘points’
plotGeneScore: no visible global function definition for ‘matlines’
plotGeneScore: no visible global function definition for ‘legend’
plotGeneScore: no visible global function definition for ‘dev.off’
plotSig: no visible global function definition for ‘points’
plotSig: no visible global function definition for ‘colors’
plotSig: no visible global function definition for ‘legend’
plotSig: no visible global function definition for ‘dev.off’
plotSigGeneSet: no visible global function definition for ‘par’
plotSigGeneSet: no visible global function definition for ‘layout’
plotSigGeneSet: no visible global function definition for ‘lines’
plotSigGeneSet : <anonymous>: no visible global function definition for
  ‘lines’
plotSigGeneSet: no visible global function definition for ‘colors’
plotSigGeneSet: no visible global function definition for ‘text’
plotSigGeneSet: no visible global function definition for ‘density’
plotSigGeneSet: no visible global function definition for ‘legend’
plotSigGeneSet: no visible global function definition for ‘dev.off’
runSeqGSEA: no visible global function definition for ‘makeCluster’
runSeqGSEA: no visible global function definition for ‘write.table’
signifES : <anonymous>: no visible global function definition for
  ‘median’
writeScores: no visible global function definition for ‘write.table’
writeSigGeneSet: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  %do% %dopar% colors density dev.off foreach i j layout legend lines
  makeCluster matlines median p.adjust par points read.table text
  write.table
Consider adding
  importFrom("grDevices", "colors", "dev.off")
  importFrom("graphics", "layout", "legend", "lines", "matlines", "par",
             "points", "text")
  importFrom("stats", "density", "median", "p.adjust")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
topDSGenes         10.664  0.004  10.685
normFactor         10.168  0.016  10.205
scoreNormalization  9.508  0.008   9.559
DSresultGeneTable   9.388  0.004   9.425
DSpermutePval       8.816  0.024   8.855
DSpermute4GSEA      8.588  0.008   8.618
DSresultExonTable   8.516  0.008   8.537
genpermuteMat       8.412  0.004   8.430
topDSExons          8.156  0.004   8.170
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.



Installation output

SeqGSEA.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL SeqGSEA
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘SeqGSEA’ ...
** using staged installation
** R
** data
** 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
** 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
** 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
** testing if installed package keeps a record of temporary installation path
* DONE (SeqGSEA)

Tests output


Example timings

SeqGSEA.Rcheck/SeqGSEA-Ex.timings

nameusersystemelapsed
DENBStat4GSEA0.6000.0000.599
DENBStatPermut4GSEA0.7240.0280.752
DENBTest0.6640.0160.679
DEpermutePval0.6280.0000.627
DSpermute4GSEA8.5880.0088.618
DSpermutePval8.8160.0248.855
DSresultExonTable8.5160.0088.537
DSresultGeneTable9.3880.0049.425
GSEAresultTable2.1440.0362.186
GSEnrichAnalyze2.2160.0042.227
ReadCountSet-class0.0000.0000.002
SeqGeneSet-class0.0040.0000.002
calES0.0080.0000.009
calES.perm2.4320.0002.434
convertEnsembl2Symbol000
convertSymbol2Ensembl000
counts-methods0.020.000.02
estiExonNBstat1.0200.0161.038
estiGeneNBstat1.0640.0001.063
exonID0.0880.0200.106
exonTestability0.0280.0000.029
geneID0.1160.0200.133
geneList0.0040.0000.006
genePermuteScore0.0040.0000.007
geneScore0.0040.0000.004
geneSetDescs0.0040.0000.003
geneSetNames0.0000.0000.002
geneSetSize0.0000.0000.003
geneTestability0.0280.0000.029
genpermuteMat8.4120.0048.430
getGeneCount0.0200.0000.016
label0.0120.0000.012
loadExonCountData0.0000.0000.002
loadGenesets000
newGeneSets0.0000.0000.002
newReadCountSet0.0800.0000.078
normFactor10.168 0.01610.205
plotES2.2720.0002.280
plotGeneScore0.0920.0080.099
plotSig2.1760.0002.178
plotSigGeneSet2.4040.0002.408
rankCombine0.0040.0040.008
runDESeq0.0880.0000.088
runSeqGSEA0.0040.0000.001
scoreNormalization9.5080.0089.559
size0.0040.0000.001
subsetByGenes0.0280.0000.030
topDEGenes1.4520.0001.453
topDSExons8.1560.0048.170
topDSGenes10.664 0.00410.685
topGeneSets2.9320.0002.935
writeScores0.0120.0000.010
writeSigGeneSet2.3840.0042.401