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This page was generated on 2024-03-27 11:38:06 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1927/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqGSEA 1.42.0  (landing page)
Xi Wang
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/SeqGSEA
git_branch: RELEASE_3_18
git_last_commit: 09222b3
git_last_commit_date: 2023-10-24 09:53:39 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for SeqGSEA on merida1


To the developers/maintainers of the SeqGSEA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SeqGSEA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SeqGSEA
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SeqGSEA_1.42.0.tar.gz
StartedAt: 2024-03-26 08:35:00 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 08:46:54 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 713.7 seconds
RetCode: 0
Status:   OK  
CheckDir: SeqGSEA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SeqGSEA_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/SeqGSEA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.42.0’
* 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 ... OK
* 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
DENBStat4GSEA: no visible global function definition for ‘colData’
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 ‘colData’
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’
nbinomTestForMatrices : <anonymous>: no visible global function
  definition for ‘dnbinom’
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’
runDESeq: no visible global function definition for ‘DataFrame’
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% DataFrame colData colors density dev.off dnbinom 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", "dnbinom", "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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
DENBStatPermut4GSEA 21.838  0.316  24.889
topDEGenes          21.976  0.143  22.993
DEpermutePval       21.499  0.234  24.823
topDSExons          12.890  0.116  13.537
normFactor          12.262  0.285  14.156
DSresultGeneTable   12.319  0.216  14.738
DSresultExonTable   12.276  0.237  14.886
scoreNormalization  12.145  0.152  13.632
DSpermutePval       12.011  0.113  13.669
topDSGenes          11.905  0.094  12.643
DSpermute4GSEA      11.707  0.192  12.972
genpermuteMat       10.928  0.187  12.355
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.



Installation output

SeqGSEA.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SeqGSEA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘SeqGSEA’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SeqGSEA)

Tests output


Example timings

SeqGSEA.Rcheck/SeqGSEA-Ex.timings

nameusersystemelapsed
DENBStat4GSEA4.1700.1624.755
DENBStatPermut4GSEA21.838 0.31624.889
DENBTest3.7720.0774.731
DEpermutePval21.499 0.23424.823
DSpermute4GSEA11.707 0.19212.972
DSpermutePval12.011 0.11313.669
DSresultExonTable12.276 0.23714.886
DSresultGeneTable12.319 0.21614.738
GSEAresultTable3.7080.0464.255
GSEnrichAnalyze4.3770.0394.842
ReadCountSet-class0.0020.0010.003
SeqGeneSet-class0.0020.0020.004
calES0.0110.0060.018
calES.perm3.6320.0203.843
convertEnsembl2Symbol000
convertSymbol2Ensembl000
counts-methods0.0210.0030.024
estiExonNBstat1.0900.0231.161
estiGeneNBstat1.0920.0141.191
exonID0.1070.1900.366
exonTestability0.0300.0020.040
geneID0.1300.1890.384
geneList0.0060.0010.008
genePermuteScore0.0080.0030.011
geneScore0.0060.0020.008
geneSetDescs0.0040.0020.008
geneSetNames0.0030.0020.005
geneSetSize0.0040.0020.005
geneTestability0.0330.0020.037
genpermuteMat10.928 0.18712.355
getGeneCount0.0310.0020.038
label0.0200.0040.031
loadExonCountData0.0020.0020.006
loadGenesets0.0000.0010.002
newGeneSets0.0050.0010.007
newReadCountSet0.1990.0050.216
normFactor12.262 0.28514.156
plotES3.6980.0613.862
plotGeneScore0.2010.0090.287
plotSig3.5430.0403.718
plotSigGeneSet3.2950.0463.511
rankCombine0.0120.0050.020
runDESeq2.5850.0242.755
runSeqGSEA0.0020.0030.006
scoreNormalization12.145 0.15213.632
size0.0040.0020.006
subsetByGenes0.0580.0050.064
topDEGenes21.976 0.14322.993
topDSExons12.890 0.11613.537
topDSGenes11.905 0.09412.643
topGeneSets3.6430.0284.038
writeScores0.0120.0030.017
writeSigGeneSet3.6530.0304.013