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This page was generated on 2025-10-07 12:08 -0400 (Tue, 07 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1965/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqGSEA 1.49.0  (landing page)
Xi Wang
Snapshot Date: 2025-10-06 13:45 -0400 (Mon, 06 Oct 2025)
git_url: https://git.bioconductor.org/packages/SeqGSEA
git_branch: devel
git_last_commit: 178db7c
git_last_commit_date: 2025-04-15 10:23:38 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SeqGSEA on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: SeqGSEA
Version: 1.49.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SeqGSEA_1.49.0.tar.gz
StartedAt: 2025-10-07 12:04:45 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 12:11:51 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 425.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SeqGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SeqGSEA_1.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SeqGSEA.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.49.0’
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ReadCountSet-class.Rd: eSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
topDEGenes          14.168  0.115  14.324
DENBStatPermut4GSEA 13.781  0.227  14.171
DEpermutePval       13.600  0.164  13.801
normFactor           8.773  0.036   8.842
topDSExons           8.491  0.040   8.568
DSresultGeneTable    8.441  0.044   8.512
scoreNormalization   8.378  0.035   8.439
topDSGenes           8.267  0.012   8.305
DSresultExonTable    8.241  0.036   8.600
DSpermutePval        8.130  0.072   8.332
genpermuteMat        7.799  0.024   7.847
DSpermute4GSEA       7.541  0.067   7.632
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.


Installation output

SeqGSEA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SeqGSEA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘SeqGSEA’ ...
** this is package ‘SeqGSEA’ version ‘1.49.0’
** 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
DENBStat4GSEA2.1940.0922.293
DENBStatPermut4GSEA13.781 0.22714.171
DENBTest3.2830.0883.384
DEpermutePval13.600 0.16413.801
DSpermute4GSEA7.5410.0677.632
DSpermutePval8.1300.0728.332
DSresultExonTable8.2410.0368.600
DSresultGeneTable8.4410.0448.512
GSEAresultTable2.2180.0562.282
GSEnrichAnalyze2.1880.0002.194
ReadCountSet-class0.0020.0000.002
SeqGeneSet-class0.0010.0000.001
calES0.0040.0030.007
calES.perm2.2030.0002.209
convertEnsembl2Symbol0.0010.0000.000
convertSymbol2Ensembl000
counts-methods0.0080.0040.013
estiExonNBstat0.7830.0270.812
estiGeneNBstat0.7950.0000.798
exonID0.0130.0280.041
exonTestability0.0200.0000.021
geneID0.0360.0120.048
geneList0.0050.0000.005
genePermuteScore0.0060.0000.006
geneScore0.0030.0000.003
geneSetDescs0.0020.0000.002
geneSetNames0.0020.0000.002
geneSetSize0.0000.0020.002
geneTestability0.0200.0020.022
genpermuteMat7.7990.0247.847
getGeneCount0.020.000.02
label0.0120.0000.013
loadExonCountData0.0010.0000.002
loadGenesets000
newGeneSets0.0030.0000.002
newReadCountSet0.1320.0080.140
normFactor8.7730.0368.842
plotES2.9990.1363.145
plotGeneScore0.1330.0000.133
plotSig2.2060.0002.212
plotSigGeneSet2.1780.0002.184
rankCombine0.0090.0000.009
runDESeq1.6890.0001.694
runSeqGSEA0.0010.0000.002
scoreNormalization8.3780.0358.439
size0.0020.0000.002
subsetByGenes0.0340.0000.034
topDEGenes14.168 0.11514.324
topDSExons8.4910.0408.568
topDSGenes8.2670.0128.305
topGeneSets2.0910.0042.102
writeScores0.0070.0000.007
writeSigGeneSet2.1590.0042.167