Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-04-22 13:17 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 1966/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqGSEA 1.48.0  (landing page)
Xi Wang
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/SeqGSEA
git_branch: RELEASE_3_21
git_last_commit: ea0980a
git_last_commit_date: 2025-04-15 10:23:38 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'DESeq2' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SeqGSEA on lconway

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: 1.48.0
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_1.48.0.tar.gz
StartedAt: 2025-04-21 23:31:02 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 23:36:49 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 346.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SeqGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SeqGSEA.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.48.0’
* 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 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 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
topDEGenes          11.385  0.085  11.547
DENBStatPermut4GSEA 11.228  0.101  11.422
DEpermutePval       11.026  0.091  11.188
DSresultGeneTable    6.169  0.105   6.319
DSpermute4GSEA       5.694  0.137   5.872
DSpermutePval        5.497  0.116   5.665
topDSExons           5.501  0.098   5.632
scoreNormalization   5.398  0.168   5.619
topDSGenes           5.313  0.133   5.484
normFactor           5.218  0.115   5.381
DSresultExonTable    5.199  0.096   5.324
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.


Installation output

SeqGSEA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SeqGSEA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SeqGSEA’ ...
** this is package ‘SeqGSEA’ version ‘1.48.0’
** 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
DENBStat4GSEA1.7870.1051.914
DENBStatPermut4GSEA11.228 0.10111.422
DENBTest2.0060.0382.060
DEpermutePval11.026 0.09111.188
DSpermute4GSEA5.6940.1375.872
DSpermutePval5.4970.1165.665
DSresultExonTable5.1990.0965.324
DSresultGeneTable6.1690.1056.319
GSEAresultTable1.7210.0141.745
GSEnrichAnalyze1.6940.0261.735
ReadCountSet-class0.0020.0010.002
SeqGeneSet-class0.0010.0010.001
calES0.0060.0030.009
calES.perm1.7110.0271.768
convertEnsembl2Symbol000
convertSymbol2Ensembl0.0000.0000.001
counts-methods0.0130.0020.014
estiExonNBstat0.4700.0240.498
estiGeneNBstat0.4720.0190.495
exonID0.0460.0600.106
exonTestability0.0200.0020.022
geneID0.0600.0780.139
geneList0.0030.0000.003
genePermuteScore0.0060.0020.007
geneScore0.0030.0010.005
geneSetDescs0.0020.0010.003
geneSetNames0.0020.0010.003
geneSetSize0.0020.0010.003
geneTestability0.0180.0020.020
genpermuteMat4.5190.1904.745
getGeneCount0.0150.0020.016
label0.0090.0010.010
loadExonCountData0.0010.0010.001
loadGenesets0.0000.0010.001
newGeneSets0.0020.0010.002
newReadCountSet0.0970.0010.098
normFactor5.2180.1155.381
plotES1.9020.0251.945
plotGeneScore0.1070.0050.113
plotSig1.6980.0121.718
plotSigGeneSet1.6590.0121.679
rankCombine0.0080.0030.012
runDESeq1.2930.0101.312
runSeqGSEA0.0020.0010.003
scoreNormalization5.3980.1685.619
size0.0020.0010.002
subsetByGenes0.0320.0020.033
topDEGenes11.385 0.08511.547
topDSExons5.5010.0985.632
topDSGenes5.3130.1335.484
topGeneSets1.7230.0171.750
writeScores0.0060.0020.009
writeSigGeneSet1.7880.0141.813