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This page was generated on 2024-07-12 17:41 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 1945/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqGSEA 1.44.0  (landing page)
Xi Wang
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/SeqGSEA
git_branch: RELEASE_3_19
git_last_commit: 3dbebc5
git_last_commit_date: 2024-04-30 10:31:23 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.44.0
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_1.44.0.tar.gz
StartedAt: 2024-07-11 11:40:50 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 11:54:25 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 815.2 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_1.44.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SeqGSEA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.44.0’
* 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 ... 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
topDEGenes          24.783  0.280  29.415
DENBStatPermut4GSEA 23.722  0.233  28.306
DEpermutePval       23.554  0.283  29.028
DSpermutePval       13.783  0.164  17.100
normFactor          13.658  0.131  16.948
topDSGenes          13.641  0.122  16.278
topDSExons          13.005  0.174  15.396
DSresultGeneTable   13.007  0.108  15.991
scoreNormalization  12.872  0.098  15.368
DSresultExonTable   12.850  0.109  15.632
DSpermute4GSEA      12.429  0.236  15.465
genpermuteMat       11.861  0.199  14.586
DENBStat4GSEA        4.790  0.396   6.550
plotES               4.398  0.061   5.538
plotSig              4.249  0.087   5.403
plotSigGeneSet       4.251  0.038   5.262
GSEnrichAnalyze      4.211  0.034   5.192
GSEAresultTable      4.196  0.046   5.294
calES.perm           4.200  0.031   5.212
topGeneSets          4.150  0.034   5.106
writeSigGeneSet      4.145  0.031   5.067
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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
DENBStat4GSEA4.7900.3966.550
DENBStatPermut4GSEA23.722 0.23328.306
DENBTest4.0590.0424.857
DEpermutePval23.554 0.28329.028
DSpermute4GSEA12.429 0.23615.465
DSpermutePval13.783 0.16417.100
DSresultExonTable12.850 0.10915.632
DSresultGeneTable13.007 0.10815.991
GSEAresultTable4.1960.0465.294
GSEnrichAnalyze4.2110.0345.192
ReadCountSet-class0.0020.0020.005
SeqGeneSet-class0.0020.0020.004
calES0.0120.0080.025
calES.perm4.2000.0315.212
convertEnsembl2Symbol0.0000.0010.000
convertSymbol2Ensembl0.0000.0000.001
counts-methods0.0200.0040.077
estiExonNBstat1.2210.0211.549
estiGeneNBstat1.2070.0141.440
exonID0.1060.1990.341
exonTestability0.0530.0030.067
geneID0.1260.1980.367
geneList0.0090.0000.011
genePermuteScore0.0080.0030.014
geneScore0.0060.0030.010
geneSetDescs0.0040.0030.008
geneSetNames0.0040.0020.007
geneSetSize0.0030.0020.005
geneTestability0.0360.0020.041
genpermuteMat11.861 0.19914.586
getGeneCount0.0350.0020.040
label0.0210.0020.026
loadExonCountData0.0020.0020.004
loadGenesets0.0000.0010.001
newGeneSets0.0050.0020.009
newReadCountSet0.2320.0030.276
normFactor13.658 0.13116.948
plotES4.3980.0615.538
plotGeneScore0.2140.0090.290
plotSig4.2490.0875.403
plotSigGeneSet4.2510.0385.262
rankCombine0.0130.0050.025
runDESeq2.9420.0253.488
runSeqGSEA0.0040.0030.006
scoreNormalization12.872 0.09815.368
size0.0030.0020.006
subsetByGenes0.0590.0040.076
topDEGenes24.783 0.28029.415
topDSExons13.005 0.17415.396
topDSGenes13.641 0.12216.278
topGeneSets4.1500.0345.106
writeScores0.0120.0030.017
writeSigGeneSet4.1450.0315.067