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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1894/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqGSEA 1.45.0  (landing page)
Xi Wang
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/SeqGSEA
git_branch: devel
git_last_commit: fd1d162
git_last_commit_date: 2024-04-30 10:31:23 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for SeqGSEA on palomino6

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: 1.45.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SeqGSEA_1.45.0.tar.gz
StartedAt: 2024-07-16 04:03:14 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 04:16:44 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 809.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SeqGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SeqGSEA_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/SeqGSEA.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SeqGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqGSEA' version '1.45.0'
* 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 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
DSpermutePval       95.69   0.42   93.89
DSpermute4GSEA      52.67   0.11   55.27
normFactor          12.88  33.81   59.25
DSresultGeneTable   16.93  21.17   40.85
genpermuteMat       17.91   6.33   30.50
scoreNormalization  20.73   0.10   17.22
topDEGenes          13.53   0.18   14.11
DSresultExonTable   12.33   1.17   18.81
GSEAresultTable     12.38   0.05   12.50
writeSigGeneSet     12.04   0.04    9.89
topDSExons          11.55   0.24   18.22
plotES              11.39   0.28   12.31
topDSGenes          11.03   0.28   11.61
DENBStatPermut4GSEA 10.50   0.05   11.30
DEpermutePval       10.34   0.16   10.78
estiExonNBstat       8.59   0.06    9.99
calES.perm           4.88   0.02    6.84
newReadCountSet      1.89   0.00   10.30
* 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
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/SeqGSEA.Rcheck/00check.log'
for details.


Installation output

SeqGSEA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SeqGSEA
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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
DENBStat4GSEA1.210.161.36
DENBStatPermut4GSEA10.50 0.0511.30
DENBTest2.10.02.1
DEpermutePval10.34 0.1610.78
DSpermute4GSEA52.67 0.1155.27
DSpermutePval95.69 0.4293.89
DSresultExonTable12.33 1.1718.81
DSresultGeneTable16.9321.1740.85
GSEAresultTable12.38 0.0512.50
GSEnrichAnalyze4.640.094.95
ReadCountSet-class000
SeqGeneSet-class000
calES0.000.000.02
calES.perm4.880.026.84
convertEnsembl2Symbol000
convertSymbol2Ensembl000
counts-methods0.010.000.01
estiExonNBstat8.590.069.99
estiGeneNBstat0.720.140.93
exonID0.080.020.15
exonTestability0.020.000.07
geneID0.080.030.13
geneList000
genePermuteScore0.030.000.05
geneScore0.000.000.06
geneSetDescs0.000.000.04
geneSetNames0.010.000.07
geneSetSize0.000.000.06
geneTestability0.030.000.08
genpermuteMat17.91 6.3330.50
getGeneCount000
label000
loadExonCountData0.000.020.02
loadGenesets000
newGeneSets000
newReadCountSet 1.89 0.0010.30
normFactor12.8833.8159.25
plotES11.39 0.2812.31
plotGeneScore0.090.000.09
plotSig1.160.081.24
plotSigGeneSet2.750.023.23
rankCombine000
runDESeq2.380.012.40
runSeqGSEA000
scoreNormalization20.73 0.1017.22
size0.020.000.02
subsetByGenes0.010.000.01
topDEGenes13.53 0.1814.11
topDSExons11.55 0.2418.22
topDSGenes11.03 0.2811.61
topGeneSets1.200.031.25
writeScores0.000.020.02
writeSigGeneSet12.04 0.04 9.89