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This page was generated on 2024-05-04 11:41:06 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 May 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    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for SeqGSEA on kunpeng2


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: 1.44.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SeqGSEA_1.44.0.tar.gz
StartedAt: 2024-05-04 11:56:23 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 12:03:25 -0000 (Sat, 04 May 2024)
EllapsedTime: 422.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SeqGSEA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SeqGSEA_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SeqGSEA.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
DENBStatPermut4GSEA 14.067  0.204  14.299
topDEGenes          14.006  0.104  14.140
DEpermutePval       13.926  0.131  14.087
topDSGenes           9.737  0.108   9.866
DSpermute4GSEA       9.381  0.124   9.525
genpermuteMat        9.026  0.084   9.127
topDSExons           8.946  0.036   9.001
DSpermutePval        8.907  0.040   8.965
DSresultGeneTable    8.914  0.032   8.964
normFactor           8.893  0.008   8.918
DSresultExonTable    8.873  0.016   8.909
scoreNormalization   8.852  0.020   8.888
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.


Installation output

SeqGSEA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL SeqGSEA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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
DENBStat4GSEA2.9940.2233.224
DENBStatPermut4GSEA14.067 0.20414.299
DENBTest2.7690.0122.786
DEpermutePval13.926 0.13114.087
DSpermute4GSEA9.3810.1249.525
DSpermutePval8.9070.0408.965
DSresultExonTable8.8730.0168.909
DSresultGeneTable8.9140.0328.964
GSEAresultTable2.2190.0882.312
GSEnrichAnalyze2.2330.0032.241
ReadCountSet-class0.0010.0000.002
SeqGeneSet-class0.0000.0000.001
calES0.0060.0000.007
calES.perm2.2310.0192.254
convertEnsembl2Symbol0.0010.0000.000
convertSymbol2Ensembl000
counts-methods0.0090.0040.012
estiExonNBstat0.8150.0040.820
estiGeneNBstat0.8350.0040.841
exonID0.0270.0120.039
exonTestability0.0210.0000.021
geneID0.0410.0040.045
geneList0.0040.0000.005
genePermuteScore0.0060.0000.006
geneScore0.0040.0000.003
geneSetDescs0.0020.0000.002
geneSetNames0.0020.0000.002
geneSetSize0.0020.0000.002
geneTestability0.0230.0000.023
genpermuteMat9.0260.0849.127
getGeneCount0.0210.0000.022
label0.0120.0000.012
loadExonCountData0.0020.0000.001
loadGenesets000
newGeneSets0.0030.0000.003
newReadCountSet0.1330.0040.137
normFactor8.8930.0088.918
plotES2.3500.0472.403
plotGeneScore0.1120.0010.113
plotSig2.1930.0032.203
plotSigGeneSet2.3410.0122.357
rankCombine0.0100.0000.011
runDESeq1.6820.0041.689
runSeqGSEA0.0010.0000.001
scoreNormalization8.8520.0208.888
size0.0020.0000.002
subsetByGenes0.0310.0040.035
topDEGenes14.006 0.10414.140
topDSExons8.9460.0369.001
topDSGenes9.7370.1089.866
topGeneSets2.1540.0042.163
writeScores0.0070.0000.007
writeSigGeneSet2.2310.0042.240