| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-03 02:36:24 -0000 (Fri, 03 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4039 |
| 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 | ||||
|
To the developers/maintainers of the SeqGSEA package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1832/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqGSEA 1.39.0 (landing page) Xi Wang
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: SeqGSEA |
| Version: 1.39.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SeqGSEA_1.39.0.tar.gz |
| StartedAt: 2023-02-02 20:09:30 -0000 (Thu, 02 Feb 2023) |
| EndedAt: 2023-02-02 20:30:16 -0000 (Thu, 02 Feb 2023) |
| EllapsedTime: 1245.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SeqGSEA.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SeqGSEA_1.39.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SeqGSEA.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.39.0’
* 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 R 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DENBStatPermut4GSEA 15.628 0.008 31.303
topDEGenes 15.578 0.016 18.523
DEpermutePval 14.924 0.007 28.006
topDSGenes 9.523 0.004 10.082
normFactor 9.403 0.012 12.486
DSresultGeneTable 8.826 0.008 12.098
scoreNormalization 8.812 0.018 11.947
DSpermute4GSEA 8.780 0.012 12.838
DSresultExonTable 8.736 0.008 10.249
topDSExons 8.656 0.008 8.965
DSpermutePval 8.627 0.012 9.017
genpermuteMat 7.996 0.014 9.311
DENBTest 2.720 0.036 5.506
DENBStat4GSEA 2.445 0.072 5.024
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘SeqGSEA.Rnw’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘SeqGSEA.Rnw’
...
> gene.score.perm <- genePermuteScore(DEscore.perm,
+ DSscore.perm, DEweight = 0.5)
> gene.set <- loadGenesets(geneset.file, geneIDs, geneID.type = "ensembl",
+ genesetsize.min = 5, genesetsize.max = 1000)
When sourcing ‘SeqGSEA.R’:
Error: Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 479008 bytes received
Execution halted
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.
SeqGSEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SeqGSEA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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)
SeqGSEA.Rcheck/SeqGSEA-Ex.timings
| name | user | system | elapsed | |
| DENBStat4GSEA | 2.445 | 0.072 | 5.024 | |
| DENBStatPermut4GSEA | 15.628 | 0.008 | 31.303 | |
| DENBTest | 2.720 | 0.036 | 5.506 | |
| DEpermutePval | 14.924 | 0.007 | 28.006 | |
| DSpermute4GSEA | 8.780 | 0.012 | 12.838 | |
| DSpermutePval | 8.627 | 0.012 | 9.017 | |
| DSresultExonTable | 8.736 | 0.008 | 10.249 | |
| DSresultGeneTable | 8.826 | 0.008 | 12.098 | |
| GSEAresultTable | 2.255 | 0.000 | 3.984 | |
| GSEnrichAnalyze | 2.237 | 0.000 | 2.525 | |
| ReadCountSet-class | 0.002 | 0.000 | 0.002 | |
| SeqGeneSet-class | 0.000 | 0.001 | 0.001 | |
| calES | 0.004 | 0.003 | 0.006 | |
| calES.perm | 2.198 | 0.000 | 2.348 | |
| convertEnsembl2Symbol | 0 | 0 | 0 | |
| convertSymbol2Ensembl | 0 | 0 | 0 | |
| counts-methods | 0.013 | 0.000 | 0.014 | |
| estiExonNBstat | 0.794 | 0.011 | 0.807 | |
| estiGeneNBstat | 0.801 | 0.000 | 0.816 | |
| exonID | 0.032 | 0.024 | 0.057 | |
| exonTestability | 0.023 | 0.000 | 0.022 | |
| geneID | 0.043 | 0.035 | 0.083 | |
| geneList | 0.005 | 0.000 | 0.005 | |
| genePermuteScore | 0.003 | 0.004 | 0.006 | |
| geneScore | 0.004 | 0.000 | 0.003 | |
| geneSetDescs | 0.002 | 0.000 | 0.002 | |
| geneSetNames | 0.002 | 0.000 | 0.002 | |
| geneSetSize | 0.002 | 0.000 | 0.002 | |
| geneTestability | 0.024 | 0.001 | 0.025 | |
| genpermuteMat | 7.996 | 0.014 | 9.311 | |
| getGeneCount | 0.022 | 0.000 | 0.035 | |
| label | 0.013 | 0.000 | 0.014 | |
| loadExonCountData | 0.001 | 0.000 | 0.029 | |
| loadGenesets | 0 | 0 | 0 | |
| newGeneSets | 0.003 | 0.000 | 0.003 | |
| newReadCountSet | 0.121 | 0.000 | 0.140 | |
| normFactor | 9.403 | 0.012 | 12.486 | |
| plotES | 2.286 | 0.004 | 3.213 | |
| plotGeneScore | 0.123 | 0.000 | 0.124 | |
| plotSig | 2.186 | 0.004 | 2.193 | |
| plotSigGeneSet | 2.260 | 0.000 | 2.329 | |
| rankCombine | 0.006 | 0.004 | 0.010 | |
| runDESeq | 1.850 | 0.000 | 1.969 | |
| runSeqGSEA | 0.000 | 0.002 | 0.002 | |
| scoreNormalization | 8.812 | 0.018 | 11.947 | |
| size | 0.002 | 0.000 | 0.002 | |
| subsetByGenes | 0.032 | 0.004 | 0.037 | |
| topDEGenes | 15.578 | 0.016 | 18.523 | |
| topDSExons | 8.656 | 0.008 | 8.965 | |
| topDSGenes | 9.523 | 0.004 | 10.082 | |
| topGeneSets | 2.223 | 0.000 | 2.562 | |
| writeScores | 0.007 | 0.000 | 0.007 | |
| writeSigGeneSet | 2.217 | 0.000 | 2.320 | |