Xi Wang
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/SeqGSEA |
| git_branch: RELEASE_3_13 |
| git_last_commit: 2ecabac |
| git_last_commit_date: 2021-05-19 11:58:27 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:52 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1737/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqGSEA 1.32.0 (landing page) Xi Wang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SeqGSEA |
| Version: 1.32.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SeqGSEA_1.32.0.tar.gz |
| StartedAt: 2021-10-14 23:54:40 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-15 00:02:35 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 475.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SeqGSEA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SeqGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SeqGSEA_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SeqGSEA.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.32.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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
DENBStatPermut4GSEA 33.152 0.173 33.360
topDEGenes 32.378 0.075 32.501
DEpermutePval 30.403 0.041 30.461
DSresultExonTable 8.792 0.225 9.021
normFactor 8.524 0.275 8.803
DSpermutePval 8.507 0.200 8.715
DSresultGeneTable 8.294 0.222 8.525
scoreNormalization 8.240 0.222 8.467
topDSGenes 8.091 0.209 8.307
topDSExons 7.843 0.259 8.106
genpermuteMat 7.797 0.254 8.055
DSpermute4GSEA 7.122 0.261 7.394
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.13-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.
SeqGSEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SeqGSEA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)
SeqGSEA.Rcheck/SeqGSEA-Ex.timings
| name | user | system | elapsed | |
| DENBStat4GSEA | 4.517 | 0.143 | 4.669 | |
| DENBStatPermut4GSEA | 33.152 | 0.173 | 33.360 | |
| DENBTest | 4.490 | 0.018 | 4.510 | |
| DEpermutePval | 30.403 | 0.041 | 30.461 | |
| DSpermute4GSEA | 7.122 | 0.261 | 7.394 | |
| DSpermutePval | 8.507 | 0.200 | 8.715 | |
| DSresultExonTable | 8.792 | 0.225 | 9.021 | |
| DSresultGeneTable | 8.294 | 0.222 | 8.525 | |
| GSEAresultTable | 2.584 | 0.036 | 2.621 | |
| GSEnrichAnalyze | 2.358 | 0.005 | 2.365 | |
| ReadCountSet-class | 0.001 | 0.000 | 0.002 | |
| SeqGeneSet-class | 0.000 | 0.000 | 0.001 | |
| calES | 0.006 | 0.002 | 0.008 | |
| calES.perm | 2.740 | 0.006 | 2.747 | |
| convertEnsembl2Symbol | 0.000 | 0.001 | 0.000 | |
| convertSymbol2Ensembl | 0.000 | 0.000 | 0.001 | |
| counts-methods | 0.020 | 0.002 | 0.021 | |
| estiExonNBstat | 0.955 | 0.060 | 1.016 | |
| estiGeneNBstat | 0.856 | 0.023 | 0.880 | |
| exonID | 0.072 | 0.081 | 0.153 | |
| exonTestability | 0.031 | 0.001 | 0.033 | |
| geneID | 0.090 | 0.108 | 0.199 | |
| geneList | 0.005 | 0.001 | 0.006 | |
| genePermuteScore | 0.005 | 0.001 | 0.006 | |
| geneScore | 0.004 | 0.001 | 0.005 | |
| geneSetDescs | 0.003 | 0.001 | 0.003 | |
| geneSetNames | 0.002 | 0.001 | 0.003 | |
| geneSetSize | 0.003 | 0.002 | 0.004 | |
| geneTestability | 0.026 | 0.001 | 0.028 | |
| genpermuteMat | 7.797 | 0.254 | 8.055 | |
| getGeneCount | 0.026 | 0.001 | 0.027 | |
| label | 0.020 | 0.002 | 0.022 | |
| loadExonCountData | 0.001 | 0.001 | 0.002 | |
| loadGenesets | 0 | 0 | 0 | |
| newGeneSets | 0.002 | 0.001 | 0.003 | |
| newReadCountSet | 0.136 | 0.001 | 0.137 | |
| normFactor | 8.524 | 0.275 | 8.803 | |
| plotES | 2.791 | 0.014 | 2.806 | |
| plotGeneScore | 0.160 | 0.004 | 0.165 | |
| plotSig | 2.723 | 0.010 | 2.737 | |
| plotSigGeneSet | 2.733 | 0.010 | 2.747 | |
| rankCombine | 0.012 | 0.003 | 0.014 | |
| runDESeq | 3.486 | 0.005 | 3.493 | |
| runSeqGSEA | 0.002 | 0.001 | 0.003 | |
| scoreNormalization | 8.240 | 0.222 | 8.467 | |
| size | 0.003 | 0.001 | 0.003 | |
| subsetByGenes | 0.044 | 0.003 | 0.090 | |
| topDEGenes | 32.378 | 0.075 | 32.501 | |
| topDSExons | 7.843 | 0.259 | 8.106 | |
| topDSGenes | 8.091 | 0.209 | 8.307 | |
| topGeneSets | 2.513 | 0.006 | 2.519 | |
| writeScores | 0.006 | 0.001 | 0.007 | |
| writeSigGeneSet | 2.566 | 0.023 | 2.591 | |