Xi Wang
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SeqGSEA |
| Branch: RELEASE_3_8 |
| Last Commit: 9ef68f0 |
| Last Changed Date: 2019-01-04 13:07:10 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:56:51 -0400 (Tue, 16 Apr 2019).
| Package 1421/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SeqGSEA 1.22.1 Xi Wang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: SeqGSEA |
| Version: 1.22.1 |
| 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_1.22.1.tar.gz |
| StartedAt: 2019-04-16 02:43:15 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:48:06 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 290.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SeqGSEA.Rcheck |
| Warnings: 1 |
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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_1.22.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.22.1’
* 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
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 ‘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’
plotES : <anonymous>: no visible global function definition for
‘density’
plotES: no visible global function definition for ‘density’
plotES: no visible global function definition for ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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’
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% colors density dev.off foreach i j layout legend lines
makeCluster matlines median p.adjust par plot points read.table text
write.table
Consider adding
importFrom("grDevices", "colors", "dev.off")
importFrom("graphics", "layout", "legend", "lines", "matlines", "par",
"plot", "points", "text")
importFrom("stats", "density", "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 ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'SeqGeneSet,numeric,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 or elapsed time > 5s
user system elapsed
runSeqGSEA 15.485 0.369 33.124
DSresultExonTable 9.528 0.215 9.895
DSpermutePval 9.152 0.360 9.628
DSresultGeneTable 8.893 0.294 9.328
topDSGenes 8.479 0.276 8.889
topDSExons 8.446 0.241 8.768
normFactor 8.319 0.274 8.680
scoreNormalization 8.128 0.249 8.445
DSpermute4GSEA 8.073 0.262 8.432
genpermuteMat 7.812 0.278 8.197
* 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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.8-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/3.5/Resources/library’ * installing *source* package ‘SeqGSEA’ ... ** 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 * DONE (SeqGSEA)
SeqGSEA.Rcheck/SeqGSEA-Ex.timings
| name | user | system | elapsed | |
| DENBStat4GSEA | 0.606 | 0.008 | 0.628 | |
| DENBStatPermut4GSEA | 1.064 | 0.075 | 1.149 | |
| DENBTest | 0.978 | 0.032 | 1.018 | |
| DEpermutePval | 0.799 | 0.018 | 0.827 | |
| DSpermute4GSEA | 8.073 | 0.262 | 8.432 | |
| DSpermutePval | 9.152 | 0.360 | 9.628 | |
| DSresultExonTable | 9.528 | 0.215 | 9.895 | |
| DSresultGeneTable | 8.893 | 0.294 | 9.328 | |
| GSEAresultTable | 2.767 | 0.011 | 2.813 | |
| GSEnrichAnalyze | 2.839 | 0.007 | 2.871 | |
| ReadCountSet-class | 0.002 | 0.001 | 0.003 | |
| SeqGeneSet-class | 0.002 | 0.000 | 0.002 | |
| calES | 0.010 | 0.002 | 0.014 | |
| calES.perm | 2.813 | 0.005 | 2.845 | |
| convertEnsembl2Symbol | 0.355 | 0.017 | 4.130 | |
| convertSymbol2Ensembl | 0.256 | 0.010 | 3.065 | |
| counts-methods | 0.014 | 0.001 | 0.015 | |
| estiExonNBstat | 0.833 | 0.056 | 0.892 | |
| estiGeneNBstat | 0.850 | 0.035 | 0.897 | |
| exonID | 0.140 | 0.052 | 0.193 | |
| exonTestability | 0.022 | 0.001 | 0.024 | |
| geneID | 0.193 | 0.062 | 0.257 | |
| geneList | 0.008 | 0.000 | 0.008 | |
| genePermuteScore | 0.006 | 0.001 | 0.008 | |
| geneScore | 0.005 | 0.001 | 0.006 | |
| geneSetDescs | 0.002 | 0.001 | 0.003 | |
| geneSetNames | 0.002 | 0.000 | 0.003 | |
| geneSetSize | 0.002 | 0.001 | 0.002 | |
| geneTestability | 0.035 | 0.001 | 0.036 | |
| genpermuteMat | 7.812 | 0.278 | 8.197 | |
| getGeneCount | 0.040 | 0.003 | 0.043 | |
| label | 0.020 | 0.001 | 0.022 | |
| loadExonCountData | 0.335 | 0.013 | 0.354 | |
| loadGenesets | 1.275 | 0.021 | 4.379 | |
| newGeneSets | 0.002 | 0.000 | 0.002 | |
| newReadCountSet | 0.085 | 0.001 | 0.085 | |
| normFactor | 8.319 | 0.274 | 8.680 | |
| plotES | 2.915 | 0.025 | 2.976 | |
| plotGeneScore | 0.135 | 0.004 | 0.141 | |
| plotSig | 2.704 | 0.008 | 2.734 | |
| plotSigGeneSet | 2.942 | 0.007 | 2.976 | |
| rankCombine | 0.008 | 0.001 | 0.010 | |
| runDESeq | 0.492 | 0.016 | 0.515 | |
| runSeqGSEA | 15.485 | 0.369 | 33.124 | |
| scoreNormalization | 8.128 | 0.249 | 8.445 | |
| size | 0.002 | 0.001 | 0.002 | |
| subsetByGenes | 0.034 | 0.001 | 0.035 | |
| topDEGenes | 1.515 | 0.029 | 1.561 | |
| topDSExons | 8.446 | 0.241 | 8.768 | |
| topDSGenes | 8.479 | 0.276 | 8.889 | |
| topGeneSets | 2.620 | 0.018 | 2.685 | |
| writeScores | 0.009 | 0.001 | 0.011 | |
| writeSigGeneSet | 2.893 | 0.007 | 2.945 | |