BioC 2.12: CHECK report for SeqGSEA on pelham

Package: SeqGSEA

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SeqGSEA_1.0.1.tar.gz

StartedAt: 2013-05-01 10:51:37 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:59:45 -0700 (Wed, 01 May 2013)

EllapsedTime: 488.0 seconds

RetCode: 0

Status: OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/SeqGSEA.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'SeqGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqGSEA' version '1.0.1'
* 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 ... [19s/20s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* 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 binding for global variable 'i'
DSpermute4GSEA : <anonymous>: no visible binding for global variable
  'i'
calES.perm: no visible binding for global variable 'i'
calES.perm: no visible binding for global variable 'j'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [282s/292s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
topDSGenes         24.858  0.757  26.120
topDSExons         24.497  0.801  25.655
normFactor         24.296  0.733  25.465
DSresultExonTable  23.911  0.844  24.978
scoreNormalization 23.824  0.508  24.583
DSpermutePval      23.593  0.538  24.347
DSresultGeneTable  22.873  0.829  24.268
DSpermute4GSEA     22.318  0.582  23.127
genpermuteMat      21.156  0.788  22.114
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/SeqGSEA.Rcheck/00check.log'
for details.

* installing *source* package 'SeqGSEA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SeqGSEA)

name	user	system	elapsed
DENBStat4GSEA	0.959	0.028	0.995
DENBStatPermut4GSEA	1.953	0.038	2.005
DENBTest	2.217	0.037	2.281
DEpermutePval	1.746	0.041	1.900
DSpermute4GSEA	22.318	0.582	23.127
DSpermutePval	23.593	0.538	24.347
DSresultExonTable	23.911	0.844	24.978
DSresultGeneTable	22.873	0.829	24.268
GSEAresultTable	3.977	0.032	4.059
GSEnrichAnalyze	4.004	0.028	4.065
ReadCountSet-class	0.008	0.004	0.017
SeqGeneSet-class	0.007	0.003	0.011
calES	0.026	0.008	0.040
calES.perm	3.913	0.026	3.975
convertEnsembl2Symbol	0.398	0.012	2.431
convertSymbol2Ensembl	0.431	0.012	2.407
counts-methods	0.039	0.007	0.047
estiExonNBstat	2.654	0.053	2.751
estiGeneNBstat	2.141	0.079	2.246
exonID	0.056	0.063	0.119
exonTestability	0.048	0.007	0.054
geneID	0.063	0.062	0.125
geneList	0.018	0.006	0.024
genePermuteScore	0.021	0.009	0.030
geneScore	0.015	0.006	0.023
geneSetDescs	0.012	0.004	0.016
geneSetNames	0.012	0.005	0.018
geneSetSize	0.012	0.005	0.018
geneTestability	0.068	0.006	0.074
genpermuteMat	21.156	0.788	22.114
getGeneCount	0.053	0.006	0.058
label	0.034	0.005	0.040
loadExonCountData	1.309	0.026	1.344
loadGenesets	2.059	0.029	4.668
newGeneSets	0.020	0.003	0.023
newReadCountSet	0.205	0.007	0.213
normFactor	24.296	0.733	25.465
plotES	4.203	0.035	4.333
plotGeneScore	0.199	0.013	0.235
plotSig	3.910	0.026	4.045
plotSigGeneSet	4.053	0.034	4.217
rankCombine	0.042	0.013	0.055
runDESeq	0.269	0.005	0.278
scoreNormalization	23.824	0.508	24.583
size	0.012	0.004	0.016
subsetByGenes	0.088	0.005	0.094
topDEGenes	3.625	0.070	3.723
topDSExons	24.497	0.801	25.655
topDSGenes	24.858	0.757	26.120
topGeneSets	4.547	0.028	4.601
writeScores	0.022	0.008	0.031
writeSigGeneSet	4.056	0.034	4.118

Summary

Command output