BioC 2.12: CHECK report for SeqGSEA on petty

Package: SeqGSEA

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SeqGSEA_1.0.2.tar.gz

StartedAt: 2013-10-08 23:54:24 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-09 00:03:44 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 559.7 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 3.0.1 (2013-05-16)
* 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 '1.0.2'
* 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 ... [20s/21s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [327s/339s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
DSpermutePval      28.453  0.429  29.111
DSresultExonTable  28.497  0.384  29.129
topDSExons         28.199  0.498  29.067
scoreNormalization 27.585  0.467  28.433
normFactor         27.396  0.511  28.182
DSresultGeneTable  27.362  0.468  29.232
topDSGenes         26.931  0.651  27.796
DSpermute4GSEA     25.918  0.324  26.402
genpermuteMat      24.780  0.545  25.528
writeSigGeneSet     5.597  0.030   5.775
plotES              5.569  0.032   5.713
GSEnrichAnalyze     5.447  0.024   5.565
plotSigGeneSet      5.427  0.024   5.473
GSEAresultTable     5.385  0.029   5.543
calES.perm          5.258  0.019   5.346
* 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	1.105	0.028	1.161
DENBStatPermut4GSEA	2.492	0.065	2.612
DENBTest	2.047	0.036	2.098
DEpermutePval	2.096	0.027	2.156
DSpermute4GSEA	25.918	0.324	26.402
DSpermutePval	28.453	0.429	29.111
DSresultExonTable	28.497	0.384	29.129
DSresultGeneTable	27.362	0.468	29.232
GSEAresultTable	5.385	0.029	5.543
GSEnrichAnalyze	5.447	0.024	5.565
ReadCountSet-class	0.009	0.001	0.010
SeqGeneSet-class	0.011	0.002	0.014
calES	0.035	0.007	0.044
calES.perm	5.258	0.019	5.346
convertEnsembl2Symbol	0.763	0.017	3.213
convertSymbol2Ensembl	0.440	0.011	2.840
counts-methods	0.036	0.005	0.042
estiExonNBstat	2.473	0.110	2.609
estiGeneNBstat	2.920	0.128	3.059
exonID	0.062	0.054	0.116
exonTestability	0.070	0.004	0.077
geneID	0.068	0.060	0.128
geneList	0.027	0.003	0.029
genePermuteScore	0.029	0.006	0.035
geneScore	0.018	0.005	0.024
geneSetDescs	0.012	0.003	0.015
geneSetNames	0.012	0.004	0.016
geneSetSize	0.013	0.003	0.017
geneTestability	0.427	0.005	0.432
genpermuteMat	24.780	0.545	25.528
getGeneCount	0.080	0.003	0.084
label	0.038	0.004	0.043
loadExonCountData	1.345	0.034	1.385
loadGenesets	2.510	0.021	4.950
newGeneSets	0.020	0.001	0.021
newReadCountSet	0.222	0.006	0.229
normFactor	27.396	0.511	28.182
plotES	5.569	0.032	5.713
plotGeneScore	0.227	0.009	0.241
plotSig	4.829	0.024	4.860
plotSigGeneSet	5.427	0.024	5.473
rankCombine	0.036	0.011	0.048
runDESeq	0.310	0.006	0.316
scoreNormalization	27.585	0.467	28.433
size	0.013	0.004	0.018
subsetByGenes	0.101	0.005	0.107
topDEGenes	3.724	0.042	3.814
topDSExons	28.199	0.498	29.067
topDSGenes	26.931	0.651	27.796
topGeneSets	4.809	0.022	4.902
writeScores	0.027	0.006	0.239
writeSigGeneSet	5.597	0.030	5.775