BioC 2.12: CHECK report for SeqGSEA on george2

Package: SeqGSEA

Version: 1.0.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.0.2.tar.gz

StartedAt: 2013-10-09 04:53:53 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:04:08 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 614.8 seconds

RetCode: 0

Status:  OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.0.2’
* 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 ... [21s/22s] 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 ... [364s/388s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
DSpermutePval      34.922  0.044  35.731
topDSExons         33.435  0.060  35.788
DSresultGeneTable  32.974  0.044  35.063
normFactor         32.858  0.044  34.672
scoreNormalization 32.422  0.024  34.167
topDSGenes         32.322  0.052  33.541
DSresultExonTable  31.146  0.004  31.653
DSpermute4GSEA     30.658  0.044  31.692
genpermuteMat      29.610  0.044  32.149
GSEnrichAnalyze     4.920  0.032   5.341
topGeneSets         4.936  0.016   5.408
writeSigGeneSet     4.748  0.016   5.094
* 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
  ‘/home/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	1.412	0.024	1.494
DENBStatPermut4GSEA	2.580	0.012	2.641
DENBTest	2.024	0.004	2.102
DEpermutePval	2.689	0.004	2.842
DSpermute4GSEA	30.658	0.044	31.692
DSpermutePval	34.922	0.044	35.731
DSresultExonTable	31.146	0.004	31.653
DSresultGeneTable	32.974	0.044	35.063
GSEAresultTable	4.456	0.020	4.481
GSEnrichAnalyze	4.920	0.032	5.341
ReadCountSet-class	0.012	0.004	0.014
SeqGeneSet-class	0.004	0.000	0.006
calES	0.032	0.000	0.033
calES.perm	4.209	0.028	4.596
convertEnsembl2Symbol	0.536	0.040	3.079
convertSymbol2Ensembl	0.396	0.008	2.789
counts-methods	0.040	0.004	0.051
estiExonNBstat	3.512	0.008	3.715
estiGeneNBstat	2.780	0.008	2.833
exonID	0.064	0.040	0.105
exonTestability	0.064	0.000	0.063
geneID	0.096	0.036	0.131
geneList	0.024	0.000	0.026
genePermuteScore	0.040	0.004	0.047
geneScore	0.024	0.000	0.026
geneSetDescs	0.024	0.000	0.025
geneSetNames	0.028	0.000	0.025
geneSetSize	0.024	0.004	0.028
geneTestability	0.084	0.004	0.088
genpermuteMat	29.610	0.044	32.149
getGeneCount	0.060	0.004	0.073
label	0.044	0.008	0.060
loadExonCountData	1.172	0.028	1.254
loadGenesets	1.796	0.016	4.331
newGeneSets	0.028	0.000	0.026
newReadCountSet	0.264	0.004	0.270
normFactor	32.858	0.044	34.672
plotES	4.441	0.004	4.630
plotGeneScore	0.176	0.008	0.242
plotSig	4.288	0.008	4.309
plotSigGeneSet	4.528	0.028	4.830
rankCombine	0.048	0.000	0.050
runDESeq	0.292	0.000	0.295
scoreNormalization	32.422	0.024	34.167
size	0.016	0.004	0.019
subsetByGenes	0.108	0.000	0.109
topDEGenes	4.284	0.016	4.431
topDSExons	33.435	0.060	35.788
topDSGenes	32.322	0.052	33.541
topGeneSets	4.936	0.016	5.408
writeScores	0.036	0.008	0.046
writeSigGeneSet	4.748	0.016	5.094