BioC 3.0: CHECK report for SeqGSEA on perceval

Package: SeqGSEA

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SeqGSEA_1.6.0.tar.gz

StartedAt: 2015-04-10 06:16:02 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 06:23:10 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 427.4 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 --no-vignettes --timings --no-multiarch SeqGSEA_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.6.0’
* 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 ... 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 ‘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 loading without being on the library search path ... 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
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’
DENBStatPermut4GSEA: no visible global function definition for
  ‘%dopar%’
DENBStatPermut4GSEA: no visible global function definition for
  ‘foreach’
DENBStatPermut4GSEA: no visible binding for global variable ‘i’
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’
runSeqGSEA: no visible global function definition for ‘makeCluster’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [199s/216s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         23.112  0.275  32.516
DSresultGeneTable  14.663  0.079  14.839
DSpermutePval      14.414  0.069  14.491
scoreNormalization 14.375  0.048  14.444
topDSGenes         14.316  0.051  14.379
DSresultExonTable  14.067  0.106  14.218
normFactor         14.104  0.068  14.184
topDSExons         14.074  0.047  14.159
genpermuteMat      13.252  0.068  13.419
DSpermute4GSEA     12.850  0.065  12.917
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.684	0.014	0.698
DENBStatPermut4GSEA	1.539	0.022	1.561
DENBTest	1.461	0.029	1.491
DEpermutePval	1.260	0.014	1.273
DSpermute4GSEA	12.850	0.065	12.917
DSpermutePval	14.414	0.069	14.491
DSresultExonTable	14.067	0.106	14.218
DSresultGeneTable	14.663	0.079	14.839
GSEAresultTable	3.461	0.037	3.507
GSEnrichAnalyze	2.930	0.009	2.941
ReadCountSet-class	0.002	0.000	0.002
SeqGeneSet-class	0.002	0.000	0.003
calES	0.015	0.004	0.019
calES.perm	3.124	0.010	3.144
convertEnsembl2Symbol	0.165	0.011	2.682
convertSymbol2Ensembl	0.155	0.011	2.578
counts-methods	0.030	0.004	0.033
estiExonNBstat	1.450	0.015	1.473
estiGeneNBstat	1.772	0.014	1.796
exonID	0.157	0.057	0.214
exonTestability	0.035	0.003	0.039
geneID	0.221	0.052	0.272
geneList	0.006	0.000	0.006
genePermuteScore	0.012	0.002	0.014
geneScore	0.007	0.002	0.009
geneSetDescs	0.005	0.001	0.006
geneSetNames	0.005	0.001	0.005
geneSetSize	0.004	0.000	0.005
geneTestability	0.035	0.002	0.037
genpermuteMat	13.252	0.068	13.419
getGeneCount	0.037	0.002	0.039
label	0.019	0.002	0.021
loadExonCountData	0.395	0.013	0.408
loadGenesets	1.454	0.019	3.976
newGeneSets	0.005	0.001	0.004
newReadCountSet	0.107	0.001	0.108
normFactor	14.104	0.068	14.184
plotES	3.316	0.018	3.349
plotGeneScore	0.138	0.008	0.177
plotSig	3.423	0.011	3.454
plotSigGeneSet	3.101	0.013	3.143
rankCombine	0.018	0.003	0.021
runDESeq	0.165	0.003	0.168
runSeqGSEA	23.112	0.275	32.516
scoreNormalization	14.375	0.048	14.444
size	0.006	0.002	0.007
subsetByGenes	0.047	0.003	0.049
topDEGenes	2.253	0.029	2.296
topDSExons	14.074	0.047	14.159
topDSGenes	14.316	0.051	14.379
topGeneSets	2.955	0.009	2.965
writeScores	0.013	0.002	0.015
writeSigGeneSet	2.976	0.009	2.987