BioC 3.2: CHECK report for SeqGSEA on perceval

Package: SeqGSEA

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.10.0.tar.gz

StartedAt: 2015-10-27 12:12:09 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 12:17:04 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 295.1 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 SeqGSEA_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.10.0’
* 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 ... [11s/11s] 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 ... [158s/172s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         18.811  0.149  26.021
topDSExons         11.616  0.019  11.636
scoreNormalization 11.611  0.022  11.634
topDSGenes         11.557  0.026  11.582
DSpermutePval      11.440  0.038  11.479
DSresultExonTable  11.430  0.048  11.478
normFactor         11.366  0.028  11.395
DSresultGeneTable  11.180  0.045  11.226
genpermuteMat      10.443  0.025  10.468
DSpermute4GSEA     10.406  0.046  10.453
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.488	0.011	0.498
DENBStatPermut4GSEA	1.007	0.021	1.028
DENBTest	1.371	0.020	1.392
DEpermutePval	0.949	0.010	0.959
DSpermute4GSEA	10.406	0.046	10.453
DSpermutePval	11.440	0.038	11.479
DSresultExonTable	11.430	0.048	11.478
DSresultGeneTable	11.180	0.045	11.226
GSEAresultTable	2.624	0.021	2.646
GSEnrichAnalyze	2.773	0.005	2.779
ReadCountSet-class	0.003	0.001	0.002
SeqGeneSet-class	0.002	0.000	0.002
calES	0.009	0.002	0.010
calES.perm	2.544	0.003	2.547
convertEnsembl2Symbol	0.149	0.011	2.475
convertSymbol2Ensembl	0.142	0.011	2.364
counts-methods	0.021	0.001	0.022
estiExonNBstat	1.026	0.009	1.034
estiGeneNBstat	1.053	0.005	1.058
exonID	0.150	0.040	0.191
exonTestability	0.029	0.001	0.031
geneID	0.214	0.041	0.255
geneList	0.006	0.000	0.006
genePermuteScore	0.008	0.001	0.009
geneScore	0.005	0.001	0.006
geneSetDescs	0.006	0.001	0.006
geneSetNames	0.004	0.001	0.005
geneSetSize	0.003	0.001	0.004
geneTestability	0.029	0.001	0.030
genpermuteMat	10.443	0.025	10.468
getGeneCount	0.029	0.000	0.030
label	0.016	0.000	0.016
loadExonCountData	0.366	0.006	0.373
loadGenesets	1.298	0.013	3.602
newGeneSets	0.004	0.001	0.004
newReadCountSet	0.105	0.000	0.105
normFactor	11.366	0.028	11.395
plotES	2.754	0.010	2.764
plotGeneScore	0.132	0.004	0.140
plotSig	2.633	0.007	2.640
plotSigGeneSet	2.646	0.006	2.652
rankCombine	0.011	0.001	0.013
runDESeq	0.138	0.001	0.139
runSeqGSEA	18.811	0.149	26.021
scoreNormalization	11.611	0.022	11.634
size	0.003	0.001	0.003
subsetByGenes	0.043	0.001	0.044
topDEGenes	2.206	0.021	2.228
topDSExons	11.616	0.019	11.636
topDSGenes	11.557	0.026	11.582
topGeneSets	2.566	0.004	2.569
writeScores	0.008	0.001	0.008
writeSigGeneSet	2.571	0.003	2.574