BioC 3.1: CHECK report for SeqGSEA on petty

Package: SeqGSEA

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.8.1.tar.gz

StartedAt: 2015-10-09 01:56:16 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:02:52 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 395.8 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_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.8.1’
* 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 ... [16s/16s] 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 ... [208s/223s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         25.950  0.222  33.584
normFactor         15.955  0.053  16.026
scoreNormalization 15.815  0.035  15.864
DSresultGeneTable  15.092  0.081  15.179
DSresultExonTable  14.665  0.053  14.719
topDSExons         14.307  0.030  14.399
DSpermutePval      13.962  0.051  14.016
topDSGenes         13.976  0.025  14.003
DSpermute4GSEA     13.785  0.065  13.859
genpermuteMat      13.611  0.036  13.657
* 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-3.1-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.

* installing *source* package ‘SeqGSEA’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (SeqGSEA)

name	user	system	elapsed
DENBStat4GSEA	0.42	0.03	0.45
DENBStatPermut4GSEA	1.711	0.017	1.728
DENBTest	1.605	0.017	1.631
DEpermutePval	1.693	0.018	1.713
DSpermute4GSEA	13.785	0.065	13.859
DSpermutePval	13.962	0.051	14.016
DSresultExonTable	14.665	0.053	14.719
DSresultGeneTable	15.092	0.081	15.179
GSEAresultTable	3.154	0.025	3.179
GSEnrichAnalyze	2.993	0.012	3.006
ReadCountSet-class	0.004	0.001	0.004
SeqGeneSet-class	0.003	0.001	0.003
calES	0.015	0.003	0.017
calES.perm	3.710	0.007	3.723
convertEnsembl2Symbol	0.234	0.014	2.761
convertSymbol2Ensembl	0.223	0.015	2.505
counts-methods	0.020	0.002	0.022
estiExonNBstat	1.521	0.013	1.537
estiGeneNBstat	1.836	0.004	1.842
exonID	0.187	0.051	0.238
exonTestability	0.038	0.001	0.040
geneID	0.272	0.050	0.322
geneList	0.005	0.001	0.006
genePermuteScore	0.008	0.001	0.008
geneScore	0.007	0.001	0.007
geneSetDescs	0.004	0.000	0.004
geneSetNames	0.003	0.000	0.003
geneSetSize	0.004	0.001	0.005
geneTestability	0.045	0.001	0.046
genpermuteMat	13.611	0.036	13.657
getGeneCount	0.025	0.000	0.026
label	0.025	0.000	0.026
loadExonCountData	0.571	0.011	0.583
loadGenesets	2.262	0.019	4.601
newGeneSets	0.006	0.000	0.007
newReadCountSet	0.161	0.000	0.161
normFactor	15.955	0.053	16.026
plotES	3.592	0.016	3.616
plotGeneScore	0.200	0.006	0.211
plotSig	3.351	0.009	3.363
plotSigGeneSet	3.043	0.006	3.051
rankCombine	0.017	0.003	0.019
runDESeq	0.219	0.001	0.220
runSeqGSEA	25.950	0.222	33.584
scoreNormalization	15.815	0.035	15.864
size	0.005	0.000	0.005
subsetByGenes	0.049	0.001	0.051
topDEGenes	2.703	0.026	2.729
topDSExons	14.307	0.030	14.399
topDSGenes	13.976	0.025	14.003
topGeneSets	3.347	0.004	3.353
writeScores	0.01	0.00	0.01
writeSigGeneSet	3.586	0.007	3.599