BioC 3.2: CHECK report for SeqGSEA on perceval

Package: SeqGSEA

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.9.1.tar.gz

StartedAt: 2015-08-24 05:05:05 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 05:10:34 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 329.4 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 SeqGSEA_1.9.1.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 (2015-08-14 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 ‘1.9.1’
* 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 ... [13s/13s] 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 ... [177s/191s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         22.103  0.254  29.566
topDSExons         13.861  0.041  13.948
scoreNormalization 13.827  0.052  13.985
normFactor         13.635  0.072  13.802
topDSGenes         13.564  0.048  13.723
DSresultExonTable  12.911  0.063  12.992
DSpermutePval      12.612  0.069  12.726
DSresultGeneTable  12.178  0.073  12.268
genpermuteMat      11.897  0.047  11.949
DSpermute4GSEA     11.496  0.086  11.615
* 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	0.575	0.016	0.591
DENBStatPermut4GSEA	0.965	0.028	0.993
DENBTest	1.415	0.028	1.443
DEpermutePval	0.968	0.020	0.987
DSpermute4GSEA	11.496	0.086	11.615
DSpermutePval	12.612	0.069	12.726
DSresultExonTable	12.911	0.063	12.992
DSresultGeneTable	12.178	0.073	12.268
GSEAresultTable	2.562	0.030	2.591
GSEnrichAnalyze	2.496	0.009	2.506
ReadCountSet-class	0.002	0.000	0.003
SeqGeneSet-class	0.003	0.001	0.003
calES	0.009	0.002	0.011
calES.perm	2.797	0.007	2.805
convertEnsembl2Symbol	0.150	0.012	2.471
convertSymbol2Ensembl	0.133	0.012	2.378
counts-methods	0.017	0.002	0.018
estiExonNBstat	1.052	0.016	1.069
estiGeneNBstat	1.176	0.008	1.189
exonID	0.150	0.047	0.197
exonTestability	0.035	0.002	0.037
geneID	0.219	0.048	0.269
geneList	0.006	0.000	0.008
genePermuteScore	0.008	0.001	0.010
geneScore	0.005	0.001	0.005
geneSetDescs	0.003	0.001	0.004
geneSetNames	0.004	0.001	0.004
geneSetSize	0.004	0.000	0.004
geneTestability	0.028	0.000	0.028
genpermuteMat	11.897	0.047	11.949
getGeneCount	0.024	0.000	0.025
label	0.016	0.001	0.017
loadExonCountData	0.412	0.014	0.426
loadGenesets	1.401	0.019	3.764
newGeneSets	0.004	0.000	0.004
newReadCountSet	0.101	0.001	0.102
normFactor	13.635	0.072	13.802
plotES	2.610	0.009	2.619
plotGeneScore	0.133	0.006	0.143
plotSig	2.616	0.012	2.633
plotSigGeneSet	2.603	0.008	2.620
rankCombine	0.012	0.003	0.015
runDESeq	0.159	0.002	0.161
runSeqGSEA	22.103	0.254	29.566
scoreNormalization	13.827	0.052	13.985
size	0.003	0.001	0.004
subsetByGenes	0.040	0.001	0.041
topDEGenes	1.911	0.028	1.948
topDSExons	13.861	0.041	13.948
topDSGenes	13.564	0.048	13.723
topGeneSets	2.508	0.009	2.530
writeScores	0.008	0.001	0.009
writeSigGeneSet	2.407	0.006	2.415