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: 2015-11-06 09:54:31 -0800 (Fri, 06 Nov 2015)

EndedAt: 2015-11-06 09:59:17 -0800 (Fri, 06 Nov 2015)

EllapsedTime: 286.1 seconds

RetCode: 0

Status:  OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

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


* 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/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 ... [151s/165s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         17.951  0.165  25.119
DSpermutePval      11.265  0.066  11.331
DSresultExonTable  11.128  0.073  11.202
scoreNormalization 11.088  0.033  11.121
DSresultGeneTable  10.970  0.061  11.032
normFactor         10.948  0.025  10.975
topDSGenes         10.674  0.030  10.704
topDSExons         10.655  0.031  10.687
genpermuteMat      10.038  0.043  10.081
DSpermute4GSEA      9.913  0.061   9.973
* 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	0.475	0.010	0.486
DENBStatPermut4GSEA	0.975	0.019	0.995
DENBTest	1.328	0.019	1.348
DEpermutePval	0.927	0.015	0.942
DSpermute4GSEA	9.913	0.061	9.973
DSpermutePval	11.265	0.066	11.331
DSresultExonTable	11.128	0.073	11.202
DSresultGeneTable	10.970	0.061	11.032
GSEAresultTable	2.563	0.021	2.585
GSEnrichAnalyze	2.557	0.009	2.566
ReadCountSet-class	0.002	0.000	0.003
SeqGeneSet-class	0.002	0.001	0.003
calES	0.008	0.002	0.010
calES.perm	2.736	0.005	2.740
convertEnsembl2Symbol	0.143	0.009	2.411
convertSymbol2Ensembl	0.141	0.010	2.397
counts-methods	0.017	0.001	0.018
estiExonNBstat	1.001	0.012	1.012
estiGeneNBstat	1.024	0.006	1.029
exonID	0.147	0.038	0.186
exonTestability	0.024	0.002	0.025
geneID	0.210	0.038	0.249
geneList	0.006	0.000	0.005
genePermuteScore	0.008	0.001	0.008
geneScore	0.005	0.001	0.005
geneSetDescs	0.004	0.001	0.004
geneSetNames	0.003	0.000	0.003
geneSetSize	0.003	0.000	0.003
geneTestability	0.032	0.001	0.033
genpermuteMat	10.038	0.043	10.081
getGeneCount	0.022	0.001	0.023
label	0.015	0.001	0.015
loadExonCountData	0.336	0.006	0.342
loadGenesets	1.219	0.011	3.587
newGeneSets	0.003	0.000	0.003
newReadCountSet	0.091	0.001	0.092
normFactor	10.948	0.025	10.975
plotES	2.601	0.008	2.609
plotGeneScore	0.126	0.005	0.133
plotSig	2.466	0.006	2.472
plotSigGeneSet	2.489	0.011	2.500
rankCombine	0.011	0.001	0.011
runDESeq	0.135	0.002	0.136
runSeqGSEA	17.951	0.165	25.119
scoreNormalization	11.088	0.033	11.121
size	0.003	0.000	0.003
subsetByGenes	0.036	0.000	0.037
topDEGenes	1.861	0.023	1.884
topDSExons	10.655	0.031	10.687
topDSGenes	10.674	0.030	10.704
topGeneSets	2.463	0.002	2.466
writeScores	0.007	0.001	0.008
writeSigGeneSet	2.665	0.004	2.670