BioC 3.2: CHECK report for SeqGSEA on oaxaca

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 03:47:35 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:52:36 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 301.0 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_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [11s/12s] 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
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’
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’
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 ... [155s/174s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         19.807  0.160  28.248
topDSExons         11.500  0.253  11.945
normFactor         11.142  0.039  11.986
topDSGenes         10.737  0.257  11.042
scoreNormalization 10.697  0.130  11.535
DSpermutePval      10.703  0.118  10.884
DSresultExonTable  10.682  0.091  10.836
DSresultGeneTable  10.616  0.085  10.830
genpermuteMat       9.794  0.039  10.144
DSpermute4GSEA      9.663  0.168  10.039
* 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	0.453	0.012	0.467
DENBStatPermut4GSEA	1.054	0.021	1.081
DENBTest	1.040	0.017	1.071
DEpermutePval	1.054	0.014	1.088
DSpermute4GSEA	9.663	0.168	10.039
DSpermutePval	10.703	0.118	10.884
DSresultExonTable	10.682	0.091	10.836
DSresultGeneTable	10.616	0.085	10.830
GSEAresultTable	2.713	0.016	2.735
GSEnrichAnalyze	2.909	0.007	2.922
ReadCountSet-class	0.002	0.001	0.003
SeqGeneSet-class	0.002	0.000	0.003
calES	0.009	0.002	0.010
calES.perm	2.647	0.005	2.844
convertEnsembl2Symbol	0.142	0.006	2.427
convertSymbol2Ensembl	0.135	0.005	2.432
counts-methods	0.017	0.001	0.018
estiExonNBstat	0.969	0.007	1.021
estiGeneNBstat	1.004	0.004	1.121
exonID	0.130	0.042	0.195
exonTestability	0.025	0.001	0.029
geneID	0.184	0.043	0.248
geneList	0.006	0.000	0.009
genePermuteScore	0.007	0.000	0.010
geneScore	0.005	0.000	0.005
geneSetDescs	0.003	0.001	0.004
geneSetNames	0.007	0.000	0.008
geneSetSize	0.003	0.000	0.004
geneTestability	0.030	0.001	0.033
genpermuteMat	9.794	0.039	10.144
getGeneCount	0.024	0.001	0.024
label	0.017	0.001	0.017
loadExonCountData	0.761	0.009	0.844
loadGenesets	1.401	0.010	3.857
newGeneSets	0.004	0.000	0.004
newReadCountSet	0.150	0.001	0.169
normFactor	11.142	0.039	11.986
plotES	2.969	0.013	2.997
plotGeneScore	0.127	0.004	0.139
plotSig	3.024	0.007	3.037
plotSigGeneSet	2.721	0.010	2.734
rankCombine	0.011	0.001	0.011
runDESeq	0.153	0.001	0.154
runSeqGSEA	19.807	0.160	28.248
scoreNormalization	10.697	0.130	11.535
size	0.003	0.000	0.003
subsetByGenes	0.043	0.001	0.044
topDEGenes	1.780	0.021	1.811
topDSExons	11.500	0.253	11.945
topDSGenes	10.737	0.257	11.042
topGeneSets	2.655	0.005	2.690
writeScores	0.009	0.000	0.009
writeSigGeneSet	2.670	0.004	2.678