BioC 3.0: CHECK report for SeqGSEA on oaxaca

Package: SeqGSEA

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SeqGSEA_1.6.0.tar.gz

StartedAt: 2015-04-10 03:17:51 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:23:46 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 354.8 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 --no-multiarch SeqGSEA_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.0’
* 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 ... [15s/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
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 ... [166s/185s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         20.283  0.357  28.694
normFactor         11.703  0.083  11.829
scoreNormalization 11.674  0.104  12.058
DSpermutePval      11.496  0.059  11.618
DSresultExonTable  11.422  0.053  11.513
DSresultGeneTable  11.414  0.037  11.471
topDSExons         11.247  0.114  11.416
topDSGenes         11.073  0.155  11.275
DSpermute4GSEA     10.464  0.058  11.738
genpermuteMat      10.168  0.080  10.350
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.478	0.008	0.487
DENBStatPermut4GSEA	1.451	0.018	1.540
DENBTest	0.948	0.014	1.083
DEpermutePval	1.147	0.007	1.291
DSpermute4GSEA	10.464	0.058	11.738
DSpermutePval	11.496	0.059	11.618
DSresultExonTable	11.422	0.053	11.513
DSresultGeneTable	11.414	0.037	11.471
GSEAresultTable	3.207	0.019	3.232
GSEnrichAnalyze	2.981	0.008	2.998
ReadCountSet-class	0.002	0.001	0.003
SeqGeneSet-class	0.002	0.000	0.003
calES	0.014	0.003	0.016
calES.perm	2.995	0.007	3.008
convertEnsembl2Symbol	1.313	0.007	3.863
convertSymbol2Ensembl	0.164	0.006	2.774
counts-methods	0.019	0.001	0.020
estiExonNBstat	1.046	0.013	1.062
estiGeneNBstat	1.200	0.014	1.236
exonID	0.131	0.039	0.170
exonTestability	0.028	0.001	0.029
geneID	0.177	0.043	0.220
geneList	0.006	0.000	0.007
genePermuteScore	0.012	0.002	0.014
geneScore	0.009	0.002	0.010
geneSetDescs	0.006	0.001	0.007
geneSetNames	0.005	0.001	0.006
geneSetSize	0.004	0.001	0.005
geneTestability	0.034	0.001	0.035
genpermuteMat	10.168	0.080	10.350
getGeneCount	0.027	0.001	0.034
label	0.018	0.001	0.021
loadExonCountData	0.786	0.011	0.818
loadGenesets	1.564	0.011	4.313
newGeneSets	0.003	0.000	0.004
newReadCountSet	0.125	0.001	0.132
normFactor	11.703	0.083	11.829
plotES	3.182	0.014	3.203
plotGeneScore	0.127	0.004	0.135
plotSig	2.922	0.009	2.944
plotSigGeneSet	3.001	0.009	3.019
rankCombine	0.020	0.004	0.022
runDESeq	0.174	0.002	0.176
runSeqGSEA	20.283	0.357	28.694
scoreNormalization	11.674	0.104	12.058
size	0.004	0.001	0.005
subsetByGenes	0.045	0.002	0.047
topDEGenes	1.863	0.021	1.892
topDSExons	11.247	0.114	11.416
topDSGenes	11.073	0.155	11.275
topGeneSets	2.892	0.008	2.915
writeScores	0.011	0.002	0.013
writeSigGeneSet	2.731	0.009	2.765