BioC 3.1: CHECK report for SeqGSEA on morelia

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 06:12:28 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 06:16:03 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 215.2 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 (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 ‘1.8.1’
* 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 ... [8s/9s] 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 ... [107s/121s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         13.320  0.351  20.936
scoreNormalization  7.782  0.878   8.663
normFactor          7.438  0.839   8.278
DSresultGeneTable   7.491  0.261   7.771
DSresultExonTable   7.124  0.241   7.367
DSpermutePval       6.997  0.303   7.302
topDSGenes          6.773  0.409   7.183
genpermuteMat       6.519  0.234   6.753
topDSExons          6.335  0.228   6.563
DSpermute4GSEA      6.351  0.177   6.529
* 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	0.172	0.011	0.184
DENBStatPermut4GSEA	0.782	0.010	0.792
DENBTest	0.649	0.006	0.656
DEpermutePval	0.812	0.060	0.872
DSpermute4GSEA	6.351	0.177	6.529
DSpermutePval	6.997	0.303	7.302
DSresultExonTable	7.124	0.241	7.367
DSresultGeneTable	7.491	0.261	7.771
GSEAresultTable	1.635	0.007	1.642
GSEnrichAnalyze	1.562	0.006	1.567
ReadCountSet-class	0.002	0.000	0.002
SeqGeneSet-class	0.002	0.001	0.002
calES	0.006	0.001	0.006
calES.perm	1.819	0.279	2.098
convertEnsembl2Symbol	0.140	0.011	2.438
convertSymbol2Ensembl	0.110	0.007	2.432
counts-methods	0.017	0.001	0.018
estiExonNBstat	0.766	0.022	0.789
estiGeneNBstat	0.699	0.005	0.704
exonID	0.110	0.042	0.151
exonTestability	0.016	0.000	0.016
geneID	0.103	0.024	0.127
geneList	0.004	0.000	0.003
genePermuteScore	0.005	0.000	0.005
geneScore	0.002	0.001	0.003
geneSetDescs	0.002	0.000	0.002
geneSetNames	0.002	0.001	0.002
geneSetSize	0.001	0.000	0.002
geneTestability	0.018	0.000	0.018
genpermuteMat	6.519	0.234	6.753
getGeneCount	0.025	0.000	0.025
label	0.019	0.000	0.020
loadExonCountData	0.671	0.007	0.678
loadGenesets	0.887	0.017	3.181
newGeneSets	0.002	0.000	0.002
newReadCountSet	0.119	0.014	0.133
normFactor	7.438	0.839	8.278
plotES	1.805	0.014	1.818
plotGeneScore	0.210	0.002	0.216
plotSig	2.180	0.232	2.414
plotSigGeneSet	1.528	0.002	1.532
rankCombine	0.007	0.000	0.007
runDESeq	0.086	0.000	0.087
runSeqGSEA	13.320	0.351	20.936
scoreNormalization	7.782	0.878	8.663
size	0.003	0.001	0.003
subsetByGenes	0.042	0.002	0.044
topDEGenes	1.538	0.149	1.687
topDSExons	6.335	0.228	6.563
topDSGenes	6.773	0.409	7.183
topGeneSets	1.566	0.004	1.569
writeScores	0.005	0.000	0.006
writeSigGeneSet	1.522	0.003	1.524