BioC 3.2: CHECK report for SeqGSEA on linux1.bioconductor.org

Package: SeqGSEA

Version: 1.10.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.10.0.tar.gz

StartedAt: 2015-10-27 08:01:43 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:05:38 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 235.1 seconds

RetCode: 0

Status:  OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [9s/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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [142s/144s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         19.242  0.032  20.540
DSresultGeneTable  12.923  0.004  12.944
normFactor         11.081  0.004  11.094
DSpermutePval      10.976  0.008  11.000
topDSExons          9.981  0.004   9.992
DSresultExonTable   9.897  0.016   9.922
scoreNormalization  9.896  0.008   9.907
DSpermute4GSEA      9.823  0.016   9.844
genpermuteMat       9.796  0.008   9.821
topDSGenes          9.172  0.000   9.178
* 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
  ‘/home/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	0.380	0.004	0.385
DENBStatPermut4GSEA	0.786	0.000	0.788
DENBTest	1.011	0.008	1.019
DEpermutePval	0.604	0.000	0.605
DSpermute4GSEA	9.823	0.016	9.844
DSpermutePval	10.976	0.008	11.000
DSresultExonTable	9.897	0.016	9.922
DSresultGeneTable	12.923	0.004	12.944
GSEAresultTable	1.978	0.004	1.983
GSEnrichAnalyze	2.352	0.004	2.362
ReadCountSet-class	0.000	0.004	0.002
SeqGeneSet-class	0.000	0.000	0.001
calES	0.006	0.000	0.006
calES.perm	1.487	0.000	1.487
convertEnsembl2Symbol	0.081	0.000	0.419
convertSymbol2Ensembl	0.072	0.000	0.460
counts-methods	0.011	0.000	0.011
estiExonNBstat	0.822	0.000	0.822
estiGeneNBstat	0.817	0.000	0.818
exonID	0.044	0.012	0.057
exonTestability	0.016	0.000	0.016
geneID	0.054	0.016	0.071
geneList	0.003	0.000	0.004
genePermuteScore	0.002	0.004	0.005
geneScore	0.003	0.000	0.002
geneSetDescs	0.002	0.000	0.002
geneSetNames	0.002	0.000	0.001
geneSetSize	0.002	0.000	0.002
geneTestability	0.022	0.000	0.021
genpermuteMat	9.796	0.008	9.821
getGeneCount	0.018	0.000	0.018
label	0.011	0.000	0.011
loadExonCountData	0.304	0.004	0.308
loadGenesets	1.141	0.000	1.503
newGeneSets	0.002	0.000	0.002
newReadCountSet	0.057	0.000	0.058
normFactor	11.081	0.004	11.094
plotES	2.051	0.012	2.067
plotGeneScore	0.083	0.000	0.083
plotSig	2.195	0.000	2.195
plotSigGeneSet	1.583	0.000	1.583
rankCombine	0.003	0.004	0.007
runDESeq	0.09	0.00	0.09
runSeqGSEA	19.242	0.032	20.540
scoreNormalization	9.896	0.008	9.907
size	0.002	0.000	0.002
subsetByGenes	0.026	0.000	0.027
topDEGenes	1.649	0.000	1.650
topDSExons	9.981	0.004	9.992
topDSGenes	9.172	0.000	9.178
topGeneSets	1.713	0.000	1.723
writeScores	0.005	0.004	0.008
writeSigGeneSet	2.545	0.000	2.549