BioC 3.3: CHECK report for SeqGSEA on morelia

Package: SeqGSEA

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.11.0.tar.gz

StartedAt: 2015-10-22 11:11:57 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 11:15:43 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 225.7 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_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SeqGSEA.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.11.0’
* 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 ... [8s/8s] 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’
Undefined global functions or variables:
  %do% %dopar% foreach i j 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/131s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         13.195  0.162  25.495
normFactor          7.956  0.094   8.217
DSresultGeneTable   7.947  0.093   8.240
scoreNormalization  7.810  0.167   8.125
DSresultExonTable   7.796  0.138   8.128
DSpermutePval       7.798  0.106   7.960
DSpermute4GSEA      7.185  0.214   7.531
genpermuteMat       7.189  0.104   7.471
topDSGenes          6.406  0.230   6.650
topDSExons          6.091  0.253   6.345
* 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-3.3-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	0.271	0.004	0.276
DENBStatPermut4GSEA	0.773	0.021	0.793
DENBTest	0.804	0.013	0.818
DEpermutePval	0.642	0.020	0.664
DSpermute4GSEA	7.185	0.214	7.531
DSpermutePval	7.798	0.106	7.960
DSresultExonTable	7.796	0.138	8.128
DSresultGeneTable	7.947	0.093	8.240
GSEAresultTable	1.701	0.003	1.705
GSEnrichAnalyze	1.909	0.003	1.914
ReadCountSet-class	0.002	0.001	0.002
SeqGeneSet-class	0.001	0.000	0.002
calES	0.005	0.001	0.006
calES.perm	2.168	0.003	2.172
convertEnsembl2Symbol	0.119	0.005	3.075
convertSymbol2Ensembl	0.106	0.006	4.809
counts-methods	0.017	0.001	0.018
estiExonNBstat	0.741	0.021	0.762
estiGeneNBstat	0.682	0.008	0.690
exonID	0.097	0.029	0.126
exonTestability	0.025	0.001	0.026
geneID	0.186	0.046	0.231
geneList	0.007	0.000	0.007
genePermuteScore	0.007	0.001	0.008
geneScore	0.005	0.001	0.005
geneSetDescs	0.003	0.000	0.003
geneSetNames	0.002	0.001	0.003
geneSetSize	0.003	0.000	0.004
geneTestability	0.030	0.001	0.031
genpermuteMat	7.189	0.104	7.471
getGeneCount	0.016	0.002	0.017
label	0.010	0.001	0.010
loadExonCountData	0.548	0.006	0.555
loadGenesets	1.061	0.009	3.710
newGeneSets	0.002	0.001	0.003
newReadCountSet	0.081	0.000	0.082
normFactor	7.956	0.094	8.217
plotES	1.935	0.011	1.947
plotGeneScore	0.087	0.002	0.093
plotSig	1.684	0.004	1.691
plotSigGeneSet	1.984	0.006	2.103
rankCombine	0.011	0.001	0.014
runDESeq	0.141	0.001	0.169
runSeqGSEA	13.195	0.162	25.495
scoreNormalization	7.810	0.167	8.125
size	0.003	0.000	0.003
subsetByGenes	0.029	0.000	0.029
topDEGenes	1.225	0.018	1.243
topDSExons	6.091	0.253	6.345
topDSGenes	6.406	0.230	6.650
topGeneSets	1.759	0.004	1.766
writeScores	0.005	0.001	0.005
writeSigGeneSet	1.662	0.005	1.668