BioC 3.2: CHECK report for SeqGSEA on oaxaca

Package: SeqGSEA

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.10.0.tar.gz

StartedAt: 2015-10-27 07:49:50 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:53:59 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 248.2 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_1.10.0.tar.gz
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* 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 ‘1.10.0’
* 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 ... [10s/10s] 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 ... [129s/143s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         17.128  0.201  24.368
normFactor          9.368  0.153   9.528
DSresultGeneTable   9.250  0.068   9.326
scoreNormalization  8.844  0.167   9.015
topDSGenes          8.833  0.075   8.913
topDSExons          8.665  0.239   8.907
DSpermute4GSEA      8.367  0.250   8.622
DSpermutePval       8.249  0.266   8.517
DSresultExonTable   8.361  0.117   8.481
genpermuteMat       7.591  0.090   7.685
* 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	0.386	0.007	0.393
DENBStatPermut4GSEA	1.052	0.018	1.070
DENBTest	0.834	0.016	0.851
DEpermutePval	0.941	0.010	0.951
DSpermute4GSEA	8.367	0.250	8.622
DSpermutePval	8.249	0.266	8.517
DSresultExonTable	8.361	0.117	8.481
DSresultGeneTable	9.250	0.068	9.326
GSEAresultTable	2.397	0.006	2.403
GSEnrichAnalyze	2.160	0.004	2.165
ReadCountSet-class	0.002	0.000	0.003
SeqGeneSet-class	0.002	0.001	0.003
calES	0.009	0.001	0.010
calES.perm	2.263	0.009	2.273
convertEnsembl2Symbol	0.129	0.006	2.585
convertSymbol2Ensembl	0.132	0.006	2.309
counts-methods	0.017	0.001	0.018
estiExonNBstat	0.785	0.010	0.797
estiGeneNBstat	0.830	0.007	0.837
exonID	0.091	0.031	0.122
exonTestability	0.017	0.001	0.017
geneID	0.114	0.026	0.140
geneList	0.003	0.000	0.003
genePermuteScore	0.004	0.001	0.005
geneScore	0.005	0.000	0.005
geneSetDescs	0.003	0.001	0.004
geneSetNames	0.002	0.000	0.002
geneSetSize	0.002	0.001	0.002
geneTestability	0.018	0.000	0.018
genpermuteMat	7.591	0.090	7.685
getGeneCount	0.025	0.001	0.025
label	0.017	0.000	0.017
loadExonCountData	0.664	0.007	0.670
loadGenesets	1.326	0.017	3.605
newGeneSets	0.004	0.000	0.004
newReadCountSet	0.119	0.000	0.120
normFactor	9.368	0.153	9.528
plotES	2.237	0.013	2.249
plotGeneScore	0.116	0.003	0.128
plotSig	2.368	0.008	2.375
plotSigGeneSet	2.303	0.006	2.311
rankCombine	0.008	0.001	0.010
runDESeq	0.153	0.001	0.155
runSeqGSEA	17.128	0.201	24.368
scoreNormalization	8.844	0.167	9.015
size	0.002	0.000	0.003
subsetByGenes	0.028	0.001	0.029
topDEGenes	1.392	0.018	1.411
topDSExons	8.665	0.239	8.907
topDSGenes	8.833	0.075	8.913
topGeneSets	2.331	0.007	2.337
writeScores	0.008	0.000	0.009
writeSigGeneSet	2.647	0.007	2.657