BioC 2.14: CHECK report for SeqGSEA on morelia

Package: SeqGSEA

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SeqGSEA_1.4.2.tar.gz

StartedAt: 2014-10-08 01:31:45 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:37:35 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 349.3 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_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.4.2’
* 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 ... [13s/13s] 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’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 binding for global variable ‘i’
DSpermute4GSEA : <anonymous>: no visible binding for global variable
  ‘i’
calES.perm: no visible binding for global variable ‘i’
calES.perm: no visible binding for global variable ‘j’
* 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 ... [156s/202s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         19.655  0.220  26.996
normFactor         10.853  0.080  10.943
topDSGenes         10.741  0.074  10.832
topDSExons         10.666  0.078  10.764
DSpermute4GSEA     10.528  0.106  10.664
DSresultGeneTable  10.534  0.072  10.614
scoreNormalization 10.404  0.069  10.489
DSpermutePval      10.377  0.047  10.441
DSresultExonTable   9.997  0.059  10.059
genpermuteMat       9.941  0.065  10.014
loadGenesets        1.319  0.015  35.298
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.453	0.007	0.473
DENBStatPermut4GSEA	1.284	0.019	1.305
DENBTest	1.067	0.014	1.081
DEpermutePval	1.194	0.012	1.209
DSpermute4GSEA	10.528	0.106	10.664
DSpermutePval	10.377	0.047	10.441
DSresultExonTable	9.997	0.059	10.059
DSresultGeneTable	10.534	0.072	10.614
GSEAresultTable	2.982	0.011	2.997
GSEnrichAnalyze	2.929	0.010	2.940
ReadCountSet-class	0.003	0.000	0.003
SeqGeneSet-class	0.001	0.000	0.002
calES	0.013	0.002	0.015
calES.perm	2.962	0.008	2.971
convertEnsembl2Symbol	0.204	0.008	2.444
convertSymbol2Ensembl	0.154	0.007	2.245
counts-methods	0.019	0.002	0.020
estiExonNBstat	0.979	0.020	0.999
estiGeneNBstat	0.973	0.004	0.976
exonID	0.129	0.039	0.167
exonTestability	0.024	0.001	0.025
geneID	0.157	0.034	0.191
geneList	0.007	0.001	0.006
genePermuteScore	0.013	0.002	0.015
geneScore	0.007	0.001	0.009
geneSetDescs	0.004	0.001	0.004
geneSetNames	0.005	0.001	0.006
geneSetSize	0.005	0.001	0.005
geneTestability	0.044	0.002	0.045
genpermuteMat	9.941	0.065	10.014
getGeneCount	0.032	0.001	0.032
label	0.016	0.001	0.017
loadExonCountData	0.952	0.013	0.968
loadGenesets	1.319	0.015	35.298
newGeneSets	0.003	0.001	0.004
newReadCountSet	0.121	0.000	0.121
normFactor	10.853	0.080	10.943
plotES	3.267	0.014	3.282
plotGeneScore	0.112	0.004	0.124
plotSig	2.769	0.008	2.779
plotSigGeneSet	3.140	0.013	3.158
rankCombine	0.020	0.003	0.023
runDESeq	0.230	0.002	0.232
runSeqGSEA	19.655	0.220	26.996
scoreNormalization	10.404	0.069	10.489
size	0.004	0.001	0.005
subsetByGenes	0.051	0.001	0.052
topDEGenes	2.061	0.019	2.083
topDSExons	10.666	0.078	10.764
topDSGenes	10.741	0.074	10.832
topGeneSets	2.805	0.009	2.817
writeScores	0.012	0.001	0.013
writeSigGeneSet	2.837	0.009	2.848