BioC 3.0: CHECK report for SeqGSEA on zin1

Package: SeqGSEA

Version: 1.6.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.6.0.tar.gz

StartedAt: 2015-04-10 04:16:11 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:21:16 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 305.4 seconds

RetCode: 0

Status:  OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.6.0’
* 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 ... [12s/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’
* 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 ... [161s/176s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         18.941  0.044  26.394
topDSExons         12.184  0.020  12.236
DSresultGeneTable  12.089  0.008  12.115
DSpermutePval      12.017  0.004  12.141
normFactor         11.989  0.012  12.034
DSresultExonTable  11.900  0.008  11.942
scoreNormalization 11.657  0.012  11.727
topDSGenes         11.597  0.008  11.628
genpermuteMat      11.056  0.016  11.107
DSpermute4GSEA     10.909  0.004  10.933
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-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	0.400	0.000	0.411
DENBStatPermut4GSEA	1.052	0.008	1.063
DENBTest	1.484	0.012	1.499
DEpermutePval	0.928	0.000	0.929
DSpermute4GSEA	10.909	0.004	10.933
DSpermutePval	12.017	0.004	12.141
DSresultExonTable	11.900	0.008	11.942
DSresultGeneTable	12.089	0.008	12.115
GSEAresultTable	2.400	0.004	2.406
GSEnrichAnalyze	2.380	0.004	2.415
ReadCountSet-class	0.000	0.004	0.002
SeqGeneSet-class	0.000	0.004	0.001
calES	0.012	0.000	0.013
calES.perm	2.380	0.000	2.381
convertEnsembl2Symbol	0.120	0.008	2.400
convertSymbol2Ensembl	0.116	0.008	2.408
counts-methods	0.012	0.000	0.016
estiExonNBstat	1.189	0.004	1.195
estiGeneNBstat	1.056	0.000	1.060
exonID	0.052	0.032	0.086
exonTestability	0.024	0.000	0.026
geneID	0.100	0.024	0.122
geneList	0.004	0.000	0.005
genePermuteScore	0.008	0.004	0.012
geneScore	0.008	0.000	0.008
geneSetDescs	0.004	0.004	0.005
geneSetNames	0.004	0.000	0.005
geneSetSize	0.008	0.000	0.005
geneTestability	0.028	0.000	0.030
genpermuteMat	11.056	0.016	11.107
getGeneCount	0.020	0.004	0.022
label	0.012	0.004	0.015
loadExonCountData	0.324	0.004	0.327
loadGenesets	1.108	0.000	3.762
newGeneSets	0.004	0.000	0.003
newReadCountSet	0.088	0.000	0.090
normFactor	11.989	0.012	12.034
plotES	2.892	0.004	2.900
plotGeneScore	0.096	0.012	0.109
plotSig	2.389	0.008	2.449
plotSigGeneSet	2.404	0.004	2.409
rankCombine	0.016	0.000	0.018
runDESeq	0.132	0.000	0.133
runSeqGSEA	18.941	0.044	26.394
scoreNormalization	11.657	0.012	11.727
size	0.004	0.000	0.004
subsetByGenes	0.040	0.000	0.039
topDEGenes	2.208	0.004	2.220
topDSExons	12.184	0.020	12.236
topDSGenes	11.597	0.008	11.628
topGeneSets	2.480	0.012	2.506
writeScores	0.004	0.004	0.012
writeSigGeneSet	2.625	0.004	2.635