BioC 3.2: CHECK report for SeqGSEA on zin1

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: 2016-04-23 05:19:13 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:25:34 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 381.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SeqGSEA.Rcheck

Warnings: 1

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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 3.2.4 Revised (2016-03-16 r70336)
* 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 ... [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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'SeqGeneSet,numeric,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [145s/272s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
runSeqGSEA            16.236  0.060  85.200
DSpermutePval         11.750  0.016  11.825
DSresultGeneTable     11.389  0.004  11.407
scoreNormalization    11.177  0.004  11.180
DSresultExonTable     11.121  0.000  11.229
topDSGenes            11.031  0.000  11.040
topDSExons            10.948  0.004  10.948
normFactor            10.882  0.000  10.875
genpermuteMat         10.218  0.024  10.249
DSpermute4GSEA        10.072  0.008  10.083
loadGenesets           1.192  0.008  20.412
convertEnsembl2Symbol  0.090  0.004  19.186
convertSymbol2Ensembl  0.082  0.004  19.313
* 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: 1 WARNING, 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	0.220	0.004	0.224
DENBStatPermut4GSEA	0.852	0.004	0.856
DENBTest	1.570	0.003	1.582
DEpermutePval	0.734	0.000	0.733
DSpermute4GSEA	10.072	0.008	10.083
DSpermutePval	11.750	0.016	11.825
DSresultExonTable	11.121	0.000	11.229
DSresultGeneTable	11.389	0.004	11.407
GSEAresultTable	1.830	0.012	1.840
GSEnrichAnalyze	1.863	0.000	1.865
ReadCountSet-class	0.002	0.000	0.002
SeqGeneSet-class	0.001	0.000	0.001
calES	0.008	0.000	0.008
calES.perm	1.906	0.008	1.918
convertEnsembl2Symbol	0.090	0.004	19.186
convertSymbol2Ensembl	0.082	0.004	19.313
counts-methods	0.013	0.000	0.014
estiExonNBstat	1.197	0.000	1.196
estiGeneNBstat	0.986	0.000	0.988
exonID	0.048	0.024	0.072
exonTestability	0.019	0.000	0.020
geneID	0.08	0.02	0.10
geneList	0.004	0.000	0.004
genePermuteScore	0.007	0.000	0.007
geneScore	0.004	0.000	0.003
geneSetDescs	0.003	0.000	0.003
geneSetNames	0.003	0.000	0.002
geneSetSize	0.002	0.000	0.002
geneTestability	0.025	0.000	0.025
genpermuteMat	10.218	0.024	10.249
getGeneCount	0.019	0.000	0.019
label	0.013	0.000	0.013
loadExonCountData	0.361	0.000	0.361
loadGenesets	1.192	0.008	20.412
newGeneSets	0.003	0.000	0.003
newReadCountSet	0.085	0.000	0.088
normFactor	10.882	0.000	10.875
plotES	2.106	0.004	2.113
plotGeneScore	0.094	0.000	0.094
plotSig	1.803	0.004	1.806
plotSigGeneSet	1.823	0.000	1.825
rankCombine	0.005	0.000	0.009
runDESeq	0.102	0.004	0.106
runSeqGSEA	16.236	0.060	85.200
scoreNormalization	11.177	0.004	11.180
size	0.002	0.000	0.003
subsetByGenes	0.033	0.000	0.032
topDEGenes	2.196	0.004	2.199
topDSExons	10.948	0.004	10.948
topDSGenes	11.031	0.000	11.040
topGeneSets	1.741	0.000	1.742
writeScores	0.006	0.000	0.007
writeSigGeneSet	1.809	0.000	1.813