BioC 2.12: CHECK report for SeqGSEA on moscato2

Package: SeqGSEA

Version: 1.0.2

Command: rm -rf SeqGSEA.buildbin-libdir && mkdir SeqGSEA.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SeqGSEA.buildbin-libdir SeqGSEA_1.0.2.tar.gz >SeqGSEA-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=SeqGSEA.buildbin-libdir --install="check:SeqGSEA-install.out" --force-multiarch --no-vignettes --timings SeqGSEA_1.0.2.tar.gz && mv SeqGSEA.buildbin-libdir/* SeqGSEA.Rcheck/ && rmdir SeqGSEA.buildbin-libdir

StartedAt: 2013-10-09 04:11:41 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:24:31 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 769.5 seconds

RetCode: 0

Status: OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/SeqGSEA.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SeqGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqGSEA' version '1.0.2'
* 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 whether package 'SeqGSEA' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for unstated dependencies in R code ... OK
* 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [269s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
DSresultExonTable  24.16   0.00   24.17
scoreNormalization 24.08   0.01   24.11
DSresultGeneTable  23.35   0.00   23.35
topDSExons         22.56   0.00   22.56
topDSGenes         22.53   0.00   22.52
DSpermutePval      22.33   0.00   22.32
genpermuteMat      22.01   0.00   22.02
normFactor         21.95   0.00   21.95
DSpermute4GSEA     19.25   0.01   19.27
** running examples for arch 'x64' ... [291s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
DSpermutePval      26.73   0.00   26.72
DSresultExonTable  26.35   0.00   26.35
scoreNormalization 25.79   0.02   25.84
topDSGenes         24.54   0.02   24.56
DSpermute4GSEA     23.95   0.01   23.98
normFactor         23.82   0.00   23.85
DSresultGeneTable  23.51   0.02   23.53
topDSExons         22.07   0.00   22.07
genpermuteMat      20.24   0.00   20.27
plotES              5.45   0.01    5.48
writeSigGeneSet     5.40   0.00    5.40
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/SeqGSEA.Rcheck/00check.log'
for details.


install for i386

* 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

install for x64

* installing *source* package 'SeqGSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqGSEA' as SeqGSEA_1.0.2.zip
* DONE (SeqGSEA)

BioC 2.12: CHECK report for SeqGSEA on moscato2

Summary

Command output