BioC 2.12: CHECK report for GeneExpressionSignature on petty

Package: GeneExpressionSignature

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneExpressionSignature_1.6.0.tar.gz

StartedAt: 2013-10-08 22:27:52 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:31:43 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 231.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneExpressionSignature.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneExpressionSignature.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneExpressionSignature/DESCRIPTION' ... OK
* this is package 'GeneExpressionSignature' 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 'GeneExpressionSignature' can be installed ... [16s/16s] WARNING
Found the following significant warnings:
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
See '/Users/biocbuild/bbs-2.12-bioc/meat/GeneExpressionSignature.Rcheck/00install.out' for details.
* 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
* 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 ... OK
* 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 examples ... [81s/82s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ScoreGSEA         20.905  2.277  23.455
SignatureDistance 19.605  2.309  22.143
ScorePGSEA        13.837  1.763  15.782
RankMerging        9.881  0.627  10.587
* 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

WARNING: There was 1 warning.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GeneExpressionSignature.Rcheck/00check.log'
for details.

* installing *source* package 'GeneExpressionSignature' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'KEGG.db' was built under R version 3.1.0
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'KEGG.db' was built under R version 3.1.0
* DONE (GeneExpressionSignature)

name	user	system	elapsed
RankMerging	9.881	0.627	10.587
ScoreGSEA	20.905	2.277	23.455
ScorePGSEA	13.837	1.763	15.782
SignatureDistance	19.605	2.309	22.143
exampleSet	0.461	0.034	0.506
getRLs	1.580	0.070	1.661