Package: PGSEA

Version: 1.25.3

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PGSEA_1.25.3.tar.gz

StartedAt: 2011-03-17 17:07:05 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:07:55 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 50.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: PGSEA.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/PGSEA.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'PGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PGSEA' version '1.25.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'PGSEA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... WARNING
Assignments in \usage in documentation object 'kegg2smc':
  smc <- kegg2smc(min = 1, max = 284, organism = "human")

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' calls not declared from:
  GO KEGG annaffy
* checking contents of 'data' directory ... WARNING
Files not of a type allowed in a 'data' directory:
  sample.gmt
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/PGSEA.Rcheck/00check.log'
for details

* installing *source* package 'PGSEA' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (PGSEA)

name	user	system	elapsed
GOLUBmcs	0.073	0.003	0.075
PGSEA	0.731	0.013	0.744
VAIgsc	1.519	0.016	1.535
VAImcs	0.294	0.015	0.309
aggregateExprs	1.145	0.035	1.192
convertSmc	0.000	0.000	0.001
editSmc	0.029	0.002	0.031
go2smc	0.003	0.001	0.003
kegg2smc	0.002	0.000	0.002
nbEset	0.063	0.002	0.066
readGmt	0.042	0.003	0.045
readSmc	0.039	0.003	0.041
scanSmc	0.021	0.001	0.022
smcPlot	0.794	0.012	0.805
writeGmt	0.039	0.003	0.042
writeSmc	0.039	0.002	0.042