Package: PGSEA

Version: 1.25.1

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings PGSEA_1.25.1.tar.gz

StartedAt: 2011-02-13 20:59:31 -0800 (Sun, 13 Feb 2011)

EndedAt: 2011-02-13 21:00:22 -0800 (Sun, 13 Feb 2011)

EllapsedTime: 50.9 seconds

RetCode: 0

Status:  OK

CheckDir: PGSEA.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/PGSEA.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PGSEA' version '1.25.1'
* 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 package directory ... OK
* checking for portable file names ... 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' calls not declared from:
  GO KEGG annaffy
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* 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
  'openVignette()'. 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	0.06	0.00	0.07
PGSEA	1.01	0.01	1.03
VAIgsc	1.04	0.05	1.07
VAImcs	0.23	0.00	0.24
aggregateExprs	0.91	0.11	1.16
convertSmc	0	0	0
editSmc	0.03	0.00	0.04
go2smc	0.01	0.00	0.01
kegg2smc	0	0	0
nbEset	0.06	0.00	0.06
readGmt	0.07	0.00	0.07
readSmc	0.03	0.00	0.03
scanSmc	0.01	0.02	0.03
smcPlot	1.02	0.01	1.03
writeGmt	0.05	0.00	0.05
writeSmc	0.03	0.00	0.03