Package: PGSEA

Version: 1.28.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch PGSEA_1.28.0.tar.gz

StartedAt: 2012-01-09 04:51:58 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 04:53:49 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 110.9 seconds

RetCode: 0

Status:  OK

CheckDir: PGSEA.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/PGSEA.Rcheck'
* using R version 2.14.1 (2011-12-22)
* 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 '1.28.0'
* 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 whether package 'PGSEA' can be installed ... OK
* checking installed package size ... 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 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 ... NOTE
'library' or 'require' calls not declared from:
  'GO' 'KEGG'
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
               old_size new_size compress
  GOLUBmcs.rda     94Kb     58Kb    bzip2
  VAIgsc.rda       14Kb     10Kb    bzip2
  VAImcs.rda       13Kb     10Kb    bzip2
  nbEset.rda      943Kb    843Kb       xz
* checking examples ... OK
* 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

* installing *source* package 'PGSEA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'PGSEA.Rnw' 
   'PGSEA2.Rnw' 
** testing if installed package can be loaded

* DONE (PGSEA)

name	user	system	elapsed
GOLUBmcs	0.06	0.02	0.08
PGSEA	1.09	0.03	1.67
VAIgsc	1.47	0.00	1.47
VAImcs	0.26	0.00	0.27
aggregateExprs	0.44	0.06	0.55
convertSmc	0	0	0
editSmc	0.03	0.00	0.03
go2smc	0.02	0.00	0.01
kegg2smc	0	0	0
nbEset	0.31	0.00	0.32
readGmt	0.03	0.02	0.04
readSmc	0.06	0.00	0.07
scanSmc	0.02	0.01	0.03
smcPlot	0.73	0.02	0.75
writeGmt	0.05	0.00	0.04
writeSmc	0.06	0.00	0.07