Package: PGSEA

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PGSEA_1.28.0.tar.gz

StartedAt: 2012-03-24 03:11:45 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:14:13 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 148.7 seconds

RetCode: 0

Status:  OK

CheckDir: PGSEA.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/PGSEA.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.28.0'
* 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 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 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 sizes of PDF files under 'inst/doc' ... OK
* 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	0.118	0.009	0.132
PGSEA	1.156	0.156	1.338
VAIgsc	1.900	0.065	1.972
VAImcs	0.366	0.017	0.389
aggregateExprs	0.609	0.041	0.668
convertSmc	0.000	0.000	0.001
editSmc	0.241	0.004	0.247
go2smc	0.002	0.001	0.003
kegg2smc	0.002	0.001	0.002
nbEset	0.098	0.005	0.180
readGmt	0.064	0.004	0.067
readSmc	0.066	0.005	0.081
scanSmc	0.025	0.002	0.027
smcPlot	1.261	0.154	1.493
writeGmt	0.056	0.004	0.061
writeSmc	0.057	0.003	0.060