Package: PGSEA

Version: 1.27.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PGSEA_1.27.0.tar.gz

StartedAt: 2011-07-07 05:00:44 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:02:20 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 95.8 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 2.14.0 Under development (unstable) (2011-06-22 r56208)
* 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 '1.27.0'
* 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 ... 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 tools::resaveRdaFiles() or R CMD build --resave-data
               old_size new_size compress
  GOLUBmcs.rda     94Kb     57Kb    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
Loading required package: AnnotationDbi
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")'.

Loading required package: DBI


** 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	0.158	0.006	0.164
PGSEA	1.075	0.152	1.269
VAIgsc	2.249	0.059	2.367
VAImcs	0.306	0.019	0.326
aggregateExprs	0.753	0.042	0.847
convertSmc	0.001	0.000	0.000
editSmc	0.043	0.003	0.046
go2smc	0.003	0.001	0.004
kegg2smc	0.003	0.001	0.004
nbEset	0.099	0.004	0.104
readGmt	0.052	0.003	0.056
readSmc	0.049	0.004	0.053
scanSmc	0.023	0.003	0.027
smcPlot	1.258	0.156	1.571
writeGmt	0.049	0.004	0.061
writeSmc	0.052	0.006	0.058