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Package 468/658HostnameOS / ArchBUILDCHECKBUILD BIN
PGSEA 1.33.0
Karl Dykema
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PGSEA
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: PGSEA
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PGSEA_1.33.0.tar.gz
StartedAt: 2013-03-25 04:01:02 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:04:54 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 231.6 seconds
RetCode: 0
Status:  OK 
CheckDir: PGSEA.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/PGSEA.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.33.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'PGSEA' can be installed ... [14s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
aggregateExprs: warning in mget(ids, env = Env, ifnotfound = NA):
  partial argument match of 'env' to 'envir'
* 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 ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [88s/88s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
go2smc 71.708  3.074  74.939
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/PGSEA.Rcheck/00check.log'
for details.

PGSEA.Rcheck/00install.out:

* installing *source* package 'PGSEA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'PGSEA.Rnw' 
   'PGSEA2.Rnw' 
** testing if installed package can be loaded
* DONE (PGSEA)

PGSEA.Rcheck/PGSEA-Ex.timings:

nameusersystemelapsed
GOLUBmcs0.1280.0140.144
PGSEA1.1690.1311.306
VAIgsc1.5760.0921.673
VAImcs0.2940.0200.314
aggregateExprs0.5460.0650.623
convertSmc0.0120.0080.020
editSmc0.0700.0150.085
go2smc71.708 3.07474.939
kegg2smc1.1030.0481.151
nbEset0.1950.0150.210
readGmt0.0840.0140.101
readSmc0.0820.0160.099
scanSmc0.0360.0150.051
smcPlot0.6250.1250.754
writeGmt0.0540.0120.068
writeSmc0.0780.0160.095