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Package 314/444HostnameOS / ArchBUILDCHECKBUILD BIN
PGSEA 1.25.3
Karl Dykema
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PGSEA
Last Changed Rev: 52728 / Revision: 53825
Last Changed Date: 2011-02-15 09:32:09 -0800 (Tue, 15 Feb 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  ERROR  skipped  skipped 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ WARNINGS ] OK 

Summary

Package: PGSEA
Version: 1.25.3
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PGSEA_1.25.3.tar.gz
StartedAt: 2011-03-17 17:07:05 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 17:07:55 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 50.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: PGSEA.Rcheck
Warnings: 2

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/PGSEA.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* 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 '1.25.3'
* 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 ... WARNING
Assignments in \usage in documentation object 'kegg2smc':
  smc <- kegg2smc(min = 1, max = 284, organism = "human")

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' calls not declared from:
  GO KEGG annaffy
* checking contents of 'data' directory ... WARNING
Files not of a type allowed in a 'data' directory:
  sample.gmt
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/PGSEA.Rcheck/00check.log'
for details

PGSEA.Rcheck/00install.out:

* 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
  'browseVignettes()'. 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)

PGSEA.Rcheck/PGSEA-Ex.timings:

nameusersystemelapsed
GOLUBmcs0.0730.0030.075
PGSEA0.7310.0130.744
VAIgsc1.5190.0161.535
VAImcs0.2940.0150.309
aggregateExprs1.1450.0351.192
convertSmc0.0000.0000.001
editSmc0.0290.0020.031
go2smc0.0030.0010.003
kegg2smc0.0020.0000.002
nbEset0.0630.0020.066
readGmt0.0420.0030.045
readSmc0.0390.0030.041
scanSmc0.0210.0010.022
smcPlot0.7940.0120.805
writeGmt0.0390.0030.042
writeSmc0.0390.0020.042