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Package 242/553HostnameOS / ArchBUILDCHECKBUILD BIN
GOstats 2.22.0
Bioconductor Package Maintainer
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/GOstats
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / 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: GOstats
Version: 2.22.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GOstats_2.22.0.tar.gz
StartedAt: 2012-09-24 00:26:37 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:29:51 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 193.3 seconds
RetCode: 0
Status:  OK 
CheckDir: GOstats.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/GOstats.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GOstats/DESCRIPTION' ... OK
* this is package 'GOstats' version '2.22.0'
* 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 'GOstats' 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 ... NOTE
File 'GOstats/R/zzz.R':
  .onAttach calls:
    require("Biobase")

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

GOGraph: warning in mget(newN, env = dataenv, ifnotfound = NA): partial
  argument match of 'env' to 'envir'
compCorrGraph: warning in as.matrix.csr(cB, nr = dim(cB)[1], nc =
  dim(cB)[2]): partial argument match of 'nr' to 'nrow'
compCorrGraph: warning in as.matrix.csr(cB, nr = dim(cB)[1], nc =
  dim(cB)[2]): partial argument match of 'nc' to 'ncol'
compGdist: warning in matrix(0, nr = nNodes, nc = nNodes): partial
  argument match of 'nr' to 'nrow'
compGdist: warning in matrix(0, nr = nNodes, nc = nNodes): partial
  argument match of 'nc' to 'ncol'
makeGOGraph: warning in mget(newN, env = dataenv, 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 ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'GSEABase' 'geneplotter' 'org.Hs.eg.db'
* 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/GOstats.Rcheck/00check.log'
for details.

GOstats.Rcheck/00install.out:

* installing *source* package 'GOstats' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GOstatsForUnsupportedOrganisms.Rnw' 
   'GOstatsHyperG.Rnw' 
   'GOvis.Rnw' 
** testing if installed package can be loaded

* DONE (GOstats)

GOstats.Rcheck/GOstats-Ex.timings:

nameusersystemelapsed
GOHyperG000
GOLeaves0.1630.0070.170
Ndists0.0540.0040.059
compCorrGraph0.2860.0140.317
compGdist0.3230.0090.333
idx2dimnames0.0310.0040.035
makeGOGraph1.3310.0701.409
notConn0.0410.0040.045
oneGOGraph0.7130.0300.744
probeSetSummary5.1390.2255.376
shortestPath2.4690.0382.514
simLL0.3770.0220.399
triadCensus0.0010.0000.000