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Package 154/436HostnameOS / ArchBUILDCHECKBUILD BIN
GeneAnswers 1.7.0
Gang Feng and Pan Du
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers
Last Changed Rev: 50295 / Revision: 53255
Last Changed Date: 2010-10-17 22:57:44 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK [ WARNINGS ] OK 

Summary

Package: GeneAnswers
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneAnswers_1.7.0.tar.gz
StartedAt: 2011-02-24 15:42:41 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 15:49:33 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 412.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GeneAnswers.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneAnswers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAnswers' version '1.7.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneAnswers' can be installed ... 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 ... NOTE
prepare_Rd: DO.Rd:32-34: Dropping empty section \references
prepare_Rd: geneFunSummarize.Rd:21-23: Dropping empty section \details
prepare_Rd: plotGeneFunSummary.Rd:30-32: Dropping empty section \details
prepare_Rd: plotOntologyGraph.Rd:28-30: Dropping empty section \details
prepare_Rd: saveGeneFunSummary.Rd:18-20: Dropping empty section \details
prepare_Rd: saveGeneFunSummary.Rd:24-26: Dropping empty section \references
prepare_Rd: simplifyGeneFunSummary.Rd:18-20: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  DmIALite HsIALite MmIALite RnIALite
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details

GeneAnswers.Rcheck/00install.out:

* installing *source* package 'GeneAnswers' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: bitops
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
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(...) : error in rgl_init
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneAnswers)

GeneAnswers.Rcheck/GeneAnswers-Ex.timings:

nameusersystemelapsed
DO0.5300.0080.538
DOLite0.0260.0010.028
DOLiteTerm0.0040.0010.004
GeneAnswers-class18.215 0.75518.971
GeneAnswers-package16.044 0.39616.442
buildNet15.904 0.40116.305
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.0310.0050.040
drawTable1.8050.0111.816
entrez2caBIO000
geneAnnotationHeatmap0.0010.0000.001
geneAnswersBuilder15.960 0.37616.337
geneAnswersChartPlots15.514 0.42515.939
geneAnswersConceptNet16.341 0.41716.758
geneAnswersConceptRelation16.225 0.39916.625
geneAnswersConcepts15.839 0.38916.229
geneAnswersHeatmap16.037 0.41516.452
geneAnswersHomoMapping16.500 0.39616.896
geneAnswersReadable27.339 0.50827.846
geneAnswersSort16.151 0.38516.536
geneConceptNet000
geneFunSummarize6.8090.7257.559
getCategoryList0.3780.0270.468
getCategoryTerms0.1030.0050.108
getConceptTable1.9370.0221.959
getConnectedGraph13.933 0.61814.551
getDOLiteTerms0.0080.0010.009
getGOList 7.190 0.75014.469
getHomoGeneIDs0.2300.0140.260
getMultiLayerGraphIDs14.648 0.56415.212
getNextGOIDs0.0530.0020.054
getPATHList0.1590.0020.161
getPATHTerms0.0400.0020.043
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs0.0010.0000.001
getSymbols0.0400.0020.043
getTotalGeneNumber0.1910.0070.199
getcaBIOPATHList000
getcaBIOPATHTerms000
groupReport10.586 0.35811.206
humanExpr0.0070.0010.008
humanGeneInput0.0040.0010.005
mouseExpr0.0070.0010.007
mouseGeneInput0.0040.0010.005
plotGeneFunSummary2.2710.1412.412
plotGraph7.9420.8928.834
plotOntologyGraph6.1790.8457.035
sampleGroupsData0.0620.0370.407
saveGeneFunSummary1.6780.1001.778
searchEntrez000
simplifyGeneFunSummary1.4130.0771.490
topCategory000
topCategoryGenes000
topDOLite0.0010.0000.000
topDOLiteGenes0.0000.0010.001
topGO000
topGOGenes000
topPATH0.0010.0000.001
topPATHGenes000
topREACTOME.PATH0.0000.0010.000
topREACTOME.PATHGenes0.0010.0000.000
topcaBIO.PATH000