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Package 151/419HostnameOS / ArchBUILDCHECKBUILD BIN
GeneAnswers 1.6.0
Gang Feng and Pan Du
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/GeneAnswers
Last Changed Rev: 50293 / Revision: 54281
Last Changed Date: 2010-10-17 22:34:23 -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 

Summary

Package: GeneAnswers
Version: 1.6.0
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings GeneAnswers_1.6.0.tar.gz
StartedAt: 2011-03-31 06:00:07 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 06:06:53 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 406.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GeneAnswers.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/GeneAnswers.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneAnswers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneAnswers’ version ‘1.6.0’
* 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
  ‘/loc/home/biocbuild/bbs-2.7-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
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneAnswers)

GeneAnswers.Rcheck/GeneAnswers-Ex.timings:

nameusersystemelapsed
DO0.3240.0160.341
DOLite0.0480.0000.050
DOLiteTerm0.0040.0000.003
GeneAnswers-class20.393 0.44421.070
GeneAnswers-package15.729 0.09215.936
buildNet15.021 0.10015.133
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.0560.0040.140
drawTable1.4440.0121.455
entrez2caBIO000
geneAnnotationHeatmap000
geneAnswersBuilder15.929 0.12016.061
geneAnswersChartPlots17.313 0.11617.494
geneAnswersConceptNet15.893 0.08015.978
geneAnswersConceptRelation15.817 0.16415.978
geneAnswersConcepts15.993 0.12016.119
geneAnswersHeatmap15.541 0.09615.634
geneAnswersHomoMapping13.849 0.11613.961
geneAnswersReadable25.774 0.20426.138
geneAnswersSort15.633 0.08015.714
geneConceptNet0.0000.0000.001
geneFunSummarize8.840.529.43
getCategoryList0.3120.0080.380
getCategoryTerms0.1120.0000.124
getConceptTable1.4280.0121.455
getConnectedGraph13.937 0.14814.122
getDOLiteTerms0.0080.0000.007
getGOList6.6640.1648.648
getHomoGeneIDs0.1770.0080.246
getMultiLayerGraphIDs18.369 0.08818.531
getNextGOIDs0.0480.0040.057
getPATHList0.1240.0000.122
getPATHTerms0.0360.0040.041
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs0.0000.0000.001
getSymbols0.0440.0000.055
getTotalGeneNumber0.1760.0000.190
getcaBIOPATHList0.0040.0000.001
getcaBIOPATHTerms0.0000.0000.001
groupReport7.7320.0367.781
humanExpr0.0080.0000.006
humanGeneInput0.0040.0000.004
mouseExpr0.0080.0000.006
mouseGeneInput0.0040.0000.004
plotGeneFunSummary3.3240.0003.323
plotGraph8.6330.5129.141
plotOntologyGraph6.8040.6127.423
sampleGroupsData0.0680.0280.095
saveGeneFunSummary1.7120.0841.796
searchEntrez000
simplifyGeneFunSummary1.8730.0001.874
topCategory000
topCategoryGenes000
topDOLite000
topDOLiteGenes0.0000.0040.001
topGO0.0000.0000.001
topGOGenes0.0000.0000.001
topPATH0.0000.0000.001
topPATHGenes000
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000