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Package 151/419HostnameOS / ArchBUILDCHECKBUILD BIN
GeneAnswers 1.6.0
Gang Feng and Pan Du
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/GeneAnswers
Last Changed Rev: 50293 / Revision: 54588
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 

Summary

Package: GeneAnswers
Version: 1.6.0
Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings GeneAnswers_1.6.0.tar.gz
StartedAt: 2011-04-07 10:18:59 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 10:28:16 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 556.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GeneAnswers.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
  'D:/biocbld/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
Warning in fun(...) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneAnswers)

GeneAnswers.Rcheck/GeneAnswers-Ex.timings:

nameusersystemelapsed
DO0.360.000.36
DOLite0.070.000.07
DOLiteTerm000
GeneAnswers-class18.55 0.7057.40
GeneAnswers-package16.70 0.5217.21
buildNet16.14 0.3316.47
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.010.000.02
drawTable1.740.032.12
entrez2caBIO000
geneAnnotationHeatmap000
geneAnswersBuilder17.93 0.2318.21
geneAnswersChartPlots18.88 0.3219.22
geneAnswersConceptNet18.01 0.3718.40
geneAnswersConceptRelation17.14 0.2517.40
geneAnswersConcepts16.73 0.3317.08
geneAnswersHeatmap17.46 0.2717.78
geneAnswersHomoMapping18.23 0.3918.63
geneAnswersReadable30.35 0.7032.26
geneAnswersSort17.64 0.6118.25
geneConceptNet000
geneFunSummarize8.030.368.40
getCategoryList0.250.001.17
getCategoryTerms0.070.000.07
getConceptTable1.750.011.79
getConnectedGraph16.29 0.3316.64
getDOLiteTerms0.000.020.02
getGOList 7.88 0.1731.59
getHomoGeneIDs0.090.002.14
getMultiLayerGraphIDs19.89 0.4420.82
getNextGOIDs0.040.000.05
getPATHList0.140.000.14
getPATHTerms0.050.000.05
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs000
getSymbols0.040.000.06
getTotalGeneNumber0.170.010.28
getcaBIOPATHList000
getcaBIOPATHTerms000
groupReport7.560.558.64
humanExpr000
humanGeneInput0.010.000.02
mouseExpr000
mouseGeneInput0.000.010.01
plotGeneFunSummary2.610.022.63
plotGraph8.700.389.09
plotOntologyGraph7.050.517.56
sampleGroupsData0.050.030.08
saveGeneFunSummary1.830.031.86
searchEntrez000
simplifyGeneFunSummary2.110.022.13
topCategory000
topCategoryGenes000
topDOLite000
topDOLiteGenes000
topGO000
topGOGenes000
topPATH000
topPATHGenes000
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000