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Package 176/479HostnameOS / ArchBUILDCHECKBUILD BIN
GeneAnswers 1.9.0
Gang Feng , Pan Du and Tian Xia
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers
Last Changed Rev: 56090 / Revision: 56603
Last Changed Date: 2011-06-09 17:02:42 -0700 (Thu, 09 Jun 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GeneAnswers
Version: 1.9.0
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GeneAnswers_1.9.0.tar.gz
StartedAt: 2011-07-07 04:03:01 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:13:09 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 607.2 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneAnswers.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* 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 '1.9.0'
* 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 installed package size ... NOTE
  installed size is 37.8Mb
  sub-directories of 1Mb or more:
    data       1.5Mb
    doc        3.4Mb
    External  32.4Mb
* 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 ... 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 examples ... OK
* checking for unstated dependencies in vignettes ... OK
* 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

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 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 ...
*** tangling vignette sources ...
   'GeneAnswersCWAnnotation.Rnw' 
   'geneAnswers.Rnw' 
   'geneFunctionSummarize.Rnw' 
** testing if installed package can be loaded
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.

* DONE (GeneAnswers)

GeneAnswers.Rcheck/GeneAnswers-Ex.timings:

nameusersystemelapsed
DO0.540.010.56
DOLite0.030.000.04
DOLiteTerm000
DmIALite0.070.000.06
GeneAnswers-class22.93 0.7179.75
GeneAnswers-package22.24 0.3622.59
HsIALite0.170.000.17
MmIALite0.020.000.02
RnIALite0.010.000.02
buildNet22.74 0.5023.26
caBIO.PATHGenes000
caBIO2entrez000
categoryNet000
chartPlots0.030.010.20
drawTable1.840.002.05
entrez2caBIO000
geneAnnotationHeatmap000
geneAnswersBuilder20.77 0.5021.31
geneAnswersChartPlots21.42 0.4921.95
geneAnswersConceptNet20.83 0.4821.34
geneAnswersConceptRelation20.84 0.4521.30
geneAnswersConcepts22.33 0.5022.83
geneAnswersHeatmap22.59 0.4723.11
geneAnswersHomoMapping21.53 0.6122.18
geneAnswersReadable35.43 0.6637.49
geneAnswersSort20.86 0.6221.48
geneConceptNet000
geneFunSummarize6.780.467.47
getCategoryList0.230.011.09
getCategoryTerms0.080.000.13
getConceptTable1.810.031.84
getConnectedGraph20.05 0.5520.61
getDOLiteTerms0.010.000.02
getGOList10.65 0.5147.40
getHomoGeneIDs0.130.002.31
getMultiLayerGraphIDs22.45 0.6523.41
getNextGOIDs0.060.000.06
getPATHList0.140.000.14
getPATHTerms0.050.000.05
getREACTOMEPATHList000
getREACTOMEPATHTerms000
getSingleLayerGraphIDs000
getSymbols0.050.000.05
getTotalGeneNumber0.210.010.37
getcaBIOPATHList000
getcaBIOPATHTerms000
groupReport8.130.579.12
humanExpr0.020.000.02
humanGeneInput000
mouseExpr0.010.000.01
mouseGeneInput0.020.000.02
plotGeneFunSummary2.610.002.61
plotGraph8.340.328.65
plotOntologyGraph7.000.257.25
sampleGroupsData0.060.010.08
saveGeneFunSummary1.810.051.86
searchEntrez000
simplifyGeneFunSummary1.70.01.7
topCategory000
topCategoryGenes000
topDOLITE000
topDOLITEGenes000
topGO000
topGOGenes000
topPATH000
topPATHGenes000
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000