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Package 170/462HostnameOS / ArchBUILDCHECKBUILD BIN
GeneAnswers 1.9.0
Gang Feng , Pan Du and Tian Xia
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 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 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: GeneAnswers
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneAnswers_1.9.0.tar.gz
StartedAt: 2011-05-09 14:39:54 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:51:10 -0700 (Mon, 09 May 2011)
EllapsedTime: 675.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneAnswers.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/GeneAnswers.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘1.9.0’
* 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 37.7Mb
  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 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 ... 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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘geneAnswers.pdf’ from 1.5Mb to 1.3Mb
  consider running tools::compactPDF() on these files
* 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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘GeneAnswersCWAnnotation.Rnw’ 
   ‘geneAnswers.Rnw’ 
   ‘geneFunctionSummarize.Rnw’ 
** testing if installed package can be loaded

* DONE (GeneAnswers)

GeneAnswers.Rcheck/GeneAnswers-Ex.timings:

nameusersystemelapsed
DO0.7080.0170.741
DOLite0.0350.0020.038
DOLiteTerm0.0050.0010.005
DmIALite0.0880.0020.091
GeneAnswers-class30.247 2.32533.031
GeneAnswers-package26.762 1.60928.456
HsIALite0.2790.0040.283
MmIALite0.0170.0020.019
RnIALite0.0100.0010.011
buildNet25.100 1.60227.535
caBIO.PATHGenes000
caBIO2entrez000
categoryNet0.0000.0000.001
chartPlots0.0320.0090.385
drawTable2.5750.0782.744
entrez2caBIO0.0010.0000.001
geneAnnotationHeatmap0.0010.0010.001
geneAnswersBuilder25.491 1.53527.375
geneAnswersChartPlots25.322 1.57827.536
geneAnswersConceptNet24.399 1.55826.552
geneAnswersConceptRelation25.261 1.60628.490
geneAnswersConcepts25.113 1.60028.460
geneAnswersHeatmap25.003 1.60027.908
geneAnswersHomoMapping25.759 1.62428.558
geneAnswersReadable42.595 1.79946.410
geneAnswersSort25.733 1.65527.777
geneConceptNet0.0000.0010.001
geneFunSummarize 9.037 2.63812.043
getCategoryList0.4820.0400.597
getCategoryTerms0.1090.0060.127
getConceptTable2.6120.0532.694
getConnectedGraph21.912 1.53823.616
getDOLiteTerms0.0110.0030.013
getGOList12.498 1.71820.511
getHomoGeneIDs0.3000.0260.359
getMultiLayerGraphIDs26.603 1.57328.973
getNextGOIDs0.0770.0040.089
getPATHList0.2170.0030.269
getPATHTerms0.0600.0030.075
getREACTOMEPATHList0.0000.0010.001
getREACTOMEPATHTerms000
getSingleLayerGraphIDs0.0020.0010.002
getSymbols0.0610.0030.091
getTotalGeneNumber0.3000.0340.411
getcaBIOPATHList0.0010.0000.000
getcaBIOPATHTerms0.0010.0010.000
groupReport11.999 0.38015.721
humanExpr0.0100.0020.012
humanGeneInput0.0060.0010.008
mouseExpr0.0100.0020.019
mouseGeneInput0.0070.0010.008
plotGeneFunSummary2.2800.8223.531
plotGraph 9.687 2.59812.422
plotOntologyGraph 7.484 2.84611.421
sampleGroupsData0.2620.0550.404
saveGeneFunSummary1.8750.6782.700
searchEntrez0.0000.0000.001
simplifyGeneFunSummary1.8960.8162.786
topCategory0.0000.0000.001
topCategoryGenes0.0010.0010.001
topDOLITE000
topDOLITEGenes0.0000.0000.001
topGO0.0000.0000.001
topGOGenes000
topPATH0.0010.0000.000
topPATHGenes0.0010.0000.001
topREACTOME.PATH000
topREACTOME.PATHGenes000
topcaBIO.PATH000