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

* 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

* 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)

name	user	system	elapsed
DO	0.708	0.017	0.741
DOLite	0.035	0.002	0.038
DOLiteTerm	0.005	0.001	0.005
DmIALite	0.088	0.002	0.091
GeneAnswers-class	30.247	2.325	33.031
GeneAnswers-package	26.762	1.609	28.456
HsIALite	0.279	0.004	0.283
MmIALite	0.017	0.002	0.019
RnIALite	0.010	0.001	0.011
buildNet	25.100	1.602	27.535
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0.000	0.000	0.001
chartPlots	0.032	0.009	0.385
drawTable	2.575	0.078	2.744
entrez2caBIO	0.001	0.000	0.001
geneAnnotationHeatmap	0.001	0.001	0.001
geneAnswersBuilder	25.491	1.535	27.375
geneAnswersChartPlots	25.322	1.578	27.536
geneAnswersConceptNet	24.399	1.558	26.552
geneAnswersConceptRelation	25.261	1.606	28.490
geneAnswersConcepts	25.113	1.600	28.460
geneAnswersHeatmap	25.003	1.600	27.908
geneAnswersHomoMapping	25.759	1.624	28.558
geneAnswersReadable	42.595	1.799	46.410
geneAnswersSort	25.733	1.655	27.777
geneConceptNet	0.000	0.001	0.001
geneFunSummarize	9.037	2.638	12.043
getCategoryList	0.482	0.040	0.597
getCategoryTerms	0.109	0.006	0.127
getConceptTable	2.612	0.053	2.694
getConnectedGraph	21.912	1.538	23.616
getDOLiteTerms	0.011	0.003	0.013
getGOList	12.498	1.718	20.511
getHomoGeneIDs	0.300	0.026	0.359
getMultiLayerGraphIDs	26.603	1.573	28.973
getNextGOIDs	0.077	0.004	0.089
getPATHList	0.217	0.003	0.269
getPATHTerms	0.060	0.003	0.075
getREACTOMEPATHList	0.000	0.001	0.001
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0.002	0.001	0.002
getSymbols	0.061	0.003	0.091
getTotalGeneNumber	0.300	0.034	0.411
getcaBIOPATHList	0.001	0.000	0.000
getcaBIOPATHTerms	0.001	0.001	0.000
groupReport	11.999	0.380	15.721
humanExpr	0.010	0.002	0.012
humanGeneInput	0.006	0.001	0.008
mouseExpr	0.010	0.002	0.019
mouseGeneInput	0.007	0.001	0.008
plotGeneFunSummary	2.280	0.822	3.531
plotGraph	9.687	2.598	12.422
plotOntologyGraph	7.484	2.846	11.421
sampleGroupsData	0.262	0.055	0.404
saveGeneFunSummary	1.875	0.678	2.700
searchEntrez	0.000	0.000	0.001
simplifyGeneFunSummary	1.896	0.816	2.786
topCategory	0.000	0.000	0.001
topCategoryGenes	0.001	0.001	0.001
topDOLITE	0	0	0
topDOLITEGenes	0.000	0.000	0.001
topGO	0.000	0.000	0.001
topGOGenes	0	0	0
topPATH	0.001	0.000	0.000
topPATHGenes	0.001	0.000	0.001
topREACTOME.PATH	0	0	0
topREACTOME.PATHGenes	0	0	0
topcaBIO.PATH	0	0	0