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: 2011-06-22 03:03:05 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 03:14:30 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 685.7 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) (2011-06-03 r56037)
* 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 37.5Mb
  sub-directories of 1Mb or more:
    data       1.5Mb
    doc        3.2Mb
    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’ ... 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

* 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	0.713	0.016	0.731
DOLite	0.038	0.002	0.040
DOLiteTerm	0.005	0.001	0.006
DmIALite	0.094	0.002	0.096
GeneAnswers-class	30.127	2.578	34.393
GeneAnswers-package	26.081	1.542	27.795
HsIALite	0.278	0.005	0.285
MmIALite	0.016	0.002	0.017
RnIALite	0.009	0.001	0.011
buildNet	24.819	1.610	27.197
caBIO.PATHGenes	0.001	0.000	0.001
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.033	0.007	0.127
drawTable	2.574	0.055	2.685
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0.001	0.000	0.001
geneAnswersBuilder	24.438	1.535	26.451
geneAnswersChartPlots	25.139	1.593	27.575
geneAnswersConceptNet	25.597	1.571	27.783
geneAnswersConceptRelation	24.638	1.582	27.207
geneAnswersConcepts	25.305	1.600	28.416
geneAnswersHeatmap	25.828	1.610	28.735
geneAnswersHomoMapping	25.726	1.585	27.792
geneAnswersReadable	42.647	1.901	46.573
geneAnswersSort	26.967	1.569	29.190
geneConceptNet	0.001	0.001	0.001
geneFunSummarize	8.702	2.546	11.602
getCategoryList	0.489	0.043	0.752
getCategoryTerms	0.116	0.007	0.142
getConceptTable	2.697	0.069	2.925
getConnectedGraph	23.019	1.544	24.934
getDOLiteTerms	0.011	0.003	0.013
getGOList	14.143	2.049	22.983
getHomoGeneIDs	0.317	0.029	0.383
getMultiLayerGraphIDs	24.588	1.823	27.304
getNextGOIDs	0.079	0.004	0.083
getPATHList	0.222	0.004	0.226
getPATHTerms	0.060	0.003	0.063
getREACTOMEPATHList	0.001	0.000	0.000
getREACTOMEPATHTerms	0.000	0.000	0.001
getSingleLayerGraphIDs	0.002	0.001	0.003
getSymbols	0.061	0.004	0.087
getTotalGeneNumber	0.292	0.037	0.510
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	12.457	0.391	13.109
humanExpr	0.010	0.001	0.012
humanGeneInput	0.006	0.002	0.008
mouseExpr	0.009	0.001	0.011
mouseGeneInput	0.006	0.002	0.007
plotGeneFunSummary	2.545	0.850	3.457
plotGraph	9.565	3.080	12.851
plotOntologyGraph	8.264	2.778	11.067
sampleGroupsData	0.260	0.054	0.315
saveGeneFunSummary	2.175	0.970	3.150
searchEntrez	0.000	0.001	0.001
simplifyGeneFunSummary	2.173	1.191	3.370
topCategory	0	0	0
topCategoryGenes	0.000	0.000	0.001
topDOLITE	0	0	0
topDOLITEGenes	0.001	0.000	0.001
topGO	0.000	0.000	0.001
topGOGenes	0.000	0.000	0.001
topPATH	0.000	0.000	0.001
topPATHGenes	0.000	0.000	0.001
topREACTOME.PATH	0.001	0.000	0.000
topREACTOME.PATHGenes	0	0	0
topcaBIO.PATH	0	0	0