Package: GeneAnswers

Version: 1.9.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings GeneAnswers_1.9.0.tar.gz

StartedAt: 2011-05-09 13:34:21 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:42:50 -0700 (Mon, 09 May 2011)

EllapsedTime: 508.8 seconds

RetCode: 0

Status:  OK

CheckDir: GeneAnswers.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-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 37.9Mb
  sub-directories of 1Mb or more:
    data       1.5Mb
    doc        3.6Mb
    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

* 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	0.71	0.00	0.70
DOLite	0.03	0.00	0.03
DOLiteTerm	0	0	0
DmIALite	0.08	0.00	0.08
GeneAnswers-class	24.53	0.63	35.33
GeneAnswers-package	20.69	0.28	21.00
HsIALite	0.25	0.00	0.25
MmIALite	0.02	0.00	0.01
RnIALite	0	0	0
buildNet	20.50	0.14	20.86
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.01	0.03	0.22
drawTable	1.86	0.03	1.97
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0	0	0
geneAnswersBuilder	21.14	0.14	21.31
geneAnswersChartPlots	20.70	0.16	20.95
geneAnswersConceptNet	20.83	0.16	21.10
geneAnswersConceptRelation	20.32	0.23	20.59
geneAnswersConcepts	21.04	0.14	21.27
geneAnswersHeatmap	20.69	0.16	20.95
geneAnswersHomoMapping	20.59	0.14	20.94
geneAnswersReadable	30.91	0.45	31.83
geneAnswersSort	20.92	0.24	21.28
geneConceptNet	0	0	0
geneFunSummarize	6.77	0.23	7.01
getCategoryList	0.23	0.03	0.41
getCategoryTerms	0.08	0.00	0.11
getConceptTable	1.87	0.00	1.89
getConnectedGraph	18.27	0.17	18.51
getDOLiteTerms	0	0	0
getGOList	10.82	0.27	23.19
getHomoGeneIDs	0.14	0.03	0.33
getMultiLayerGraphIDs	19.16	0.06	19.53
getNextGOIDs	0.03	0.02	0.04
getPATHList	0.14	0.00	0.14
getPATHTerms	0.03	0.00	0.04
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0	0	0
getSymbols	0.04	0.00	0.06
getTotalGeneNumber	0.21	0.00	0.30
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	7.18	0.44	7.79
humanExpr	0.00	0.01	0.02
humanGeneInput	0	0	0
mouseExpr	0.01	0.00	0.01
mouseGeneInput	0	0	0
plotGeneFunSummary	1.47	0.02	1.49
plotGraph	7.14	0.19	7.33
plotOntologyGraph	5.81	0.20	6.01
sampleGroupsData	0.03	0.03	0.06
saveGeneFunSummary	1.39	0.02	1.41
searchEntrez	0	0	0
simplifyGeneFunSummary	1.49	0.01	1.51
topCategory	0	0	0
topCategoryGenes	0	0	0
topDOLITE	0	0	0
topDOLITEGenes	0.01	0.00	0.02
topGO	0	0	0
topGOGenes	0	0	0
topPATH	0	0	0
topPATHGenes	0	0	0
topREACTOME.PATH	0	0	0
topREACTOME.PATHGenes	0	0	0
topcaBIO.PATH	0	0	0