Package: GeneAnswers

Version: 1.9.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GeneAnswers_1.9.0.tar.gz

StartedAt: 2011-05-09 12:30:26 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:38:47 -0700 (Mon, 09 May 2011)

EllapsedTime: 500.4 seconds

RetCode: 0

Status:  OK

CheckDir: GeneAnswers.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GeneAnswers.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-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 37.9Mb
  sub-directories of 1Mb or more:
    External  32.4Mb
    data       1.5Mb
    doc        3.6Mb
* 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 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	0.792	0.004	0.799
DOLite	0.020	0.000	0.021
DOLiteTerm	0.004	0.000	0.004
DmIALite	0.048	0.000	0.046
GeneAnswers-class	27.606	0.472	28.096
GeneAnswers-package	19.573	0.120	19.695
HsIALite	0.136	0.000	0.137
MmIALite	0.008	0.000	0.009
RnIALite	0.004	0.000	0.005
buildNet	19.185	0.232	19.464
caBIO.PATHGenes	0	0	0
caBIO2entrez	0.000	0.004	0.000
categoryNet	0	0	0
chartPlots	0.248	0.020	0.302
drawTable	1.572	0.012	1.589
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0.000	0.000	0.001
geneAnswersBuilder	21.881	0.216	22.097
geneAnswersChartPlots	22.046	0.248	22.419
geneAnswersConceptNet	19.981	0.344	20.325
geneAnswersConceptRelation	20.801	0.192	20.999
geneAnswersConcepts	21.078	0.180	21.430
geneAnswersHeatmap	21.033	0.176	21.317
geneAnswersHomoMapping	20.581	0.132	20.731
geneAnswersReadable	36.615	0.160	37.169
geneAnswersSort	21.313	0.240	21.569
geneConceptNet	0	0	0
geneFunSummarize	7.584	0.660	8.262
getCategoryList	0.256	0.016	0.285
getCategoryTerms	0.056	0.012	0.068
getConceptTable	1.573	0.024	1.594
getConnectedGraph	18.813	0.136	18.953
getDOLiteTerms	0.004	0.004	0.008
getGOList	10.024	0.196	10.494
getHomoGeneIDs	0.144	0.016	0.160
getMultiLayerGraphIDs	22.622	0.236	22.973
getNextGOIDs	0.044	0.000	0.054
getPATHList	0.112	0.000	0.121
getPATHTerms	0.028	0.000	0.035
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0.000	0.000	0.001
getSingleLayerGraphIDs	0.000	0.000	0.001
getSymbols	0.032	0.004	0.035
getTotalGeneNumber	0.200	0.004	0.208
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	8.076	0.092	8.235
humanExpr	0.008	0.000	0.008
humanGeneInput	0.004	0.000	0.007
mouseExpr	0.008	0.000	0.011
mouseGeneInput	0.004	0.004	0.006
plotGeneFunSummary	2.368	0.020	2.389
plotGraph	9.413	0.704	10.116
plotOntologyGraph	8.153	0.728	8.887
sampleGroupsData	0.076	0.024	0.100
saveGeneFunSummary	2.092	0.116	2.233
searchEntrez	0	0	0
simplifyGeneFunSummary	1.920	0.000	1.969
topCategory	0	0	0
topCategoryGenes	0	0	0
topDOLITE	0	0	0
topDOLITEGenes	0	0	0
topGO	0	0	0
topGOGenes	0	0	0
topPATH	0	0	0
topPATHGenes	0	0	0
topREACTOME.PATH	0.000	0.000	0.001
topREACTOME.PATHGenes	0	0	0
topcaBIO.PATH	0	0	0