Package: GeneAnswers

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneAnswers_1.7.0.tar.gz

StartedAt: 2011-02-24 15:42:41 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 15:49:33 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 412.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneAnswers.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneAnswers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAnswers' version '1.7.0'
* 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 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 ... WARNING
Undocumented data sets:
  DmIALite HsIALite MmIALite RnIALite
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details

* 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
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(...) : error in rgl_init
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.530	0.008	0.538
DOLite	0.026	0.001	0.028
DOLiteTerm	0.004	0.001	0.004
GeneAnswers-class	18.215	0.755	18.971
GeneAnswers-package	16.044	0.396	16.442
buildNet	15.904	0.401	16.305
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.031	0.005	0.040
drawTable	1.805	0.011	1.816
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0.001	0.000	0.001
geneAnswersBuilder	15.960	0.376	16.337
geneAnswersChartPlots	15.514	0.425	15.939
geneAnswersConceptNet	16.341	0.417	16.758
geneAnswersConceptRelation	16.225	0.399	16.625
geneAnswersConcepts	15.839	0.389	16.229
geneAnswersHeatmap	16.037	0.415	16.452
geneAnswersHomoMapping	16.500	0.396	16.896
geneAnswersReadable	27.339	0.508	27.846
geneAnswersSort	16.151	0.385	16.536
geneConceptNet	0	0	0
geneFunSummarize	6.809	0.725	7.559
getCategoryList	0.378	0.027	0.468
getCategoryTerms	0.103	0.005	0.108
getConceptTable	1.937	0.022	1.959
getConnectedGraph	13.933	0.618	14.551
getDOLiteTerms	0.008	0.001	0.009
getGOList	7.190	0.750	14.469
getHomoGeneIDs	0.230	0.014	0.260
getMultiLayerGraphIDs	14.648	0.564	15.212
getNextGOIDs	0.053	0.002	0.054
getPATHList	0.159	0.002	0.161
getPATHTerms	0.040	0.002	0.043
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0.001	0.000	0.001
getSymbols	0.040	0.002	0.043
getTotalGeneNumber	0.191	0.007	0.199
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	10.586	0.358	11.206
humanExpr	0.007	0.001	0.008
humanGeneInput	0.004	0.001	0.005
mouseExpr	0.007	0.001	0.007
mouseGeneInput	0.004	0.001	0.005
plotGeneFunSummary	2.271	0.141	2.412
plotGraph	7.942	0.892	8.834
plotOntologyGraph	6.179	0.845	7.035
sampleGroupsData	0.062	0.037	0.407
saveGeneFunSummary	1.678	0.100	1.778
searchEntrez	0	0	0
simplifyGeneFunSummary	1.413	0.077	1.490
topCategory	0	0	0
topCategoryGenes	0	0	0
topDOLite	0.001	0.000	0.000
topDOLiteGenes	0.000	0.001	0.001
topGO	0	0	0
topGOGenes	0	0	0
topPATH	0.001	0.000	0.001
topPATHGenes	0	0	0
topREACTOME.PATH	0.000	0.001	0.000
topREACTOME.PATHGenes	0.001	0.000	0.000
topcaBIO.PATH	0	0	0