Package: GeneAnswers

Version: 1.6.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings GeneAnswers_1.6.0.tar.gz

StartedAt: 2011-04-07 06:26:34 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 06:33:24 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 410.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneAnswers.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/GeneAnswers.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘1.6.0’
* 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
  ‘/loc/home/biocbuild/bbs-2.7-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
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.332	0.004	0.337
DOLite	0.048	0.000	0.050
DOLiteTerm	0.000	0.000	0.003
GeneAnswers-class	20.785	0.360	21.782
GeneAnswers-package	15.761	0.096	15.860
buildNet	15.113	0.072	15.201
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.044	0.012	0.130
drawTable	1.448	0.004	1.489
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0	0	0
geneAnswersBuilder	15.913	0.112	16.041
geneAnswersChartPlots	17.409	0.168	17.590
geneAnswersConceptNet	15.961	0.096	16.066
geneAnswersConceptRelation	15.905	0.180	16.095
geneAnswersConcepts	15.985	0.140	16.129
geneAnswersHeatmap	15.713	0.004	15.725
geneAnswersHomoMapping	13.857	0.092	13.953
geneAnswersReadable	26.170	0.132	27.255
geneAnswersSort	15.853	0.056	15.929
geneConceptNet	0	0	0
geneFunSummarize	8.912	0.332	9.329
getCategoryList	0.320	0.012	0.416
getCategoryTerms	0.096	0.012	0.119
getConceptTable	1.436	0.008	1.464
getConnectedGraph	14.057	0.092	14.151
getDOLiteTerms	0.008	0.000	0.007
getGOList	6.629	0.128	8.693
getHomoGeneIDs	0.160	0.008	0.232
getMultiLayerGraphIDs	18.445	0.016	18.548
getNextGOIDs	0.056	0.000	0.060
getPATHList	0.124	0.000	0.123
getPATHTerms	0.040	0.000	0.041
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0.000	0.004	0.001
getSymbols	0.044	0.000	0.047
getTotalGeneNumber	0.180	0.000	0.298
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0.000	0.000	0.001
groupReport	7.740	0.068	7.830
humanExpr	0.004	0.004	0.007
humanGeneInput	0.004	0.000	0.004
mouseExpr	0.008	0.000	0.006
mouseGeneInput	0.004	0.000	0.004
plotGeneFunSummary	3.284	0.004	3.286
plotGraph	8.737	0.484	9.223
plotOntologyGraph	6.852	0.564	7.420
sampleGroupsData	0.064	0.032	0.094
saveGeneFunSummary	1.757	0.044	1.799
searchEntrez	0	0	0
simplifyGeneFunSummary	1.872	0.004	1.877
topCategory	0	0	0
topCategoryGenes	0.000	0.004	0.000
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	0	0
topREACTOME.PATHGenes	0	0	0
topcaBIO.PATH	0	0	0