Package: GeneAnswers

Version: 1.7.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings GeneAnswers_1.7.0.tar.gz

StartedAt: 2011-02-24 19:41:01 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:47:57 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 415.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneAnswers.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/GeneAnswers.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.7.0’
* 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
  ‘/loc/home/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
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.592	0.012	0.608
DOLite	0.016	0.004	0.019
DOLiteTerm	0.004	0.000	0.003
GeneAnswers-class	20.473	0.380	22.577
GeneAnswers-package	15.657	0.144	15.841
buildNet	17.769	0.152	17.972
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0.000	0.004	0.001
chartPlots	0.052	0.020	0.133
drawTable	1.324	0.004	1.339
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0.000	0.000	0.001
geneAnswersBuilder	17.401	0.212	17.876
geneAnswersChartPlots	16.285	0.188	16.526
geneAnswersConceptNet	16.609	0.100	16.728
geneAnswersConceptRelation	16.733	0.124	16.926
geneAnswersConcepts	15.721	0.200	15.990
geneAnswersHeatmap	16.989	0.152	17.196
geneAnswersHomoMapping	16.133	0.188	16.320
geneAnswersReadable	28.030	0.152	28.447
geneAnswersSort	15.625	0.100	15.937
geneConceptNet	0.000	0.000	0.001
geneFunSummarize	8.609	0.592	9.309
getCategoryList	0.320	0.004	0.393
getCategoryTerms	0.112	0.004	0.115
getConceptTable	1.448	0.012	1.459
getConnectedGraph	14.325	0.160	14.508
getDOLiteTerms	0.008	0.000	0.008
getGOList	7.984	0.164	10.028
getHomoGeneIDs	0.180	0.004	0.211
getMultiLayerGraphIDs	17.965	0.156	18.415
getNextGOIDs	0.056	0.000	0.066
getPATHList	0.128	0.000	0.128
getPATHTerms	0.040	0.004	0.043
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0.000	0.000	0.002
getSymbols	0.044	0.000	0.048
getTotalGeneNumber	0.192	0.004	0.245
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	7.753	0.080	7.868
humanExpr	0.008	0.000	0.008
humanGeneInput	0.000	0.004	0.004
mouseExpr	0.008	0.000	0.007
mouseGeneInput	0.004	0.000	0.004
plotGeneFunSummary	3.644	0.012	3.663
plotGraph	9.045	0.620	9.688
plotOntologyGraph	6.928	0.732	7.694
sampleGroupsData	0.068	0.028	0.096
saveGeneFunSummary	1.740	0.100	1.841
searchEntrez	0	0	0
simplifyGeneFunSummary	1.892	0.008	1.914
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	0	0
topREACTOME.PATHGenes	0	0	0
topcaBIO.PATH	0	0	0