Package: GeneAnswers

Version: 1.7.0

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings GeneAnswers_1.7.0.tar.gz

StartedAt: 2011-02-24 18:04:16 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:11:42 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 445.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneAnswers.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 '1.7.0'
* 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 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
  'E:/biocbld/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	0.67	0.02	0.69
DOLite	0.02	0.01	0.03
DOLiteTerm	0	0	0
GeneAnswers-class	20.56	0.58	23.06
GeneAnswers-package	17.79	0.25	18.09
buildNet	17.83	0.22	18.39
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.00	0.02	0.02
drawTable	1.80	0.06	1.86
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0	0	0
geneAnswersBuilder	18.08	0.16	18.31
geneAnswersChartPlots	18.36	0.20	18.94
geneAnswersConceptNet	18.36	0.17	18.71
geneAnswersConceptRelation	17.72	0.25	18.22
geneAnswersConcepts	16.77	0.08	17.08
geneAnswersHeatmap	17.90	0.24	18.33
geneAnswersHomoMapping	18.38	0.20	18.68
geneAnswersReadable	30.33	0.86	31.56
geneAnswersSort	17.69	0.14	17.83
geneConceptNet	0	0	0
geneFunSummarize	7.29	0.25	7.57
getCategoryList	0.41	0.00	0.49
getCategoryTerms	0.11	0.01	0.12
getConceptTable	1.95	0.08	2.10
getConnectedGraph	14.52	0.06	14.78
getDOLiteTerms	0.01	0.00	0.01
getGOList	8.50	0.29	17.03
getHomoGeneIDs	0.17	0.03	0.25
getMultiLayerGraphIDs	15.99	0.04	16.24
getNextGOIDs	0.05	0.00	0.10
getPATHList	0.14	0.02	0.15
getPATHTerms	0.01	0.02	0.03
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0.02	0.00	0.02
getSymbols	0.03	0.00	0.06
getTotalGeneNumber	0.27	0.01	0.34
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	7.17	0.50	7.81
humanExpr	0.02	0.00	0.02
humanGeneInput	0	0	0
mouseExpr	0.01	0.00	0.01
mouseGeneInput	0	0	0
plotGeneFunSummary	1.33	0.00	1.33
plotGraph	6.91	0.24	7.24
plotOntologyGraph	5.98	0.26	6.39
sampleGroupsData	0.07	0.02	0.07
saveGeneFunSummary	1.50	0.01	1.54
searchEntrez	0	0	0
simplifyGeneFunSummary	1.28	0.02	1.34
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