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 19:20:43 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:30:21 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 577.3 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: 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
  ‘/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
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.708	0.015	0.724
DOLite	0.035	0.002	0.037
DOLiteTerm	0.006	0.002	0.006
GeneAnswers-class	24.387	2.290	29.094
GeneAnswers-package	21.086	1.261	22.480
buildNet	20.877	1.295	22.392
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.032	0.007	0.209
drawTable	2.467	0.049	2.534
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0.001	0.000	0.001
geneAnswersBuilder	21.248	1.266	22.626
geneAnswersChartPlots	21.360	1.294	22.923
geneAnswersConceptNet	21.794	1.327	23.405
geneAnswersConceptRelation	21.388	1.310	22.861
geneAnswersConcepts	20.495	1.257	21.976
geneAnswersHeatmap	21.474	1.332	23.032
geneAnswersHomoMapping	21.444	1.304	22.900
geneAnswersReadable	39.137	1.499	41.148
geneAnswersSort	21.820	1.328	23.257
geneConceptNet	0.001	0.000	0.001
geneFunSummarize	10.467	2.609	13.223
getCategoryList	0.489	0.041	0.601
getCategoryTerms	0.139	0.008	0.158
getConceptTable	2.532	0.055	2.610
getConnectedGraph	19.113	1.416	20.558
getDOLiteTerms	0.011	0.003	0.015
getGOList	9.823	1.411	15.054
getHomoGeneIDs	0.299	0.025	0.684
getMultiLayerGraphIDs	19.266	1.346	20.665
getNextGOIDs	0.079	0.004	0.125
getPATHList	0.222	0.003	0.226
getPATHTerms	0.055	0.003	0.058
getREACTOMEPATHList	0.001	0.000	0.001
getREACTOMEPATHTerms	0.000	0.000	0.001
getSingleLayerGraphIDs	0.002	0.001	0.003
getSymbols	0.056	0.003	0.059
getTotalGeneNumber	0.297	0.035	0.390
getcaBIOPATHList	0.001	0.000	0.001
getcaBIOPATHTerms	0.001	0.000	0.000
groupReport	12.690	0.370	13.245
humanExpr	0.011	0.001	0.013
humanGeneInput	0.007	0.001	0.008
mouseExpr	0.010	0.001	0.011
mouseGeneInput	0.007	0.001	0.009
plotGeneFunSummary	2.329	0.815	3.146
plotGraph	9.899	2.925	12.986
plotOntologyGraph	8.605	2.617	11.317
sampleGroupsData	0.256	0.052	0.309
saveGeneFunSummary	2.310	1.060	3.396
searchEntrez	0.001	0.000	0.001
simplifyGeneFunSummary	1.880	1.493	3.392
topCategory	0	0	0
topCategoryGenes	0.001	0.000	0.000
topDOLite	0.001	0.000	0.000
topDOLiteGenes	0.001	0.000	0.000
topGO	0.000	0.000	0.001
topGOGenes	0	0	0
topPATH	0.000	0.001	0.001
topPATHGenes	0.000	0.000	0.001
topREACTOME.PATH	0.000	0.000	0.001
topREACTOME.PATHGenes	0.001	0.001	0.001
topcaBIO.PATH	0	0	0