Package: GeneAnswers

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings GeneAnswers_1.4.2.tar.gz

StartedAt: 2010-10-04 17:03:23 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:11:18 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 475.1 seconds

RetCode: 0

Status:  OK

CheckDir: GeneAnswers.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeneAnswers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAnswers' version '1.4.2'
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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
DOLite	0.112	0.003	0.124
DOLiteTerm	0.005	0.001	0.008
GeneAnswers-class	22.516	1.722	25.540
GeneAnswers-package	21.314	1.203	22.554
buildNet	21.34	1.18	23.71
categoryNet	0	0	0
chartPlots	0.031	0.006	0.057
drawTable	1.066	0.050	1.144
geneAnnotationHeatmap	0.001	0.000	0.001
geneAnswersBuilder	20.000	1.142	21.654
geneAnswersChartPlots	20.101	1.144	21.784
geneAnswersConceptNet	20.375	1.151	22.038
geneAnswersConceptRelation	21.526	1.163	23.908
geneAnswersConcepts	20.480	1.144	21.952
geneAnswersHeatmap	19.841	1.142	21.177
geneAnswersHomoMapping	19.906	1.114	21.208
geneAnswersReadable	37.676	1.284	39.912
geneAnswersSort	19.393	1.134	21.528
geneConceptNet	0	0	0
getCategoryList	0.409	0.043	0.840
getCategoryTerms	0.119	0.006	0.124
getConceptTable	1.140	0.041	1.200
getConnectedGraph	19.952	1.178	21.596
getDOLiteTerms	0.011	0.003	0.014
getGOList	6.164	0.978	9.333
getHomoGeneIDs	0.309	0.028	0.372
getMultiLayerGraphIDs	21.260	1.264	22.903
getNextGOIDs	0.084	0.003	0.087
getPATHList	0.086	0.003	0.106
getPATHTerms	0.093	0.003	0.100
getSingleLayerGraphIDs	0.002	0.000	0.002
getSymbols	0.063	0.004	0.081
groupReport	8.504	0.217	9.155
humanExpr	0.011	0.001	0.017
humanGeneInput	0.007	0.001	0.012
mouseExpr	0.010	0.002	0.011
mouseGeneInput	0.007	0.001	0.007
sampleGroupsData	0.262	0.055	0.343
searchEntrez	0	0	0
topCategory	0.000	0.000	0.001
topCategoryGenes	0	0	0
topDOLite	0.000	0.001	0.001
topDOLiteGenes	0	0	0
topGO	0	0	0
topGOGenes	0.001	0.000	0.000
topPATH	0.000	0.000	0.001
topPATHGenes	0	0	0