Package: GeneAnswers

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneAnswers_1.9.0.tar.gz

StartedAt: 2011-07-07 03:05:28 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 03:17:31 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 723.3 seconds

RetCode: 0

Status:  OK

CheckDir: GeneAnswers.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneAnswers/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAnswers' version '1.9.0'
* 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 installed package size ... NOTE
  installed size is 37.7Mb
  sub-directories of 1Mb or more:
    data       1.5Mb
    doc        3.4Mb
    External  32.4Mb
* 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                       old_size new_size compress
  DO.rda                  702Kb    417Kb       xz
  DOLite.rda               86Kb     46Kb       xz
  DmIALite.rda            114Kb     84Kb       xz
  HsIALite.rda            536Kb    414Kb       xz
  MmIALite.rda             43Kb     34Kb       xz
  RnIALite.rda             19Kb     16Kb       xz
  sampleGroupsData.rda     25Kb     17Kb    bzip2
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* 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 ...
*** tangling vignette sources ...
   'GeneAnswersCWAnnotation.Rnw' 
   'geneAnswers.Rnw' 
   'geneFunctionSummarize.Rnw' 
** testing if installed package can be loaded

* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.753	0.019	0.783
DOLite	0.042	0.003	0.046
DOLiteTerm	0.005	0.002	0.006
DmIALite	0.095	0.003	0.099
GeneAnswers-class	31.615	2.530	36.279
GeneAnswers-package	26.251	1.629	28.446
HsIALite	0.321	0.008	0.329
MmIALite	0.015	0.002	0.017
RnIALite	0.008	0.001	0.010
buildNet	25.065	1.574	26.954
caBIO.PATHGenes	0.001	0.000	0.000
caBIO2entrez	0	0	0
categoryNet	0.000	0.000	0.001
chartPlots	0.035	0.006	0.051
drawTable	2.655	0.060	2.992
entrez2caBIO	0.000	0.000	0.001
geneAnnotationHeatmap	0.001	0.000	0.002
geneAnswersBuilder	26.981	1.585	29.534
geneAnswersChartPlots	26.127	1.538	27.939
geneAnswersConceptNet	25.308	1.609	27.694
geneAnswersConceptRelation	25.223	1.605	27.472
geneAnswersConcepts	26.002	1.620	28.684
geneAnswersHeatmap	26.201	1.644	28.800
geneAnswersHomoMapping	26.458	1.614	28.999
geneAnswersReadable	43.557	1.830	46.453
geneAnswersSort	28.151	1.612	31.015
geneConceptNet	0	0	0
geneFunSummarize	8.535	2.550	11.447
getCategoryList	0.495	0.041	0.650
getCategoryTerms	0.110	0.006	0.118
getConceptTable	2.681	0.051	2.753
getConnectedGraph	23.836	1.661	25.853
getDOLiteTerms	0.010	0.003	0.013
getGOList	13.211	1.781	21.978
getHomoGeneIDs	0.316	0.026	0.400
getMultiLayerGraphIDs	24.819	1.714	27.360
getNextGOIDs	0.084	0.004	0.131
getPATHList	0.225	0.003	0.241
getPATHTerms	0.061	0.003	0.079
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0.000	0.000	0.001
getSingleLayerGraphIDs	0.001	0.000	0.002
getSymbols	0.064	0.003	0.088
getTotalGeneNumber	0.306	0.041	0.467
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0.000	0.000	0.001
groupReport	12.597	0.390	13.605
humanExpr	0.009	0.002	0.012
humanGeneInput	0.006	0.001	0.007
mouseExpr	0.009	0.002	0.019
mouseGeneInput	0.007	0.002	0.010
plotGeneFunSummary	2.576	0.779	3.696
plotGraph	8.949	2.836	12.146
plotOntologyGraph	7.728	2.634	10.578
sampleGroupsData	0.074	0.052	0.126
saveGeneFunSummary	1.984	0.895	2.937
searchEntrez	0.001	0.001	0.000
simplifyGeneFunSummary	1.978	1.042	3.082
topCategory	0	0	0
topCategoryGenes	0.000	0.000	0.001
topDOLITE	0	0	0
topDOLITEGenes	0.000	0.000	0.001
topGO	0	0	0
topGOGenes	0	0	0
topPATH	0	0	0
topPATHGenes	0.000	0.000	0.001
topREACTOME.PATH	0.001	0.000	0.000
topREACTOME.PATHGenes	0	0	0
topcaBIO.PATH	0.001	0.001	0.000