BioC 2.9: CHECK report for GeneAnswers on moscato1

Package: GeneAnswers

Version: 1.9.0

Command: mkdir GeneAnswers.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneAnswers.buildbin-libdir GeneAnswers_1.9.0.tar.gz >GeneAnswers-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=GeneAnswers.buildbin-libdir --install="check:GeneAnswers-install.out" --force-multiarch --no-vignettes --timings GeneAnswers_1.9.0.tar.gz && mv GeneAnswers.buildbin-libdir/* GeneAnswers.Rcheck/ && rmdir GeneAnswers.buildbin-libdir

StartedAt: 2011-07-07 05:00:13 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:13:56 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 823.3 seconds

RetCode: 0

Status: OK

CheckDir: GeneAnswers.Rcheck

Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* 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 '1.9.0'
* 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 37.8Mb
  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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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


install for i386

* 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

add DLL for x64

* installing *source* package 'GeneAnswers' ...
** testing if installed package can be loaded
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_1.9.0.zip

* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.36	0.00	0.65
DOLite	0.02	0.00	0.02
DOLiteTerm	0	0	0
DmIALite	0.05	0.00	0.05
GeneAnswers-class	19.95	0.64	20.59
GeneAnswers-package	17.05	0.37	17.43
HsIALite	0.15	0.00	0.16
MmIALite	0.02	0.00	0.02
RnIALite	0	0	0
buildNet	18.07	0.36	18.44
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.01	0.01	0.03
drawTable	1.53	0.00	1.54
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0	0	0
geneAnswersBuilder	16.37	0.30	16.68
geneAnswersChartPlots	17.42	0.36	17.78
geneAnswersConceptNet	15.99	0.25	16.24
geneAnswersConceptRelation	16.07	0.39	16.46
geneAnswersConcepts	17.25	0.34	17.60
geneAnswersHeatmap	17.76	0.31	18.06
geneAnswersHomoMapping	16.23	0.32	16.55
geneAnswersReadable	30.74	0.39	31.15
geneAnswersSort	18.40	0.32	18.72
geneConceptNet	0	0	0
geneFunSummarize	6.26	0.21	6.46
getCategoryList	0.36	0.00	0.36
getCategoryTerms	0.08	0.01	0.10
getConceptTable	1.80	0.00	1.79
getConnectedGraph	16.74	0.36	17.10
getDOLiteTerms	0.02	0.00	0.01
getGOList	8.64	0.23	8.88
getHomoGeneIDs	0.16	0.02	0.17
getMultiLayerGraphIDs	18.33	0.27	18.60
getNextGOIDs	0.04	0.00	0.04
getPATHList	0.13	0.00	0.13
getPATHTerms	0.01	0.01	0.03
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0	0	0
getSymbols	0.03	0.00	0.03
getTotalGeneNumber	0.2	0.0	0.2
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	7.23	0.34	7.59
humanExpr	0	0	0
humanGeneInput	0.02	0.00	0.01
mouseExpr	0	0	0
mouseGeneInput	0.01	0.00	0.02
plotGeneFunSummary	1.97	0.00	1.96
plotGraph	6.24	0.27	6.51
plotOntologyGraph	5.16	0.24	5.41
sampleGroupsData	0.05	0.02	0.07
saveGeneFunSummary	1.56	0.05	1.61
searchEntrez	0	0	0
simplifyGeneFunSummary	1.29	0.01	1.31
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