Package: GeneAnswers

Version: 1.8.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GeneAnswers_1.8.0.tar.gz

StartedAt: 2011-10-20 14:24:12 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:33:30 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 558.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneAnswers.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-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 '1.8.0'
* checking package namespace 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 36.0Mb
  sub-directories of 1Mb or more:
    data       1.5Mb
    doc        1.6Mb
    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
* 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   GeneAnswersCWAnnotation.Rnw
   geneAnswers.Rnw
   geneFunctionSummarize.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details

* installing *source* package 'GeneAnswers' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in fun(...) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
** help
*** installing help indices
** building package indices ...
** 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.

* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.40	0.00	0.41
DOLite	0.02	0.02	0.03
DOLiteTerm	0	0	0
DmIALite	0.08	0.01	0.09
GeneAnswers-class	27.11	0.88	36.72
GeneAnswers-package	21.23	0.37	21.61
HsIALite	0.17	0.00	0.17
MmIALite	0.07	0.00	0.06
RnIALite	0	0	0
buildNet	20.64	0.49	21.13
caBIO.PATHGenes	0.01	0.00	0.01
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.02	0.00	0.02
drawTable	0.96	0.00	0.96
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0	0	0
geneAnswersBuilder	20.85	0.40	21.25
geneAnswersChartPlots	20.95	0.66	21.63
geneAnswersConceptNet	20.37	0.56	20.97
geneAnswersConceptRelation	19.04	0.64	19.70
geneAnswersConcepts	20.46	0.49	21.00
geneAnswersHeatmap	22.02	0.31	22.38
geneAnswersHomoMapping	22.53	0.44	22.96
geneAnswersReadable	35.10	0.65	37.64
geneAnswersSort	21.45	0.50	21.96
geneConceptNet	0	0	0
geneFunSummarize	7.05	0.35	7.39
getCategoryList	0.17	0.01	0.34
getCategoryTerms	0.08	0.00	0.08
getConceptTable	1.11	0.03	1.14
getConnectedGraph	19.39	0.35	19.73
getDOLiteTerms	0.02	0.00	0.02
getGOList	11.83	0.79	65.81
getHomoGeneIDs	0.10	0.00	0.14
getMultiLayerGraphIDs	21.88	0.54	22.47
getNextGOIDs	0.05	0.00	0.04
getPATHList	0.05	0.00	0.05
getPATHTerms	0.03	0.01	0.05
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0	0	0
getSymbols	0.03	0.00	0.14
getTotalGeneNumber	0.20	0.03	0.42
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	6.36	0.50	6.93
humanExpr	0	0	0
humanGeneInput	0.01	0.00	0.02
mouseExpr	0	0	0
mouseGeneInput	0.02	0.00	0.01
plotGeneFunSummary	2.42	0.00	2.43
plotGraph	7.95	0.28	8.23
plotOntologyGraph	6.64	0.36	7.00
sampleGroupsData	0.07	0.00	0.06
saveGeneFunSummary	1.88	0.07	1.94
searchEntrez	0	0	0
simplifyGeneFunSummary	1.86	0.00	1.86
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