Package: GeneAnswers

Version: 1.10.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GeneAnswers_1.10.0.tar.gz

StartedAt: 2012-01-09 02:57:00 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 03:07:41 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 640.8 seconds

RetCode: 0

Status:  OK

CheckDir: GeneAnswers.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.14.1 (2011-12-22)
* 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 '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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
* 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 ... NOTE
File 'GeneAnswers/R/zzz.R':
  .onLoad calls:
    require(Biobase)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* 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 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 ... 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
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'graph' seems equivalent to one from package 'IRanges' and is not turning on duplicate class definitions for this class
Warning in library.dynam("Rgraphviz", package = "Rgraphviz") :
  use of library.dynam() without specifying both 'package' and 'lib.loc' is deprecated
Warning in fun(libname, pkgname) :
  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 ...
*** tangling vignette sources ...
   'GeneAnswersCWAnnotation.Rnw' 
   'geneAnswers.Rnw' 
   'geneFunctionSummarize.Rnw' 
** testing if installed package can be loaded
Warning in library.dynam("Rgraphviz", package = "Rgraphviz") :
  use of library.dynam() without specifying both 'package' and 'lib.loc' is deprecated
Warning message:
In fun(libname, pkgname) : 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	0.50	0.04	0.53
DOLite	0.01	0.00	0.02
DOLiteTerm	0.02	0.00	0.01
DmIALite	0.04	0.00	0.05
GeneAnswers-class	28.14	1.03	38.06
GeneAnswers-package	22.03	0.45	22.48
HsIALite	0.16	0.00	0.16
MmIALite	0.01	0.00	0.01
RnIALite	0.02	0.00	0.02
buildNet	23.14	0.59	23.73
caBIO.PATHGenes	0	0	0
caBIO2entrez	0	0	0
categoryNet	0	0	0
chartPlots	0.05	0.00	0.05
drawTable	0.95	0.00	0.95
entrez2caBIO	0	0	0
geneAnnotationHeatmap	0	0	0
geneAnswersBuilder	21.61	0.75	22.36
geneAnswersChartPlots	20.46	0.60	21.04
geneAnswersConceptNet	23.01	0.43	23.46
geneAnswersConceptRelation	22.07	0.69	22.75
geneAnswersConcepts	22.34	0.66	23.01
geneAnswersHeatmap	22.97	0.59	23.58
geneAnswersHomoMapping	24.05	0.72	24.77
geneAnswersReadable	35.92	0.52	38.17
geneAnswersSort	23.47	0.64	24.12
geneConceptNet	0	0	0
geneFunSummarize	8.25	0.39	8.64
getCategoryList	0.21	0.01	0.47
getCategoryTerms	0.07	0.00	0.07
getConceptTable	0.92	0.02	0.94
getConnectedGraph	19.99	0.59	20.59
getDOLiteTerms	0	0	0
getGOList	11.13	0.53	62.06
getHomoGeneIDs	0.11	0.00	0.42
getMultiLayerGraphIDs	23.08	0.57	23.89
getNextGOIDs	0.03	0.01	0.05
getPATHList	0.05	0.00	0.04
getPATHTerms	0.13	0.02	0.14
getREACTOMEPATHList	0	0	0
getREACTOMEPATHTerms	0	0	0
getSingleLayerGraphIDs	0	0	0
getSymbols	0.03	0.00	0.08
getTotalGeneNumber	0.22	0.00	0.26
getcaBIOPATHList	0	0	0
getcaBIOPATHTerms	0	0	0
groupReport	6.39	0.60	7.11
humanExpr	0.01	0.00	0.02
humanGeneInput	0	0	0
mouseExpr	0	0	0
mouseGeneInput	0.01	0.00	0.02
plotGeneFunSummary	2.25	0.03	2.28
plotGraph	9.28	0.30	9.58
plotOntologyGraph	5.61	0.37	5.98
sampleGroupsData	0.06	0.00	0.06
saveGeneFunSummary	1.86	0.00	1.86
searchEntrez	0	0	0
simplifyGeneFunSummary	1.30	0.06	1.36
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