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Package 246/658HostnameOS / ArchBUILDCHECKBUILD BIN
GeneAnswers 1.17.0
Gang Feng , Pan Du and Tian Xia
Snapshot Date: 2013-03-22 17:01:19 -0700 (Fri, 22 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers
Last Changed Rev: 70052 / Revision: 74721
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GeneAnswers
Version: 1.17.0
Command: rm -rf GeneAnswers.buildbin-libdir && mkdir GeneAnswers.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneAnswers.buildbin-libdir GeneAnswers_1.17.0.tar.gz >GeneAnswers-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=GeneAnswers.buildbin-libdir --install="check:GeneAnswers-install.out" --force-multiarch --no-vignettes --timings GeneAnswers_1.17.0.tar.gz && mv GeneAnswers.buildbin-libdir/* GeneAnswers.Rcheck/ && rmdir GeneAnswers.buildbin-libdir
StartedAt: 2013-03-23 02:10:49 -0700 (Sat, 23 Mar 2013)
EndedAt: 2013-03-23 02:30:18 -0700 (Sat, 23 Mar 2013)
EllapsedTime: 1168.8 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneAnswers.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/GeneAnswers.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-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 '1.17.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GeneAnswers' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 35.8Mb
  sub-directories of 1Mb or more:
    External  32.4Mb
    data       1.0Mb
    doc        1.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace 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 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'.

plotGeneFunSummary: warning in require(lib, character = TRUE): partial
  argument match of 'character' to 'character.only'
saveGeneFunSummary: warning in require(lib, character = TRUE): partial
  argument match of 'character' to 'character.only'
* 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [477s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        55.30   0.70   62.04
GeneAnswers-class          28.92   1.10   38.40
getConnectedGraph          26.84   0.63   27.47
geneAnswersSort            25.41   0.53   25.94
buildNet                   25.24   0.49   25.72
geneAnswersConceptNet      25.08   0.61   25.69
geneAnswersChartPlots      24.96   0.62   25.61
getMultiLayerGraphIDs      24.18   0.59   24.82
geneAnswersBuilder         23.76   0.59   24.36
geneAnswersConceptRelation 23.82   0.53   24.35
geneAnswersHeatmap         23.29   0.53   23.82
geneAnswersConcepts        22.53   0.52   23.07
GeneAnswers-package        22.33   0.65   22.97
geneAnswersHomoMapping     22.25   0.70   22.95
getGOList                  21.55   1.01   36.06
groupReport                 8.86   0.38    9.43
geneFunSummarize            5.69   0.19    5.89
plotGraph                   5.58   0.26    5.85
** running examples for arch 'x64' ... [475s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        55.05   0.88   55.94
GeneAnswers-class          32.57   1.11   33.70
getMultiLayerGraphIDs      30.85   0.98   31.84
geneAnswersConceptNet      28.94   0.86   29.80
geneAnswersChartPlots      28.64   0.96   29.60
geneAnswersHeatmap         26.15   0.94   27.08
getConnectedGraph          26.02   0.75   26.77
geneAnswersHomoMapping     25.88   0.84   26.73
geneAnswersConceptRelation 25.49   0.95   26.44
buildNet                   25.38   0.63   26.04
geneAnswersBuilder         24.94   0.94   25.90
geneAnswersSort            24.39   0.84   25.23
GeneAnswers-package        23.73   0.61   24.33
geneAnswersConcepts        23.04   0.81   23.85
getGOList                  17.58   0.60   18.18
groupReport                10.23   0.41   10.77
plotGraph                   5.73   0.28    6.01
plotOntologyGraph           4.80   0.24    5.04
* 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

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details.

GeneAnswers.Rcheck/00install.out:


install for i386

* installing *source* package 'GeneAnswers' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GeneAnswersCWAnnotation.Rnw' 
   'geneAnswers.Rnw' 
   'geneFunctionSummarize.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'GeneAnswers' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_1.17.0.zip
* DONE (GeneAnswers)