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BioC 2.12: CHECK report for GeneAnswers on moscato2

This page was generated on 2013-10-09 09:38:44 -0700 (Wed, 09 Oct 2013).

Package 250/671HostnameOS / ArchBUILDCHECKBUILD BIN
GeneAnswers 2.2.1
Gang Feng , Pan Du and Tian Xia
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GeneAnswers
Last Changed Rev: 75810 / Revision: 81334
Last Changed Date: 2013-04-19 09:55:42 -0700 (Fri, 19 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GeneAnswers
Version: 2.2.1
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_2.2.1.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_2.2.1.tar.gz && mv GeneAnswers.buildbin-libdir/* GeneAnswers.Rcheck/ && rmdir GeneAnswers.buildbin-libdir
StartedAt: 2013-10-09 02:12:31 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:36:27 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 1436.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GeneAnswers.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/GeneAnswers.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '2.2.1'
* 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 ... WARNING
Found the following significant warnings:
  Warning: package 'igraph' was built under R version 3.0.2
  Warning: package 'igraph' was built under R version 3.0.2
  Warning: package 'igraph' was built under R version 3.0.2
See 'E:/biocbld/bbs-2.12-bioc/meat/GeneAnswers.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 35.3Mb
  sub-directories of 1Mb or more:
    External  32.4Mb
    data       1.0Mb
    doc        1.4Mb
* 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'.
* checking Rd files ... OK
* 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' ... [596s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        73.79   1.37   75.16
GeneAnswers-class          35.39   1.36   36.77
getConnectedGraph          32.81   1.56   34.37
getMultiLayerGraphIDs      32.26   1.34   33.64
geneAnswersConceptRelation 32.13   1.13   33.25
geneAnswersHeatmap         30.89   1.25   32.13
geneAnswersConceptNet      30.50   1.13   31.65
geneAnswersSort            30.62   0.97   31.59
GeneAnswers-package        30.36   1.12   31.48
geneAnswersChartPlots      29.61   1.05   30.69
geneAnswersHomoMapping     29.28   0.95   30.25
buildNet                   28.53   1.06   29.60
geneAnswersConcepts        27.86   1.06   28.94
geneAnswersBuilder         26.91   0.92   27.83
getGOList                  19.39   1.13   91.68
** running examples for arch 'x64' ... [580s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
geneAnswersReadable        83.81   1.63   85.46
GeneAnswers-class          44.20   2.26   46.46
getMultiLayerGraphIDs      39.11   1.66   40.76
geneAnswersHeatmap         35.85   1.50   37.35
GeneAnswers-package        35.53   1.64   37.17
geneAnswersSort            33.85   1.16   35.00
geneAnswersHomoMapping     33.54   1.30   34.84
buildNet                   32.38   1.41   33.79
geneAnswersBuilder         31.92   1.17   33.10
geneAnswersConcepts        31.81   1.14   32.98
geneAnswersConceptRelation 29.91   1.45   31.35
geneAnswersChartPlots      30.22   1.10   31.32
getConnectedGraph          30.30   0.97   31.28
geneAnswersConceptNet      28.90   1.14   30.05
getGOList                  19.61   0.78   20.39
* 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

WARNING: There was 1 warning.
NOTE: There were 2 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
Warning: package 'igraph' was built under R version 3.0.2
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'igraph' was built under R version 3.0.2

install for x64

* installing *source* package 'GeneAnswers' ...
** testing if installed package can be loaded
Warning: package 'igraph' was built under R version 3.0.2
* MD5 sums
packaged installation of 'GeneAnswers' as GeneAnswers_2.2.1.zip
* DONE (GeneAnswers)