Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 234/631HostnameOS / ArchBUILDCHECKBUILD BIN
GeneAnswers 1.17.0
Gang Feng , Pan Du and Tian Xia
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers
Last Changed Rev: 70052 / Revision: 72575
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 
lamb2 Linux (openSUSE 11.4) / 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 

Summary

Package: GeneAnswers
Version: 1.17.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GeneAnswers_1.17.0.tar.gz
StartedAt: 2013-01-16 02:41:06 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 02:52:30 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 684.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneAnswers.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GeneAnswers.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GeneAnswers’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 35.7Mb
  sub-directories of 1Mb or more:
    External  32.4Mb
    data       1.1Mb
    doc        1.8Mb
* 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
geneAnswersReadable        52.719  0.504  53.374
GeneAnswers-class          37.066  0.752  37.911
geneAnswersConceptNet      29.906  0.320  30.241
geneAnswersConcepts        28.202  0.272  28.474
geneAnswersHomoMapping     27.874  0.296  28.169
geneAnswersHeatmap         27.530  0.404  27.959
geneAnswersBuilder         27.617  0.308  27.952
getMultiLayerGraphIDs      27.606  0.232  27.845
geneAnswersSort            26.958  0.292  27.290
getConnectedGraph          25.886  0.456  26.351
geneAnswersChartPlots      25.906  0.228  26.134
buildNet                   25.202  0.268  25.495
geneAnswersConceptRelation 25.069  0.372  25.449
GeneAnswers-package        24.454  0.380  24.842
getGOList                  15.469  0.292  16.052
plotGraph                  10.217  0.608  10.841
geneFunSummarize            9.748  0.680  10.510
groupReport                 9.508  0.112   9.640
plotOntologyGraph           6.704  0.692   7.403
* 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
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GeneAnswers.Rcheck/00check.log’
for details.

GeneAnswers.Rcheck/00install.out:

* 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

* DONE (GeneAnswers)

GeneAnswers.Rcheck/GeneAnswers-Ex.timings:

nameusersystemelapsed
DO0.9040.0320.939
DOLite0.0360.0000.037
DOLiteTerm0.0080.0000.014
DmIALite0.0880.0000.089
GeneAnswers-class37.066 0.75237.911
GeneAnswers-package24.454 0.38024.842
HsIALite0.2120.0120.225
MmIALite0.0120.0040.018
RnIALite0.0120.0000.011
buildNet25.202 0.26825.495
caBIO.PATHGenes0.0040.0000.003
caBIO2entrez0.0040.0000.003
categoryNet0.0040.0000.003
chartPlots0.0960.0080.117
drawTable0.9200.0120.933
entrez2caBIO0.0000.0000.003
geneAnnotationHeatmap0.0040.0000.005
geneAnswersBuilder27.617 0.30827.952
geneAnswersChartPlots25.906 0.22826.134
geneAnswersConceptNet29.906 0.32030.241
geneAnswersConceptRelation25.069 0.37225.449
geneAnswersConcepts28.202 0.27228.474
geneAnswersHeatmap27.530 0.40427.959
geneAnswersHomoMapping27.874 0.29628.169
geneAnswersReadable52.719 0.50453.374
geneAnswersSort26.958 0.29227.290
geneConceptNet0.0040.0000.005
geneFunSummarize 9.748 0.68010.510
getCategoryList0.1960.0120.269
getCategoryTerms0.0840.0000.085
getConceptTable1.0960.0241.126
getConnectedGraph25.886 0.45626.351
getDOLiteTerms0.0120.0040.016
getGOList15.469 0.29216.052
getHomoGeneIDs0.1040.0000.135
getMultiLayerGraphIDs27.606 0.23227.845
getNextGOIDs0.080.000.08
getPATHList0.0720.0040.075
getPATHTerms0.0480.0040.049
getREACTOMEPATHList0.0040.0000.004
getREACTOMEPATHTerms0.0000.0040.005
getSingleLayerGraphIDs0.0040.0040.012
getSymbols0.0520.0080.066
getTotalGeneNumber0.4120.0080.447
getcaBIOPATHList0.0040.0000.004
getcaBIOPATHTerms0.0040.0000.003
groupReport9.5080.1129.640
humanExpr0.0120.0000.011
humanGeneInput0.0080.0000.008
mouseExpr0.0080.0040.010
mouseGeneInput0.0080.0000.008
plotGeneFunSummary1.9600.0642.027
plotGraph10.217 0.60810.841
plotOntologyGraph6.7040.6927.403
sampleGroupsData0.0720.0240.094
saveGeneFunSummary1.7210.0161.740
searchEntrez0.4760.0120.491
simplifyGeneFunSummary1.5000.1001.601
topCategory0.0040.0040.005
topCategoryGenes0.0440.0000.044
topDOLITE0.0040.0000.003
topDOLITEGenes0.0000.0040.004
topGO0.0000.0040.004
topGOGenes0.0000.0080.004
topPATH0.0000.0040.004
topPATHGenes0.0040.0000.004
topREACTOME.PATH0.0440.0000.044
topREACTOME.PATHGenes0.0040.0000.003
topcaBIO.PATH0.0040.0000.004