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BioC 2.12: CHECK report for GeneAnswers on george2

This page was generated on 2013-10-09 09:37:35 -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: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GeneAnswers_2.2.1.tar.gz
StartedAt: 2013-10-09 01:55:20 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:13:22 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 1082.3 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneAnswers.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/GeneAnswers.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘GeneAnswers’ can be installed ... [23s/23s] OK
* checking installed package size ... NOTE
  installed size is 35.3Mb
  sub-directories of 1Mb or more:
    External  32.4Mb
    data       1.1Mb
    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
* 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 ... [13m/14m] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
geneAnswersReadable        113.643  0.788 115.301
GeneAnswers-class           68.613  1.468  70.689
getMultiLayerGraphIDs       53.655  1.084  56.386
getConnectedGraph           52.515  0.656  53.780
geneAnswersHomoMapping      49.435  0.500  50.849
geneAnswersBuilder          48.379  0.452  49.545
geneAnswersSort             47.983  0.556  48.779
geneAnswersChartPlots       46.663  0.748  48.139
geneAnswersConcepts         45.994  0.472  46.882
geneAnswersConceptNet       45.907  0.556  47.124
geneAnswersHeatmap          45.171  0.300  45.596
buildNet                    44.763  0.460  45.600
GeneAnswers-package         44.422  0.300  45.236
geneAnswersConceptRelation  39.083  0.248  39.499
getGOList                   29.010  0.432  30.943
* 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 2 notes.
See
  ‘/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
** testing if installed package can be loaded
* DONE (GeneAnswers)

GeneAnswers.Rcheck/GeneAnswers-Ex.timings:

nameusersystemelapsed
DO1.1440.0201.167
DOLite0.0400.0080.046
DOLiteTerm0.0240.0000.021
DmIALite0.1000.0080.107
GeneAnswers-class68.613 1.46870.689
GeneAnswers-package44.422 0.30045.236
HsIALite0.2720.0080.278
MmIALite0.0200.0000.023
RnIALite0.0120.0000.014
buildNet44.763 0.46045.600
caBIO.PATHGenes0.0080.0000.006
caBIO2entrez0.0040.0000.006
categoryNet0.0080.0000.006
chartPlots0.1160.0160.157
drawTable1.5760.0281.609
entrez2caBIO0.0040.0000.005
geneAnnotationHeatmap0.0080.0000.009
geneAnswersBuilder48.379 0.45249.545
geneAnswersChartPlots46.663 0.74848.139
geneAnswersConceptNet45.907 0.55647.124
geneAnswersConceptRelation39.083 0.24839.499
geneAnswersConcepts45.994 0.47246.882
geneAnswersHeatmap45.171 0.30045.596
geneAnswersHomoMapping49.435 0.50050.849
geneAnswersReadable113.643 0.788115.301
geneAnswersSort47.983 0.55648.779
geneConceptNet0.0080.0000.007
getCategoryList0.2880.0320.374
getCategoryTerms0.1280.0040.132
getConceptTable1.4050.0081.413
getConnectedGraph52.515 0.65653.780
getDOLiteTerms0.0120.0040.021
getGOList29.010 0.43230.943
getHomoGeneIDs0.5280.0120.539
getMultiLayerGraphIDs53.655 1.08456.386
getNextGOIDs0.4880.0040.493
getPATHList0.0800.0040.084
getPATHTerms0.0520.0040.057
getREACTOMEPATHList0.0080.0000.006
getREACTOMEPATHTerms0.0080.0000.005
getSingleLayerGraphIDs0.0160.0000.014
getSymbols0.0640.0160.080
getTotalGeneNumber0.3040.0400.348
getcaBIOPATHList0.0000.0080.007
getcaBIOPATHTerms0.0040.0000.006
groupReport1.2920.0241.319
humanExpr0.0160.0040.017
humanGeneInput0.0120.0000.012
mouseExpr0.0080.0040.013
mouseGeneInput0.0000.0120.013
sampleGroupsData0.2800.0440.328
searchEntrez0.0040.0000.005
topCategory0.0040.0000.004
topCategoryGenes0.0080.0000.006
topDOLITE0.0040.0000.006
topDOLITEGenes0.0080.0000.006
topGO0.0040.0040.008
topGOGenes0.0000.0080.008
topPATH0.0000.0080.008
topPATHGenes0.0040.0040.008
topREACTOME.PATH0.0000.0080.008
topREACTOME.PATHGenes0.1920.0040.197
topcaBIO.PATH0.0080.0000.006