BioC 2.12: CHECK report for GeneAnswers on pelham

Package: GeneAnswers

Version: 2.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneAnswers_2.2.1.tar.gz

StartedAt: 2013-05-01 05:40:54 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:59:47 -0700 (Wed, 01 May 2013)

EllapsedTime: 1133.9 seconds

RetCode: 0

Status: OK

CheckDir: GeneAnswers.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneAnswers.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [20s/21s] OK
* checking installed package size ... NOTE
  installed size is 35.2Mb
  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
* 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 ... [14m/15m] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
geneAnswersReadable        94.147  5.928 103.708
GeneAnswers-class          63.550  4.752  80.400
getMultiLayerGraphIDs      53.796  3.251  58.773
geneAnswersBuilder         51.211  2.950  56.805
getConnectedGraph          51.109  2.545  55.599
geneAnswersChartPlots      50.423  2.813  55.005
geneAnswersSort            49.681  2.787  55.077
geneAnswersConceptNet      49.492  2.781  53.795
geneAnswersHomoMapping     49.521  2.672  53.709
GeneAnswers-package        48.986  3.162  55.633
geneAnswersConcepts        49.104  2.561  53.288
buildNet                   48.395  2.900  54.074
geneAnswersHeatmap         47.128  2.934  51.971
geneAnswersConceptRelation 45.094  3.004  49.810
getGOList                  30.494  2.645  41.817
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/GeneAnswers.Rcheck/00check.log'
for details.

* 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)

name	user	system	elapsed
DO	0.918	0.044	0.989
DOLite	0.048	0.011	0.064
DOLiteTerm	0.010	0.004	0.014
DmIALite	0.118	0.014	0.135
GeneAnswers-class	63.550	4.752	80.400
GeneAnswers-package	48.986	3.162	55.633
HsIALite	0.354	0.026	0.423
MmIALite	0.023	0.016	0.180
RnIALite	0.013	0.015	0.032
buildNet	48.395	2.900	54.074
caBIO.PATHGenes	0.002	0.004	0.006
caBIO2entrez	0.002	0.004	0.006
categoryNet	0.002	0.005	0.007
chartPlots	0.034	0.013	0.137
drawTable	2.009	0.123	2.508
entrez2caBIO	0.002	0.004	0.006
geneAnnotationHeatmap	0.004	0.006	0.011
geneAnswersBuilder	51.211	2.950	56.805
geneAnswersChartPlots	50.423	2.813	55.005
geneAnswersConceptNet	49.492	2.781	53.795
geneAnswersConceptRelation	45.094	3.004	49.810
geneAnswersConcepts	49.104	2.561	53.288
geneAnswersHeatmap	47.128	2.934	51.971
geneAnswersHomoMapping	49.521	2.672	53.709
geneAnswersReadable	94.147	5.928	103.708
geneAnswersSort	49.681	2.787	55.077
geneConceptNet	0.002	0.005	0.009
getCategoryList	0.371	0.039	0.462
getCategoryTerms	0.113	0.013	0.131
getConceptTable	1.931	0.129	2.110
getConnectedGraph	51.109	2.545	55.599
getDOLiteTerms	0.012	0.007	0.019
getGOList	30.494	2.645	41.817
getHomoGeneIDs	0.813	0.056	0.886
getMultiLayerGraphIDs	53.796	3.251	58.773
getNextGOIDs	0.413	0.056	0.483
getPATHList	0.105	0.015	0.122
getPATHTerms	0.058	0.009	0.070
getREACTOMEPATHList	0.002	0.004	0.007
getREACTOMEPATHTerms	0.002	0.004	0.006
getSingleLayerGraphIDs	0.007	0.010	0.018
getSymbols	0.070	0.011	0.084
getTotalGeneNumber	0.405	0.050	0.464
getcaBIOPATHList	0.003	0.006	0.009
getcaBIOPATHTerms	0.003	0.004	0.007
groupReport	1.845	0.115	2.004
humanExpr	0.011	0.008	0.018
humanGeneInput	0.007	0.007	0.014
mouseExpr	0.009	0.006	0.016
mouseGeneInput	0.006	0.006	0.013
sampleGroupsData	0.184	0.082	0.267
searchEntrez	0.003	0.005	0.008
topCategory	0.003	0.005	0.007
topCategoryGenes	0.002	0.005	0.007
topDOLITE	0.002	0.006	0.008
topDOLITEGenes	0.002	0.007	0.008
topGO	0.003	0.006	0.008
topGOGenes	0.002	0.006	0.009
topPATH	0.002	0.007	0.009
topPATHGenes	0.002	0.007	0.009
topREACTOME.PATH	0.003	0.010	0.013
topREACTOME.PATHGenes	0.111	0.027	0.139
topcaBIO.PATH	0.002	0.004	0.006

Summary

Command output