BioC 2.12: CHECK report for GeneAnswers on pelham

Package: GeneAnswers

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneAnswers_1.17.0.tar.gz

StartedAt: 2013-03-23 05:27:37 -0700 (Sat, 23 Mar 2013)

EndedAt: 2013-03-23 05:44:55 -0700 (Sat, 23 Mar 2013)

EllapsedTime: 1038.4 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 beta (2013-03-21 r62346)
* 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 '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 ... [22s/23s] OK
* checking installed package size ... NOTE
  installed size is 35.7Mb
  sub-directories of 1Mb or more:
    External  32.4Mb
    data       1.0Mb
    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 ... [13m/13m] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
geneAnswersReadable        89.484  5.839  97.607
GeneAnswers-class          52.661  4.958  65.634
geneAnswersConceptRelation 40.928  2.804  44.102
getMultiLayerGraphIDs      40.094  3.292  44.102
getConnectedGraph          40.288  2.683  43.511
geneAnswersChartPlots      39.847  2.588  43.698
buildNet                   39.506  2.648  43.246
geneAnswersConceptNet      39.405  2.681  42.390
geneAnswersBuilder         39.287  2.693  43.345
geneAnswersHeatmap         39.403  2.519  42.444
GeneAnswers-package        38.238  2.994  43.489
geneAnswersHomoMapping     37.918  2.639  41.409
geneAnswersSort            37.389  2.626  40.517
geneAnswersConcepts        36.720  2.681  39.865
getGOList                  27.700  2.998  35.854
groupReport                18.354  1.057  19.885
plotGraph                   9.328  1.358  10.756
geneFunSummarize            8.430  1.431  10.057
plotOntologyGraph           7.777  1.326   9.180
* 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
  '/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
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
   'GeneAnswersCWAnnotation.Rnw' 
   'geneAnswers.Rnw' 
   'geneFunctionSummarize.Rnw' 
** testing if installed package can be loaded
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.955	0.038	1.010
DOLite	0.047	0.016	0.064
DOLiteTerm	0.011	0.004	0.016
DmIALite	0.121	0.013	0.134
GeneAnswers-class	52.661	4.958	65.634
GeneAnswers-package	38.238	2.994	43.489
HsIALite	0.354	0.023	0.410
MmIALite	0.022	0.011	0.033
RnIALite	0.012	0.011	0.024
buildNet	39.506	2.648	43.246
caBIO.PATHGenes	0.002	0.004	0.007
caBIO2entrez	0.003	0.004	0.006
categoryNet	0.002	0.004	0.007
chartPlots	0.035	0.023	0.098
drawTable	1.490	0.108	1.704
entrez2caBIO	0.003	0.004	0.006
geneAnnotationHeatmap	0.005	0.006	0.011
geneAnswersBuilder	39.287	2.693	43.345
geneAnswersChartPlots	39.847	2.588	43.698
geneAnswersConceptNet	39.405	2.681	42.390
geneAnswersConceptRelation	40.928	2.804	44.102
geneAnswersConcepts	36.720	2.681	39.865
geneAnswersHeatmap	39.403	2.519	42.444
geneAnswersHomoMapping	37.918	2.639	41.409
geneAnswersReadable	89.484	5.839	97.607
geneAnswersSort	37.389	2.626	40.517
geneConceptNet	0.003	0.005	0.007
geneFunSummarize	8.430	1.431	10.057
getCategoryList	0.296	0.033	0.395
getCategoryTerms	0.112	0.013	0.158
getConceptTable	1.447	0.100	1.630
getConnectedGraph	40.288	2.683	43.511
getDOLiteTerms	0.011	0.007	0.019
getGOList	27.700	2.998	35.854
getHomoGeneIDs	0.428	0.030	0.464
getMultiLayerGraphIDs	40.094	3.292	44.102
getNextGOIDs	0.201	0.013	0.223
getPATHList	0.094	0.012	0.107
getPATHTerms	0.057	0.008	0.065
getREACTOMEPATHList	0.003	0.004	0.007
getREACTOMEPATHTerms	0.002	0.005	0.007
getSingleLayerGraphIDs	0.008	0.010	0.017
getSymbols	0.064	0.012	0.076
getTotalGeneNumber	0.401	0.083	0.486
getcaBIOPATHList	0.003	0.004	0.008
getcaBIOPATHTerms	0.002	0.005	0.007
groupReport	18.354	1.057	19.885
humanExpr	0.010	0.007	0.016
humanGeneInput	0.008	0.008	0.016
mouseExpr	0.009	0.008	0.017
mouseGeneInput	0.011	0.011	0.023
plotGeneFunSummary	2.063	0.321	2.411
plotGraph	9.328	1.358	10.756
plotOntologyGraph	7.777	1.326	9.180
sampleGroupsData	0.069	0.104	0.185
saveGeneFunSummary	1.918	0.286	2.231
searchEntrez	0.003	0.004	0.008
simplifyGeneFunSummary	2.743	0.317	3.179
topCategory	0.002	0.004	0.007
topCategoryGenes	0.002	0.005	0.007
topDOLITE	0.003	0.005	0.007
topDOLITEGenes	0.003	0.004	0.007
topGO	0.002	0.005	0.007
topGOGenes	0.002	0.005	0.008
topPATH	0.003	0.005	0.008
topPATHGenes	0.002	0.005	0.007
topREACTOME.PATH	0.003	0.005	0.009
topREACTOME.PATHGenes	0.002	0.005	0.008
topcaBIO.PATH	0.003	0.006	0.009

Summary

Command output