BioC 2.12: CHECK report for GeneAnswers on petty

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 02:31:17 -0700 (Sat, 23 Mar 2013)

EndedAt: 2013-03-23 02:46:14 -0700 (Sat, 23 Mar 2013)

EllapsedTime: 897.8 seconds

RetCode: 0

Status: OK

CheckDir: GeneAnswers.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneAnswers.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [20s/20s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [11m/11m] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
geneAnswersReadable        76.102  4.184  80.408
GeneAnswers-class          44.407  3.812  48.373
geneAnswersConcepts        38.128  1.953  40.134
geneAnswersBuilder         37.492  1.914  39.484
geneAnswersConceptRelation 37.258  2.042  39.437
geneAnswersChartPlots      37.103  2.081  39.317
getConnectedGraph          36.999  2.040  39.141
GeneAnswers-package        35.328  2.819  38.288
geneAnswersHomoMapping     34.877  1.894  36.814
geneAnswersConceptNet      33.439  2.068  35.647
geneAnswersHeatmap         33.164  2.011  35.226
geneAnswersSort            33.072  1.983  35.177
buildNet                   33.025  2.023  35.151
getMultiLayerGraphIDs      28.855  2.193  31.168
getGOList                  21.018  2.125  25.964
groupReport                13.314  0.661  14.043
plotGraph                  10.542  2.697  13.338
plotOntologyGraph           9.243  2.862  12.176
geneFunSummarize            7.225  2.110   9.475
* 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
** help
*** installing help indices
** building package indices
** installing vignettes
   'GeneAnswersCWAnnotation.Rnw' 
   'geneAnswers.Rnw' 
   'geneFunctionSummarize.Rnw' 
** testing if installed package can be loaded
* DONE (GeneAnswers)

name	user	system	elapsed
DO	0.789	0.034	0.825
DOLite	0.069	0.008	0.079
DOLiteTerm	0.010	0.006	0.016
DmIALite	0.117	0.010	0.127
GeneAnswers-class	44.407	3.812	48.373
GeneAnswers-package	35.328	2.819	38.288
HsIALite	0.418	0.017	0.437
MmIALite	0.095	0.013	0.111
RnIALite	0.014	0.008	0.024
buildNet	33.025	2.023	35.151
caBIO.PATHGenes	0.003	0.004	0.006
caBIO2entrez	0.002	0.005	0.007
categoryNet	0.003	0.005	0.007
chartPlots	0.034	0.014	0.058
drawTable	1.633	0.085	1.727
entrez2caBIO	0.003	0.006	0.009
geneAnnotationHeatmap	0.005	0.011	0.017
geneAnswersBuilder	37.492	1.914	39.484
geneAnswersChartPlots	37.103	2.081	39.317
geneAnswersConceptNet	33.439	2.068	35.647
geneAnswersConceptRelation	37.258	2.042	39.437
geneAnswersConcepts	38.128	1.953	40.134
geneAnswersHeatmap	33.164	2.011	35.226
geneAnswersHomoMapping	34.877	1.894	36.814
geneAnswersReadable	76.102	4.184	80.408
geneAnswersSort	33.072	1.983	35.177
geneConceptNet	0.002	0.004	0.007
geneFunSummarize	7.225	2.110	9.475
getCategoryList	0.376	0.046	0.456
getCategoryTerms	0.124	0.019	0.144
getConceptTable	1.820	0.093	1.916
getConnectedGraph	36.999	2.040	39.141
getDOLiteTerms	0.010	0.008	0.019
getGOList	21.018	2.125	25.964
getHomoGeneIDs	0.358	0.030	0.405
getMultiLayerGraphIDs	28.855	2.193	31.168
getNextGOIDs	0.204	0.016	0.220
getPATHList	0.073	0.012	0.085
getPATHTerms	0.047	0.011	0.058
getREACTOMEPATHList	0.002	0.004	0.007
getREACTOMEPATHTerms	0.048	0.014	0.062
getSingleLayerGraphIDs	0.006	0.007	0.012
getSymbols	0.073	0.013	0.086
getTotalGeneNumber	0.317	0.040	0.358
getcaBIOPATHList	0.003	0.006	0.009
getcaBIOPATHTerms	0.003	0.004	0.007
groupReport	13.314	0.661	14.043
humanExpr	0.009	0.006	0.014
humanGeneInput	0.006	0.005	0.012
mouseExpr	0.008	0.006	0.024
mouseGeneInput	0.006	0.006	0.022
plotGeneFunSummary	1.996	0.594	2.595
plotGraph	10.542	2.697	13.338
plotOntologyGraph	9.243	2.862	12.176
sampleGroupsData	0.073	0.051	0.124
saveGeneFunSummary	1.923	0.900	2.839
searchEntrez	0.003	0.007	0.010
simplifyGeneFunSummary	1.810	1.208	3.044
topCategory	0.002	0.007	0.010
topCategoryGenes	0.033	0.018	0.052
topDOLITE	0.002	0.006	0.009
topDOLITEGenes	0.002	0.007	0.010
topGO	0.002	0.008	0.009
topGOGenes	0.031	0.015	0.046
topPATH	0.002	0.007	0.009
topPATHGenes	0.002	0.008	0.011
topREACTOME.PATH	0.002	0.007	0.009
topREACTOME.PATHGenes	0.003	0.006	0.008
topcaBIO.PATH	0.002	0.007	0.009

Summary

Command output