BioC 2.12: CHECK report for GeneAnswers on petty

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: 2013-10-08 22:27:29 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:44:23 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 1014.1 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 3.0.1 (2013-05-16)
* 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 ... [23s/23s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [12m/13m] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
geneAnswersReadable        102.927  4.839 108.438
GeneAnswers-class           54.451  3.788  59.151
getMultiLayerGraphIDs       45.206  2.850  48.211
getConnectedGraph           43.578  2.180  46.066
geneAnswersBuilder          43.148  2.467  46.227
geneAnswersConceptNet       42.367  2.431  45.073
geneAnswersConcepts         42.520  2.277  45.412
geneAnswersChartPlots       42.358  2.377  45.126
geneAnswersHomoMapping      42.217  2.323  44.831
geneAnswersSort             41.559  2.382  44.057
geneAnswersHeatmap          40.543  2.607  43.452
buildNet                    40.218  2.498  43.218
GeneAnswers-package         38.962  2.734  42.494
geneAnswersConceptRelation  38.621  2.734  41.783
getGOList                   25.431  1.962  27.707
* 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	1.013	0.043	1.098
DOLite	0.058	0.011	0.078
DOLiteTerm	0.010	0.004	0.013
DmIALite	0.142	0.013	0.171
GeneAnswers-class	54.451	3.788	59.151
GeneAnswers-package	38.962	2.734	42.494
HsIALite	0.414	0.029	0.443
MmIALite	0.026	0.020	0.047
RnIALite	0.013	0.019	0.032
buildNet	40.218	2.498	43.218
caBIO.PATHGenes	0.002	0.005	0.007
caBIO2entrez	0.002	0.004	0.006
categoryNet	0.002	0.004	0.007
chartPlots	0.037	0.013	0.074
drawTable	1.856	0.101	1.982
entrez2caBIO	0.002	0.003	0.005
geneAnnotationHeatmap	0.004	0.005	0.010
geneAnswersBuilder	43.148	2.467	46.227
geneAnswersChartPlots	42.358	2.377	45.126
geneAnswersConceptNet	42.367	2.431	45.073
geneAnswersConceptRelation	38.621	2.734	41.783
geneAnswersConcepts	42.520	2.277	45.412
geneAnswersHeatmap	40.543	2.607	43.452
geneAnswersHomoMapping	42.217	2.323	44.831
geneAnswersReadable	102.927	4.839	108.438
geneAnswersSort	41.559	2.382	44.057
geneConceptNet	0.002	0.004	0.007
getCategoryList	0.344	0.032	0.404
getCategoryTerms	0.140	0.013	0.153
getConceptTable	1.803	0.137	1.953
getConnectedGraph	43.578	2.180	46.066
getDOLiteTerms	0.012	0.006	0.018
getGOList	25.431	1.962	27.707
getHomoGeneIDs	0.694	0.063	0.773
getMultiLayerGraphIDs	45.206	2.850	48.211
getNextGOIDs	0.379	0.043	0.421
getPATHList	0.112	0.011	0.125
getPATHTerms	0.066	0.008	0.074
getREACTOMEPATHList	0.002	0.003	0.006
getREACTOMEPATHTerms	0.002	0.004	0.006
getSingleLayerGraphIDs	0.008	0.010	0.018
getSymbols	0.079	0.012	0.091
getTotalGeneNumber	0.365	0.042	0.407
getcaBIOPATHList	0.003	0.004	0.006
getcaBIOPATHTerms	0.002	0.003	0.006
groupReport	1.813	0.099	1.918
humanExpr	0.012	0.005	0.017
humanGeneInput	0.008	0.005	0.014
mouseExpr	0.010	0.006	0.016
mouseGeneInput	0.008	0.006	0.013
sampleGroupsData	0.076	0.062	0.141
searchEntrez	0.003	0.005	0.008
topCategory	0.002	0.004	0.006
topCategoryGenes	0.002	0.004	0.006
topDOLITE	0.002	0.003	0.006
topDOLITEGenes	0.003	0.003	0.006
topGO	0.002	0.004	0.006
topGOGenes	0.003	0.004	0.006
topPATH	0.003	0.003	0.005
topPATHGenes	0.002	0.004	0.006
topREACTOME.PATH	0.002	0.003	0.006
topREACTOME.PATHGenes	0.003	0.004	0.006
topcaBIO.PATH	0.002	0.004	0.006