GeneAnswers 1.17.0
Gang Feng , Pan Du and Tian Xia
| Snapshot Date: 2013-03-22 17:01:19 -0700 (Fri, 22 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers | | Last Changed Rev: 70052 / Revision: 74721 | | Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/GeneAnswers.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘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 ... [26s/27s] OK
* checking installed package size ... NOTE
installed size is 35.8Mb
sub-directories of 1Mb or more:
External 32.4Mb
data 1.1Mb
doc 1.9Mb
* 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/14m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneAnswersReadable 111.767 1.064 115.878
GeneAnswers-class 65.052 1.524 70.522
geneAnswersSort 47.447 0.736 48.667
geneAnswersHomoMapping 46.974 0.384 49.111
geneAnswersChartPlots 46.655 0.660 48.200
geneAnswersConcepts 43.187 0.976 45.870
GeneAnswers-package 43.779 0.248 46.619
geneAnswersConceptRelation 42.450 0.632 43.298
geneAnswersBuilder 41.226 0.420 43.063
geneAnswersConceptNet 40.627 0.456 42.712
getMultiLayerGraphIDs 40.110 0.504 41.532
getConnectedGraph 39.931 0.584 40.737
buildNet 39.067 0.528 41.277
geneAnswersHeatmap 39.331 0.200 39.587
getGOList 27.238 0.544 29.264
groupReport 18.977 0.096 20.286
geneFunSummarize 12.637 1.036 14.342
plotGraph 11.225 0.596 12.069
plotOntologyGraph 9.889 0.700 10.609
* 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
‘/home/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)