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 '/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)