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 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)