GeneAnswers 1.13.1
Gang Feng , Pan Du and Tian Xia
| Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers | | Last Changed Rev: 65499 / Revision: 66885 | | Last Changed Date: 2012-04-27 12:36:57 -0700 (Fri, 27 Apr 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | ERROR | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | ERROR |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | ERROR | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GeneAnswers.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.13.1'
* 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 whether package 'GeneAnswers' can be installed ... 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... ERROR
Running examples in 'GeneAnswers-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: groupReport
> ### Title: Generate a multigroup Concepts-genes analysis report
> ### Aliases: groupReport
> ### Keywords: methods
>
> ### ** Examples
>
> data(sampleGroupsData)
> gAKEGGL <- lapply(sampleGroupsData, geneAnswersBuilder, 'org.Hs.eg.db', categoryType='KEGG', pvalueT=0.1, verbose=FALSE)
Loading required package: org.Hs.eg.db
[1] "GeneAnswers instance has been successfully created!"
[1] "GeneAnswers instance has been successfully created!"
[1] "GeneAnswers instance has been successfully created!"
[1] "GeneAnswers instance has been successfully created!"
[1] "GeneAnswers instance has been successfully created!"
[1] "GeneAnswers instance has been successfully created!"
> output<- getConceptTable(gAKEGGL, catTerm=FALSE, items='geneNum')
> groupReport(output[[1]], gAKEGGL, matrixOfHeatmap=output[[2]], clusterTable=NULL, fileName='KEGGtest.html', catType='KEGG', colorValueColumn=colnames(sampleGroupsData[[1]])[-1])
Loading required package: KEGG.db
[1] "Warning: some genes do not have valid symbols!"
Error in graph(t(el), directed = directed) :
At structure_generators.c:84 : Invalid (negative) vertex id, Invalid vertex id
Calls: groupReport ... .list2graph -> .makeGraph -> graph.edgelist -> graph -> .Call
Execution halted
* 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)