EnrichmentBrowser 2.0.15
Ludwig Geistlinger
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/EnrichmentBrowser | | Last Changed Rev: 116547 / Revision: 116712 | | Last Changed Date: 2016-04-19 07:09:39 -0700 (Tue, 19 Apr 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings EnrichmentBrowser_2.0.15.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.0.15’
* 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 ‘EnrichmentBrowser’ can be installed ... [30s/30s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘pathview:::parseKGML2Graph2’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘EnrichmentBrowser-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ebrowser
> ### Title: Seamless navigation through enrichment analysis results
> ### Aliases: ebrowser
>
> ### ** Examples
>
> # expression data from file
> exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser")
> pdat.file <- system.file("extdata/pData.tab", package="EnrichmentBrowser")
> fdat.file <- system.file("extdata/fData.tab", package="EnrichmentBrowser")
>
> # getting all human KEGG gene sets
> # hsa.gs <- get.kegg.genesets("hsa")
> gs.file <- system.file("extdata/hsa_kegg_gs.gmt", package="EnrichmentBrowser")
> hsa.gs <- parse.genesets.from.GMT(gs.file)
>
> # set-based enrichment analysis
> ebrowser( meth="ora",
+ exprs=exprs.file, pdat=pdat.file, fdat=fdat.file,
+ gs=hsa.gs, org="hsa", nr.show=3)
Read expression data ...
Normalize ...
Transform probe expression to gene expression ...
DE analysis ...
Execute ORA ...
100 permutations completed
200 permutations completed
300 permutations completed
400 permutations completed
500 permutations completed
600 permutations completed
700 permutations completed
800 permutations completed
900 permutations completed
1000 permutations completed
Creating gene report ...
Creating set view ...
Creating kegg view ...
Info: Downloading xml files for hsa05410, 1/1 pathways..
Info: Downloading png files for hsa05410, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.2-bioc/meat/EnrichmentBrowser.Rcheck/EnrichmentBrowser/results
Info: Writing image file hsa05410.kpath.png
Info: Downloading xml files for hsa04350, 1/1 pathways..
Info: Downloading png files for hsa04350, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.2-bioc/meat/EnrichmentBrowser.Rcheck/EnrichmentBrowser/results
Info: Writing image file hsa04350.kpath.png
Info: Downloading xml files for hsa04622, 1/1 pathways..
Info: Downloading png files for hsa04622, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.2-bioc/meat/EnrichmentBrowser.Rcheck/EnrichmentBrowser/results
Info: Writing image file hsa04622.kpath.png
Genewise differential expression written to de.txt
Your output files are in /home/biocbuild/bbs-3.2-bioc/meat/EnrichmentBrowser.Rcheck/EnrichmentBrowser/results !
Produce html report ...
>
> # compile a gene regulatory network from KEGG pathways
> # hsa.grn <- compile.grn.from.kegg("hsa")
> pwys <- system.file("extdata/hsa_kegg_pwys.zip", package="EnrichmentBrowser")
> hsa.grn <- compile.grn.from.kegg(pwys)
>
> # network-based enrichment analysis
> ebrowser( meth="ggea",
+ exprs=exprs.file, pdat=pdat.file, fdat=fdat.file,
+ gs=hsa.gs, grn=hsa.grn, org="hsa", nr.show=3 )
Read expression data ...
Normalize ...
Transform probe expression to gene expression ...
DE analysis ...
Execute GGEA ...
Creating gene report ...
Creating set view ...
Creating kegg view ...
Info: Downloading xml files for hsa04390, 1/1 pathways..
Info: Downloading png files for hsa04390, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Error in readPNG(paste(kegg.dir, "/", pathway.name, ".png", sep = "")) :
libpng error: Read Error
Calls: ebrowser ... make.kpath.html -> pathview -> keggview.native -> readPNG -> .Call
Execution halted
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.2-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.
* installing *source* package ‘EnrichmentBrowser’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
* DONE (EnrichmentBrowser)