compEpiTools 1.0.4
Kamal Kishore
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/compEpiTools | | Last Changed Rev: 101596 / Revision: 102249 | | Last Changed Date: 2015-03-30 07:52:59 -0700 (Mon, 30 Mar 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | ERROR | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ ERROR ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch compEpiTools_1.0.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/compEpiTools.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compEpiTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compEpiTools’ version ‘1.0.4’
* 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 ‘compEpiTools’ can be installed ... [55s/99s] 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 ... OK
* 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 ‘compEpiTools-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotStallingIndex
> ### Title: Stalling Index plots
> ### Aliases: plotStallingIndex
>
> ### ** Examples
>
> require(TxDb.Mmusculus.UCSC.mm9.knownGene)
Loading required package: TxDb.Mmusculus.UCSC.mm9.knownGene
Loading required package: GenomicFeatures
Attaching package: ‘GenomicFeatures’
The following object is masked from ‘package:topGO’:
genes
> require(org.Mm.eg.db)
Loading required package: org.Mm.eg.db
> txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
> isActiveSeq(txdb) <- c(rep(FALSE,18), TRUE, rep(FALSE, length(isActiveSeq(txdb))-19))
> # pointing to Pol2 BAM file
> # BAM file from the GEO GSM1234478 sample, limited to chr19:3200000-4000000
> Pol2bam <- system.file("extdata", "Pol2.bam", package="compEpiTools")
> # loading Pol2 peaks as a GRanges object
> # built based on the BED file from the GEO GSM1234478 sample
> # limited to chr19:3200000-4000000
> Pol2GR <- system.file("extdata", "Pol2GR.Rda", package="compEpiTools")
> load(Pol2GR)
> egs <- distanceFromTSS(Pol2GR, txdb=txdb)
> egs <- unique(egs$nearest_gene_id)
> SI_matrix <- stallingIndex(BAMlist=list(Pol2bam), peakGRlist=list(Pol2GR),
+ genesList=list(egs), transcriptDB=txdb, countMode='gene')
Error in stallingIndex(BAMlist = list(Pol2bam), peakGRlist = list(Pol2GR), :
genesList has to contain characters ...
Execution halted
* installing *source* package ‘compEpiTools’ ...
** R
** inst
** preparing package for lazy loading
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (compEpiTools)