CoverageView 0.99.9
Ernesto Lowy
| Snapshot Date: 2014-04-01 17:43:03 -0700 (Tue, 01 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CoverageView | | Last Changed Rev: 88195 / Revision: 88289 | | Last Changed Date: 2014-03-31 10:57:37 -0700 (Mon, 31 Mar 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ ERROR ] | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/CoverageView.Rcheck'
* using R version 3.1.0 beta (2014-03-27 r65320)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoverageView/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoverageView' version '0.99.9'
* 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 whether package 'CoverageView' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'CoverageView-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cov.interval
> ### Title: arithmetic operation on an interval
> ### Aliases: cov.interval cov.interval,CoverageBamFile-method
> ### cov.interval,CoverageBigWigFile-method
> ### cov.interval,CoverageBamFile,CoverageBamFile-method
> ### cov.interval,CoverageBigWigFile,CoverageBigWigFile-method
>
> ### ** Examples
>
> ##BAM files
>
> #get treatment and control test files
> treat1file<-system.file("extdata","treat.bam",package="CoverageView")
> control1file<-system.file("extdata","ctrl.bam",package="CoverageView")
>
> #create two CoverageBamFile objects representing single-end alignments
> trm1<-CoverageBamFile(treat1file,run_type="single")
> ctl1<-CoverageBamFile(control1file,run_type="single")
>
> #calculate the ratio of the coverages for the defined genomic interval using a bin_width equal to 10 nts
> cov1=cov.interval(trm1,ctl1,chr="chrI",start=1,end=100,bin_width=10,do="ratio")
>
> #create a WIG file with the obtained vector with the ratios
> outfolder=system.file("extdata",package="CoverageView")
> an_outfile1=paste(outfolder,"out.wig",sep="/")
> export.wig(cov1,outfile=an_outfile1)
>
> ##BigWIG files
>
> #get a treatment and control test files
> treat2file<-system.file("extdata","treat.bw",package="CoverageView")
> control2file<-system.file("extdata","ctrl.bw",package="CoverageView")
>
> #create the 'treatment' and 'control' CoverageBigWigFile objects
> trm2<-CoverageBigWigFile(path=treat2file,reads_mapped=28564510)
> ctl2<-CoverageBigWigFile(path=control2file,reads_mapped=26713667)
>
> #calculate the ratio of the coverages for the defined genomic interval
> cov2=cov.interval(trm2,ctl2,bin_width=1,chr="chrI",start=1,end=1000,do='ratio')
Warning in seqinfo(ranges) :
Invalid argument
lseek(5, 64, invalid 'whence' value (106)) failed
Error in seqinfo(ranges) : UCSC library operation failed
Calls: cov.interval ... .class1 -> BigWigSelection -> seqinfo -> seqinfo -> .Call
Execution halted
** running examples for arch 'x64' ... [31s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
cov.matrix 8.19 0.05 8.24
install for i386
* installing *source* package 'CoverageView' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'CoverageView' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoverageView' as CoverageView_0.99.9.zip
* DONE (CoverageView)