[Bioc-devel] Problem running Perl script with R-devel

[Dan Tenenbaum]

Hi Charles,

----- Original Message -----
> From: "Charles Warden" <cwarden at coh.org>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: bioc-devel at r-project.org
> Sent: Monday, January 27, 2014 10:56:45 AM
> Subject: RE: [Bioc-devel] Problem running Perl script with R-devel
> 
> Hi Dan,
> 
> Thanks for your prompt response. To simplify things, I'll provide the
> code for the truncated dataset:
> 
> library("COHCAP")
> 
> dir <- system.file("extdata", package="COHCAP")
> beta.file <- file.path(dir,"GSE42308_truncated.txt")
> sample.file <- file.path(dir,"sample_GSE42308.txt")
> project.folder <-
> "T:\\BIC\\cwarden\\Methylation_Package\\Protocol_Exchange\\minfi_example"
> project.name <- "450k_avg_by_island_test"
> beta.table <- COHCAP.annotate(beta.file, project.name,
> project.folder,
> 				platform="450k-UCSC")
> 
> 
> filtered.sites <- COHCAP.site(sample.file, beta.table, project.name,
> 				project.folder, ref="parental")
> 
> And here is the sessionInfo() and warning() outputs:
> 
> Warning message:
> running command 'perl C:/Program
> Files/R/R-devel/library/COHCAP/Perl/create_wig_files.pl
> T:\BIC\cwarden\Methylation_Package\Protocol_Exchange\minfi_example/CpG_Site/450k_avg_by_island_test_wig/temp.txt
> T:\BIC\cwarden\Methylation_Package\Protocol_Exchange\minfi_example/CpG_Site/450k_avg_by_island_test_wig'
> had status 2
> 
> > sessionInfo()
> R Under development (unstable) (2014-01-20 r64849)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> 
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] COHCAP_0.99.5     COHCAPanno_0.99.2 WriteXLS_3.3.1
> 
> loaded via a namespace (and not attached):
> [1] tools_3.1.0
> 
> Please let me know if you need anything else.
> 

I can't reproduce the problem on either mac or windows. I changed project.folder to tempdir() but otherwise left your code alone.

Do you have a perl command in your PATH? 

What's the output of traceback() after you get the error? What are the arguments being passed to system()?

Dan



> Thanks,
> Charles
> 
> -----Original Message-----
> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
> Sent: Monday, January 27, 2014 10:51 AM
> To: Warden, Charles
> Cc: bioc-devel at r-project.org
> Subject: Re: [Bioc-devel] Problem running Perl script with R-devel
> 
> Hi Charles,
> 
> 
> ----- Original Message -----
> > From: "Charles Warden" <cwarden at coh.org>
> > To: bioc-devel at r-project.org
> > Sent: Monday, January 27, 2014 10:45:42 AM
> > Subject: [Bioc-devel] Problem running Perl script with R-devel
> > 
> > Hi,
> > 
> > I am testing out my newly released COHCAP package:
> > 
> > http://bioconductor.org/packages/devel/bioc/html/COHCAP.html
> > 
> > I didn't see any warnings when I created the package, and there
> > weren't any warnings when Bioconductor tests the package (on any of
> > the operating systems).
> > 
> > However, I have been testing the package using R-devel (since the
> > package is a currently only available as a devel package, it looks
> > like I can only use lazy loading with R-devel), and I've noticed
> > that the Perl command (creating the .wig files within the function
> > COHCAP.site()) doesn't work properly for either the truncated demo
> > dataset that is included with the package or the entire dataset
> > that
> > I am trying to use to test the package.
> > 
> > To be clear, I can download COHCAP and COHCAPanno and use R CMD
> > INSTALL to run the package in the normal version of R (v.3.0.2),
> > and
> > the package runs just fine with both the truncated and full
> > datasets.
> > 
> > I am trying to provide users with instructions on how to use the
> > package while it is only available as a devel version.  I'm trying
> > to make the instructions as simple as possible, so I was hoping to
> > use the lazy loading via biocLite("COHCAP").
> > 
> > I am running R-devel on Windows (v.3.1.0 pre-release) and the
> > system() command script is existing with status 2.
> > 
> > Does anyone know what is causing this error to specifically occur
> > with R-devel?
> > 
> 
> Can you provide the exact commands you entered which caused the
> error? As well as the output of sessionInfo()?
> Thanks,
> Dan
> 
> 
> 
> > Thanks,
> > Charles
> > 
> > 
> > 
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