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

Dan Tenenbaum dtenenba at fhcrc.org
Mon Jan 27 19:50:31 CET 2014

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,
> Charles
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