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

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?

Thanks,
Charles



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