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

2014-01-28 Thread Warden, Charles
To: Warden, Charles Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Problem running Perl script with R-devel - Original Message - From: Charles Warden cwar...@coh.org To: Charles Warden cwar...@coh.org, Dan Tenenbaum dtene...@fhcrc.org Cc: bioc-devel@r-project.org Sent: Monday

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

2014-01-28 Thread Dan Tenenbaum
Hi Charles, - Original Message - From: Charles Warden cwar...@coh.org To: Dan Tenenbaum dtene...@fhcrc.org Cc: bioc-devel@r-project.org Sent: Tuesday, January 28, 2014 2:12:09 PM Subject: RE: [Bioc-devel] Problem running Perl script with R-devel Hi, For those interested

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

2014-01-27 Thread Dan Tenenbaum
Hi Charles, - Original Message - From: Charles Warden cwar...@coh.org To: bioc-devel@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:

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

2014-01-27 Thread Warden, Charles
, 2014 10:51 AM To: Warden, Charles Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Problem running Perl script with R-devel Hi Charles, - Original Message - From: Charles Warden cwar...@coh.org To: bioc-devel@r-project.org Sent: Monday, January 27, 2014 10:45:42 AM Subject: [Bioc

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

2014-01-27 Thread Warden, Charles
Tenenbaum' Cc: bioc-devel@r-project.org 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

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

2014-01-27 Thread Dan Tenenbaum
- Original Message - From: Charles Warden cwar...@coh.org To: Charles Warden cwar...@coh.org, Dan Tenenbaum dtene...@fhcrc.org Cc: bioc-devel@r-project.org Sent: Monday, January 27, 2014 11:19:46 AM Subject: RE: [Bioc-devel] Problem running Perl script with R-devel Hi Dan

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

2014-01-27 Thread Dan Tenenbaum
- Original Message - From: Dan Tenenbaum dtene...@fhcrc.org To: Charles Warden cwar...@coh.org Cc: bioc-devel@r-project.org Sent: Monday, January 27, 2014 11:26:43 AM Subject: Re: [Bioc-devel] Problem running Perl script with R-devel - Original Message - From

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

2014-01-27 Thread Dan Tenenbaum
- Original Message - From: Charles Warden cwar...@coh.org To: Dan Tenenbaum dtene...@fhcrc.org Cc: bioc-devel@r-project.org Sent: Monday, January 27, 2014 11:38:10 AM Subject: RE: [Bioc-devel] Problem running Perl script with R-devel Hi Dan, 1) When I first ran the code

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

2014-01-27 Thread Warden, Charles
11:54 AM To: Warden, Charles Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Problem running Perl script with R-devel - Original Message - From: Charles Warden cwar...@coh.org To: Dan Tenenbaum dtene...@fhcrc.org Cc: bioc-devel@r-project.org Sent: Monday, January 27, 2014 11:38

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

2014-01-27 Thread Henrik Bengtsson
): [1] tools_3.1.0 Please let me know if you need anything else. Thanks, Charles -Original Message- From: Dan Tenenbaum [mailto:dtene...@fhcrc.org] Sent: Monday, January 27, 2014 10:51 AM To: Warden, Charles Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Problem running Perl

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

2014-01-27 Thread Dan Tenenbaum
- Original Message - From: Charles Warden cwar...@coh.org To: Charles Warden cwar...@coh.org, Dan Tenenbaum dtene...@fhcrc.org Cc: bioc-devel@r-project.org Sent: Monday, January 27, 2014 11:19:46 AM Subject: RE: [Bioc-devel] Problem running Perl script with R-devel Hi Dan

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

2014-01-27 Thread Warden, Charles
: Monday, January 27, 2014 12:38 PM To: Warden, Charles Cc: Dan Tenenbaum; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Problem running Perl script with R-devel Some quick ideas: 1. Before making the full call, call res - system2(perlbin, -v) to assert no errors about running Perl itself

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

2014-01-27 Thread Warden, Charles
] Sent: Monday, January 27, 2014 12:41 PM To: Warden, Charles Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Problem running Perl script with R-devel - Original Message - From: Charles Warden cwar...@coh.org To: Charles Warden cwar...@coh.org, Dan Tenenbaum dtene...@fhcrc.org Cc