[Bioc-devel] graphite build error on George2

On 03/28/2013 03:20 AM, Enrica wrote:
Dear Bioconductor,

I'm one of the authors of the graphite package.

I've noticed that the build host george2 seems to have a problem building
the package. In particular, it seems there is a segmentation fault caused
by the function sp_moralize(). This belongs to the CRAN package gRbase,
which we indirectly depend upon because we use topologyGSA (CRAN) and
clipper (BioC).

Unfortunately, we have been thus far unable to reproduce the error on our
Linux systems. Those include: Debian Testing - 64 bit, Ubuntu 12.10 and
Ubuntu LTS 12.04.1. We are in touch with the clipper package maintainer
that has the same problem.

We would clearly like understand how to fix this in time for the 2.12
release, but being unable to reproduce the issue makes things quite
difficult. Do you have any suggestion?
The basic approach is outlined here

   http://bioconductor.org/developers/c-debugging/
probably my response is a little too brief for your problem! I'd start by 
creating the source code for the vignette

   R CMD Stangle graphite/inst/doc/graphite.Rnw

and then

   ## sanity check -- does the vignette run?
   R -f graphite.R
   R -d valgrind -f graphite.R

Martin
Martin

Thanks in advance!

Best,
Enrica

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[Bioc-devel] graphite build error on George2

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