[Bioc-devel] graphite build error on George2

[Martin Morgan]

On 03/28/2013 05:40 AM, Martin Morgan wrote:
> 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
>>
>>     [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>


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