[Bioc-devel] graphite build error on George2

[Dan Tenenbaum]

On Thu, Mar 28, 2013 at 6:28 AM, Enrica <enrica.calura at gmail.com> wrote:
> Dear Martin,
>
> we tried that and everything worked correctly.
>
> As I was trying to stress in my previous message, we are unable to
> reproduce that segfault reported in george2 build logs. In other
> terms, george2 is the only host to our knowledge exhibiting such
> problem.


graphite and clipper are building without error today after upgrading
to R-3.0 RC.

Dan


>
> It is hard for us to make any hypotesis about the real cause of the
> problem without knowing the exact configuration of such host.
>
> Thanks again for the help.
>
> Best regards,
> Enrica
>
>
>
> 2013/3/28 Martin Morgan <mtmorgan at fhcrc.org>:
>> 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]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>
>>
>>
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>>
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>
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