[Bioc-devel] graphite build error on George2

[Enrica]

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.

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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