On Thu, Mar 28, 2013 at 6:28 AM, Enrica enrica.cal...@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 mtmor...@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
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