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 >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >>> >>> >> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel