[Debian-med-packaging] Bug#577386: Fwd: Bio3D problems with R 2.11.

[Barry Grant]

---------- Forwarded message ----------
From: Barry Grant <bgrant at mccammon.ucsd.edu>
Date: Mon, Apr 12, 2010 at 3:27 PM
Subject: Re: Bio3D problems with R 2.11.
To: Charles Plessy <plessy at debian.org>


Dear Charles,
I have updated the Bio3D package so it should now install correctly
with the R 2.11.0
< http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.0-8.tar.gz >
Thanks again for your bug report.
All best,
Barry

On Mon, Apr 12, 2010 at 11:11 AM, Barry Grant <bgrant at mccammon.ucsd.edu> wrote:
> Thanks for the note Charles, I will have a look into this issue and
> get back to you.
> All best,
> Barry
>
>
> On Sun, Apr 11, 2010 at 5:51 AM, Charles Plessy <plessy at debian.org> wrote:
>> Dear Barry,
>>
>> Bio3D is distributed in its version 1.0-7 by Debian, and in one of our
>> automated QA tests, we realised that our package will not build with the latest
>> version of R that we distribute, the initial beta release (r51661) of R 2.11.0.
>>
>> You can find below a tail of the build log, with the error that stops the build.
>>
>> I am not intimate with R development, so I can not tell if it is a regression in
>> R 2.11.0, or a change to which Bio3D has to adapt. What is your impression?
>>
>> Best regards,
>>
>> -- Charles Plessy, Debian Med packaging team, Tsurumi, Kanagawa, Japan.
>>
>> Le Sun, Apr 11, 2010 at 10:15:57AM +0200, Lucas Nussbaum a écrit :
>>> Source: r-other-bio3d
>>> Version: 1.0-7-1
>>> Severity: serious
>>> Tags: squeeze sid
>>> User: debian-qa at lists.debian.org
>>> Usertags: qa-ftbfs-20100410 qa-ftbfs
>>> Justification: FTBFS on amd64
>>>
>>> Hi,
>>>
>>> During a rebuild of all packages in sid, your package failed to build on
>>> amd64.
>>>
>>> Relevant part:
>>> >  /usr/bin/fakeroot debian/rules binary
>>> > test -x debian/rules
>>> > dh_testroot
>>> > dh_clean -k
>>> > dh_installdirs -A
>>> > mkdir -p "."
>>> > dh_installdirs              usr/lib/R/site-library
>>> > if test -f /usr/bin/xvfb-run; then                  \
>>> >                      xvfb-run                       \
>>> >                             R CMD INSTALL -l /build/user-r-other-bio3d_1.0-7-1-amd64-lI2VR2/r-other-bio3d-1.0-7/debian/r-other-bio3d/usr/lib/R/site-library --clean     \
>>> >                                      . ;    \
>>> >             else                                                    \
>>> >                      R CMD INSTALL -l /build/user-r-other-bio3d_1.0-7-1-amd64-lI2VR2/r-other-bio3d-1.0-7/debian/r-other-bio3d/usr/lib/R/site-library        \
>>> >                                     --clean  . ;\
>>> >             fi
>>> > * installing *source* package 'bio3d' ...
>>> > ** R
>>> > Error in parse(outFile) : embedded nul in string: '\0'
>>> > ERROR: unable to collate files for package 'bio3d'
>>> > * removing '/build/user-r-other-bio3d_1.0-7-1-amd64-lI2VR2/r-other-bio3d-1.0-7/debian/r-other-bio3d/usr/lib/R/site-library/bio3d'
>>> > make: *** [R_any_arch] Error 1
>>>
>>> The full build log is available from:
>>>    http://people.debian.org/~lucas/logs/2010/04/10/r-other-bio3d_1.0-7-1_lsid64.buildlog
>>>
>>> A list of current common problems and possible solutions is available at
>>> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
>>>
>>> About the archive rebuild: The rebuild was done on about 50 AMD64 nodes
>>> of the Grid'5000 platform, using a clean chroot.  Internet was not
>>> accessible from the build systems.
>>>
>>> --
>>> | Lucas Nussbaum
>>> | lucas at lucas-nussbaum.net   http://www.lucas-nussbaum.net/ |
>>> | jabber: lucas at nussbaum.fr             GPG: 1024D/023B3F4F |
>>>
>>>
>>>
>>> _______________________________________________
>>> Debian-med-packaging mailing list
>>> Debian-med-packaging at lists.alioth.debian.org
>>> http://lists.alioth.debian.org/mailman/listinfo/debian-med-packaging
>>
>
>
>
> --
> B. J. Grant PhD
> Department of Chemistry & Biochemistry
> University of California, San Diego
> La Jolla, CA 92093-0365, USA
> <  http://mccammon.ucsd.edu/~bgrant/  >
>



--
B. J. Grant PhD
Department of Chemistry & Biochemistry
University of California, San Diego
La Jolla, CA 92093-0365, USA
<  http://mccammon.ucsd.edu/~bgrant/  >



-- 
B. J. Grant PhD
Department of Chemistry & Biochemistry
University of California, San Diego
La Jolla, CA 92093-0365, USA
<  http://mccammon.ucsd.edu/~bgrant/  >