---------- Forwarded message ---------- From: Barry Grant <bgr...@mccammon.ucsd.edu> Date: Mon, Apr 12, 2010 at 3:27 PM Subject: Re: Bio3D problems with R 2.11. To: Charles Plessy <ple...@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 <bgr...@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 <ple...@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...@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 >>> | lu...@lucas-nussbaum.net http://www.lucas-nussbaum.net/ | >>> | jabber: lu...@nussbaum.fr GPG: 1024D/023B3F4F | >>> >>> >>> >>> _______________________________________________ >>> Debian-med-packaging mailing list >>> debian-med-packag...@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/ > -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
