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

[Charles Plessy]

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 |
> 
> 
> 
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