[Debian-med-packaging] Bug#643852: mafft: FTBFS on ia64: partQalignmm.c:210:1: internal compiler error: in code_motion_path_driver, at sel-sched.c:6575

[Luca Capello]

Package: gcc-4.6
Version: 4.6.1-9
Severity: normal
Affects: mafft
Usertags: unige.ch-jmlab

Hi there!

While looking if it would be possible to backport mafft to squeeze I
discovered that mafft FTBFS on ia64 [1] and I could reproduce it on
merulo.d.o [2], from where the output and attached file come.  Given
that is seems to be a bug in gcc, reporting to this latter package (with
the version available on the sid dchroot on merulo.d.o) and adding the
Affects: to the former (and cc:ing its maintainer).

--8<---------------cut here---------------start------------->8---
dpkg-buildpackage -rfakeroot -D -us -uc
dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS = 
dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = 
dpkg-buildpackage: source package mafft
dpkg-buildpackage: source version 6.860-1
[...]
make[1]: Entering directory `/home/gismo/mafft-6.860'
/usr/bin/make -C core PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft
make[2]: Entering directory `/home/gismo/mafft-6.860/core'
gcc  -Denablemultithread -O3 -c mtxutl.c
gcc  -Denablemultithread -O3 -c io.c
gcc  -Denablemultithread -O3 -c mltaln9.c
gcc  -Denablemultithread -O3 -c tddis.c
gcc  -Denablemultithread -O3 -c constants.c
gcc  -Denablemultithread -O3 -c nj.c
gcc  -Denablemultithread -O3 -c partQalignmm.c  
partQalignmm.c: In function 'part_imp_match_init_strictQ':
partQalignmm.c:210:1: internal compiler error: in code_motion_path_driver, at sel-sched.c:6575
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.6/README.Bugs> for instructions.
Preprocessed source stored into /tmp/ccOGbQFN.out file, please attach this to your bugreport.
make[2]: *** [partQalignmm.o] Error 1
make[2]: Leaving directory `/home/gismo/mafft-6.860/core'
make[1]: *** [override_dh_auto_build] Error 2
make[1]: Leaving directory `/home/gismo/mafft-6.860'
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
--8<---------------cut here---------------end--------------->8---

[1] <https://buildd.debian.org/status/fetch.php?pkg=mafft&arch=ia64&ver=6.860-1&stamp=1316327156>
[2] <http://db.debian.org/machines.cgi?host=merulo>

Thx, bye,
Gismo / Luca

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