Re: [RKI-Spam-Verdacht]Maq: Strange 64bit issue

[Charles Plessy <plessy@debian.org>]

Le Mon, Jul 07, 2008 at 04:09:56PM +0200, Andreas Tille a écrit :
> 
> a colleague of mine stumbled upon Maq at
> 
>    http://sourceforge.net/projects/maq/

> /usr/lib/gcc/i486-linux-gnu/4.3.1/libstdc++.a when searching for -lstdc++
> /usr/bin/ld: cannot find -lstdc++
> collect2: ld returned 1 exit status
> 
> on a recent unstable (on testing it is the same error message excep the
> gcc version string is 4.2.4 instead of 4.3.1).
 
> Any comments to a completely 64 bit uneducated person?

Hi Andreas,

you may have more luck on the debian-amd64 mailing list…

Anyway, Maq had a nice advertisement in a recent review published in
Genome Research, and it is therefore definitely one of the programs we
must add to our collection before the end of the year. I just imported
a rudimentary packaging in our subversion repository. Unfortunately, the
binary building also fails on my machine (powerpc):

g++ -DHAVE_CONFIG_H -I.     -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o pair_stat.o pair_stat.ccg++ -DHAVE_CONFIG_H -I.     -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o indel_soa.o indel_soa.ccindel_soa.cc: In function ‘void fill_counter(bit32_t*, int, nst_bfa1_t*, void*)’:
indel_soa.cc:42: warning: suggest parentheses around + or - inside shift
indel_soa.cc:56: warning: suggest parentheses around + or - inside shift
cc -DHAVE_CONFIG_H -I.     -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c maqmap.c
cc -DHAVE_CONFIG_H -I.     -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c maqmap_conv.c
g++ -DHAVE_CONFIG_H -I.     -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o altchr.o altchr.cc
cc -DHAVE_CONFIG_H -I.     -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c submap.c
g++ -DHAVE_CONFIG_H -I.     -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o rmdup.o rmdup.cc
cc -DHAVE_CONFIG_H -I.     -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c simulate.c
simulate.c: In function ‘simustat_core’:
simulate.c:374: internal compiler error: in expand_expr_real_1, at expr.c:9199
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.3/README.Bugs> for instructions.
make[2]: *** [simulate.o] Erreur 1
make[2]: quittant le répertoire « /home/charles/src/maq-0.6.7 »
make[1]: *** [all] Erreur 2
make[1]: quittant le répertoire « /home/charles/src/maq-0.6.7 »
make: *** [debian/stamp-makefile-build] Erreur 2
dpkg-buildpackage: échec: debian/rules build a produit une erreur de sortie de type 2
debuild: fatal error at line 1319:
dpkg-buildpackage -rfakeroot -D -us -uc failed

Have a nice day,

-- 
Charles Plessy
Debian-Med packaging team,
Tsurumi, Kanagawa, Japan