gcc-4.3 build failure on G5 powerpc.
Dear all,
I am trying to build a program, `Maq', in order to make a Debian package
of it. Unfortunately, gcc crashes when compiling it on powerpc:
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
/usr/bin/make -C .
make[1]: Entering directory `/home/charles/debian/debian-med/trunk/packages/maq/build-area/maq-0.6.7'
cd . && /bin/sh /home/charles/debian/debian-med/trunk/packages/maq/build-area/maq-0.6.7/missing --run autoheader
rm -f stamp-h1
touch config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
/usr/bin/make all-am
make[2]: Entering directory `/home/charles/debian/debian-med/trunk/packages/maq/build-area/maq-0.6.7'
cc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c main.c
cc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c const.c
cc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c seq.c
cc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c bfa.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o read.o read.cc
cc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c fasta2bfa.c
cc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c fastq2bfq.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o merge.o merge.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o match_aux.o match_aux.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o match.o match.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o sort_mapping.o sort_mapping.cc
sort_mapping.cc: In function ‘int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)’:
sort_mapping.cc:59: warning: suggest parentheses around arithmetic in operand of ^
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o assemble.o assemble.cc
assemble.cc: In function ‘base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)’:
assemble.cc:106: warning: suggest parentheses around arithmetic in operand of |
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o pileup.o pileup.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o mapcheck.o mapcheck.cc
cc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c get_pos.c
cc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c assopt.c
cc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c aux_utils.c
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o rbcc.o rbcc.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o subsnp.o subsnp.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o pair_stat.o pair_stat.cc
g++ -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -g -O2 -g -Wall -O2 -c -o indel_soa.o indel_soa.cc
indel_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] Error 1
make[2]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/maq/build-area/maq-0.6.7'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/charles/debian/debian-med/trunk/packages/maq/build-area/maq-0.6.7'
make: *** [debian/stamp-makefile-build] Error 2
dpkg-buildpackage: failure: debian/rules build gave error exit status 2
Command dpkg-buildpackage -us -uc failed in <unknown>, how to continue now? [Qri?]: Q
Aborting.
The crash does not happen with DEB_BUILD_OPTIONS=noopt set…
The preliminary debian package is in Debian-Med's Subversion repository:
svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/
Maq is on Sourceforge:
http://downloads.sourceforge.net/maq/maq-0.6.7.tar.bz2
Do you think that it is a bug in Maq or in gcc ?
Have a nice day,
--
Charles Plessy
Debian-Med packaging team
Tsurumi, Kanagawa, Japan
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