[Debian-med-packaging] Bug#667161: fastx-toolkit: ftbfs with GCC-4.7

[Matthias Klose]

Package: fastx-toolkit
Version: 0.0.13.1-1
Severity: important
Tags: sid wheezy
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-4.7

The package fails to build in a test rebuild on at least amd64 with
gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
severity of this report may be raised before the wheezy release.

../libfastx/sequence_alignment.h:146:32: error: 'ssize_t' does not name a type

The full build log can be found at:
http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/fastx-toolkit_0.0.13.1-1_unstable-gcc47.log
The last lines of the build log are at the end of this report.

Some hints on fixing these issues can be found at
http://gcc.gnu.org/gcc-4.7/porting_to.html

To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

[...]
make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_reverse_complement'
Making all in fastx_collapser
make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_collapser'
g++ -DHAVE_CONFIG_H -I. -I../..   -I../libfastx -D_FORTIFY_SOURCE=2  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -c -o fastx_collapser.o fastx_collapser.cpp
/bin/bash ../../libtool --tag=CXX   --mode=link g++  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1  -Wl,-z,relro -o fastx_collapser fastx_collapser.o ../libfastx/libfastx.a  
libtool: link: g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastx_collapser fastx_collapser.o  ../libfastx/libfastx.a
make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_collapser'
Making all in fastx_uncollapser
make[4]: Entering directory `/«PKGBUILDDIR»/src/fastx_uncollapser'
g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/gtextutils   -I../libfastx  -I../libfastx -D_FORTIFY_SOURCE=2  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -c -o fastx_uncollapser.o fastx_uncollapser.cpp
/bin/bash ../../libtool --tag=CXX   --mode=link g++  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1  -Wl,-z,relro -o fastx_uncollapser fastx_uncollapser.o -lgtextutils   ../libfastx/libfastx.a  
libtool: link: g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -Wl,-z -Wl,relro -o fastx_uncollapser fastx_uncollapser.o  -lgtextutils ../libfastx/libfastx.a
make[4]: Leaving directory `/«PKGBUILDDIR»/src/fastx_uncollapser'
Making all in seqalign_test
make[4]: Entering directory `/«PKGBUILDDIR»/src/seqalign_test'
g++ -DHAVE_CONFIG_H -I. -I../..   -I../libfastx -D_FORTIFY_SOURCE=2  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -c -o seqalign_test.o seqalign_test.cpp
In file included from seqalign_test.cpp:5:0:
../libfastx/sequence_alignment.h:146:32: error: 'ssize_t' does not name a type
../libfastx/sequence_alignment.h:146:40: error: ISO C++ forbids declaration of 'query_index' with no type [-fpermissive]
../libfastx/sequence_alignment.h:146:59: error: 'ssize_t' does not name a type
../libfastx/sequence_alignment.h:146:67: error: ISO C++ forbids declaration of 'target_index' with no type [-fpermissive]
../libfastx/sequence_alignment.h:244:37: error: 'ssize_t' has not been declared
../libfastx/sequence_alignment.h:244:63: error: 'ssize_t' has not been declared
make[4]: *** [seqalign_test.o] Error 1
make[4]: Leaving directory `/«PKGBUILDDIR»/src/seqalign_test'
make[3]: *** [all-recursive] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [debian/stamp-makefile-build] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2