[Debian-med-packaging] Bug#667161: FASTX-Toolkit faisl to build with GCC-4.7.

[Charles Plessy]

Dear Gordon,

Debian distributes FASTX-Toolkit, and after a mass-rebuild against GCC 4.7, we
noticed the following error:

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

You can see below for more context.

Do you think you can release an updated version of FASTX-Toolkit ?

I am sending a copy of this message in our public bug tracker
(667161 at bugs.debian.org).  Please feel free to do the same in your answer. 
The archive is available at the following URL.

  http://bugs.debian.org/667161

Have a nice day,

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

Le Tue, Apr 03, 2012 at 11:08:46PM +0000, Matthias Klose a écrit :
> 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
> 
> 
> 

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-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan