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 (667...@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-...@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 > > > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". 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