[Debian-med-packaging] Bug#853677: t-coffee: ftbfs with GCC-7

[Matthias Klose]

Package: src:t-coffee
Version: 11.00.8cbe486-5
Severity: normal
Tags: sid buster
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-7

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-7/g++-7, but succeeds to build with gcc-6/g++-6. The
severity of this report may be raised before the buster release.
There is no need to fix this issue in time for the stretch release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc7-20170126/t-coffee_11.00.8cbe486-5_unstable_gcc7.log
The last lines of the build log are at the end of this report.

To build with GCC 7, either set CC=gcc-7 CXX=g++-7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-7/porting_to.html

[...]
In file included from /usr/include/stdio.h:938:0,
                 from util_lib/util_constraints_list.c:29:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: format output between 6 and 4503 bytes into a destination of size 1000
       __bos (__s), __fmt, __va_arg_pack ());
                                           ^
util_lib/util_constraints_list.c:611:9: warning: '%s' directive writing between 0 and 500 bytes into a region of size 100 [-Wformat-overflow=]
 Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL)
         ^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
                 from util_lib/util_constraints_list.c:29:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: format output between 1 and 501 bytes into a destination of size 100
       __bos (__s), __fmt, __va_arg_pack ());
                                           ^
util_lib/util_constraints_list.c:611:9: warning: '%s' directive writing between 0 and 500 bytes into a region of size 100 [-Wformat-overflow=]
 Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL)
         ^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
                 from util_lib/util_constraints_list.c:29:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: format output between 1 and 501 bytes into a destination of size 100
       __bos (__s), __fmt, __va_arg_pack ());
                                           ^
util_lib/util_constraints_list.c:611:9: warning: '%s' directive writing between 0 and 999 bytes into a region of size 499 [-Wformat-overflow=]
 Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL)
         ^~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:938:0,
                 from util_lib/util_constraints_list.c:29:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: format output between 6 and 4503 bytes into a destination of size 1000
       __bos (__s), __fmt, __va_arg_pack ());
                                           ^
 Linking...
g++: error: util_lib/aln_convertion_util.o: No such file or directory
g++: error: util_lib/util.o: No such file or directory
makefile:8: recipe for target 't_coffee' failed
make[2]: [t_coffee] Error 1 (ignored)
make[2]: Leaving directory '/<<PKGBUILDDIR>>/t_coffee_source'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test -O--sourcedirectory=t_coffee_source
   create-stamp debian/debhelper-build-stamp
 fakeroot debian/rules binary
dh binary --sourcedirectory=t_coffee_source
   dh_testroot -O--sourcedirectory=t_coffee_source
   dh_prep -O--sourcedirectory=t_coffee_source
   dh_auto_install -O--sourcedirectory=t_coffee_source
   dh_install -O--sourcedirectory=t_coffee_source
dh_install: Cannot find (any matches for) "t_coffee_source/t_coffee" (tried in "." and "debian/tmp")
dh_install: t-coffee missing files: t_coffee_source/t_coffee
dh_install: missing files, aborting
debian/rules:13: recipe for target 'binary' failed
make: *** [binary] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2