[Debian-med-packaging] Bug#853666: spades: ftbfs with GCC-7

[Matthias Klose]

Package: src:spades
Version: 3.9.1+dfsg-1
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/spades_3.9.1+dfsg-1_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

[...]
                  ^~~~~~~~
/<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/dev_support/segfault_handler.hpp:21:33: error: expected ')' before 'const'
     segfault_handler(callback_t const &cb = 0) {
                                 ^~~~~
/<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/dev_support/segfault_handler.hpp:35:12: error: 'callback_t' does not name a type; did you mean 'clock_t'?
     static callback_t &callback() {
            ^~~~~~~~~~
            clock_t
/<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/dev_support/segfault_handler.hpp: In destructor 'segfault_handler::~segfault_handler()':
/<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/dev_support/segfault_handler.hpp:30:9: error: 'callback' was not declared in this scope
         callback() = 0;
         ^~~~~~~~
/<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/dev_support/segfault_handler.hpp:30:9: note: suggested alternative: 'calloc'
         callback() = 0;
         ^~~~~~~~
         calloc
/<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/dev_support/segfault_handler.hpp: In static member function 'static void segfault_handler::handler(int)':
/<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/dev_support/segfault_handler.hpp:45:17: error: 'callback' was not declared in this scope
             if (callback())
                 ^~~~~~~~
/<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/dev_support/segfault_handler.hpp:45:17: note: suggested alternative: 'calloc'
             if (callback())
                 ^~~~~~~~
                 calloc
In file included from /<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/data_structures/sequence/seq.hpp:38:0,
                 from /<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/data_structures/sequence/sequence.hpp:16,
                 from /<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/data_structures/indices/edge_info_updater.hpp:12,
                 from /<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/data_structures/indices/edge_position_index.hpp:11,
                 from /<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/pipeline/graph_pack.hpp:10,
                 from /<<BUILDDIR>>/spades-3.9.1+dfsg/src/projects/spades/launch.hpp:12,
                 from /<<BUILDDIR>>/spades-3.9.1+dfsg/src/projects/spades/main.cpp:15:
/<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/data_structures/sequence/nucl.hpp: In member function 'bool nucl_complement_functor::operator()(char) const':
/<<BUILDDIR>>/spades-3.9.1+dfsg/src/modules/data_structures/sequence/nucl.hpp:84:19: warning: ?: using integer constants in boolean context [-Wint-in-bool-context]
         return cc ? cc : 'N';
                ~~~^~~~~~~~~~
projects/spades/CMakeFiles/spades.dir/build.make:62: recipe for target 'projects/spades/CMakeFiles/spades.dir/main.cpp.o' failed
make[4]: *** [projects/spades/CMakeFiles/spades.dir/main.cpp.o] Error 1
make[4]: Leaving directory '/<<BUILDDIR>>/spades-3.9.1+dfsg/build_spades'
CMakeFiles/Makefile2:1421: recipe for target 'projects/spades/CMakeFiles/spades.dir/all' failed
make[3]: *** [projects/spades/CMakeFiles/spades.dir/all] Error 2
make[3]: Leaving directory '/<<BUILDDIR>>/spades-3.9.1+dfsg/build_spades'
Makefile:149: recipe for target 'all' failed
make[2]: *** [all] Error 2
make[2]: Leaving directory '/<<BUILDDIR>>/spades-3.9.1+dfsg/build_spades'
debian/rules:41: recipe for target 'override_dh_auto_build' failed
make[1]: *** [override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/spades-3.9.1+dfsg'
debian/rules:23: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2