[Debian-med-packaging] Bug#957836: spoa: ftbfs with GCC-10

[Matthias Klose]

Package: src:spoa
Version: 3.0.1-1
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

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-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/spoa_3.0.1-1_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html

[...]
      |                    ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/alignment_engine.cpp:41:20: error: ‘invalid_argument’ is not a member of ‘std’
   41 |         throw std::invalid_argument("[spoa::createAlignmentEngine] error: "
      |                    ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/alignment_engine.cpp:45:20: error: ‘invalid_argument’ is not a member of ‘std’
   45 |         throw std::invalid_argument("[spoa::createAlignmentEngine] error: "
      |                    ^~~~~~~~~~~~~~~~
make[3]: *** [CMakeFiles/spoa.dir/build.make:66: CMakeFiles/spoa.dir/src/alignment_engine.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [CMakeFiles/spoa_static.dir/build.make:66: CMakeFiles/spoa_static.dir/src/alignment_engine.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
[ 31%] Building CXX object CMakeFiles/spoa_static.dir/src/graph.cpp.o
/usr/bin/c++   -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/config -I/<<PKGBUILDDIR>>/src  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG   -std=c++11 -o CMakeFiles/spoa_static.dir/src/graph.cpp.o -c /<<PKGBUILDDIR>>/src/graph.cpp
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In function ‘std::unique_ptr<spoa::AlignmentEngine> spoa::createSimdAlignmentEngine(spoa::AlignmentType, spoa::AlignmentSubtype, int8_t, int8_t, int8_t, int8_t, int8_t, int8_t)’:
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:293:74: warning: unused parameter ‘type’ [-Wunused-parameter]
  293 | std::unique_ptr<AlignmentEngine> createSimdAlignmentEngine(AlignmentType type,
      |                                                            ~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:294:22: warning: unused parameter ‘subtype’ [-Wunused-parameter]
  294 |     AlignmentSubtype subtype, std::int8_t m, std::int8_t n, std::int8_t g,
      |     ~~~~~~~~~~~~~~~~~^~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:294:43: warning: unused parameter ‘m’ [-Wunused-parameter]
  294 |     AlignmentSubtype subtype, std::int8_t m, std::int8_t n, std::int8_t g,
      |                               ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:294:58: warning: unused parameter ‘n’ [-Wunused-parameter]
  294 |     AlignmentSubtype subtype, std::int8_t m, std::int8_t n, std::int8_t g,
      |                                              ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:294:73: warning: unused parameter ‘g’ [-Wunused-parameter]
  294 |     AlignmentSubtype subtype, std::int8_t m, std::int8_t n, std::int8_t g,
      |                                                             ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:295:17: warning: unused parameter ‘e’ [-Wunused-parameter]
  295 |     std::int8_t e, std::int8_t q, std::int8_t c) {
      |     ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:295:32: warning: unused parameter ‘q’ [-Wunused-parameter]
  295 |     std::int8_t e, std::int8_t q, std::int8_t c) {
      |                    ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:295:47: warning: unused parameter ‘c’ [-Wunused-parameter]
  295 |     std::int8_t e, std::int8_t q, std::int8_t c) {
      |                                   ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function ‘virtual void spoa::SimdAlignmentEngine::prealloc(uint32_t, uint32_t)’:
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:358:50: warning: unused parameter ‘max_sequence_size’ [-Wunused-parameter]
  358 | void SimdAlignmentEngine::prealloc(std::uint32_t max_sequence_size,
      |                                    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:359:19: warning: unused parameter ‘alphabet_size’ [-Wunused-parameter]
  359 |     std::uint32_t alphabet_size) {
      |     ~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function ‘void spoa::SimdAlignmentEngine::realloc(uint32_t, uint32_t, uint32_t)’:
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:380:49: warning: unused parameter ‘matrix_width’ [-Wunused-parameter]
  380 | void SimdAlignmentEngine::realloc(std::uint32_t matrix_width,
      |                                   ~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:381:19: warning: unused parameter ‘matrix_height’ [-Wunused-parameter]
  381 |     std::uint32_t matrix_height, std::uint32_t num_codes) {
      |     ~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:381:48: warning: unused parameter ‘num_codes’ [-Wunused-parameter]
  381 |     std::uint32_t matrix_height, std::uint32_t num_codes) {
      |                                  ~~~~~~~~~~~~~~^~~~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function ‘virtual spoa::Alignment spoa::SimdAlignmentEngine::align(const char*, uint32_t, const std::unique_ptr<spoa::Graph>&)’:
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:649:50: warning: unused parameter ‘sequence’ [-Wunused-parameter]
  649 | Alignment SimdAlignmentEngine::align(const char* sequence,
      |                                      ~~~~~~~~~~~~^~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:166: CMakeFiles/spoa.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:139: CMakeFiles/spoa_static.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:133: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:13: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2