[Debian-med-packaging] Bug#957536: mia: ftbfs with GCC-10

[Matthias Klose]

Package: src:mia
Version: 2.4.6-5
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/mia_2.4.6-5_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

[...]
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d/filter && /usr/bin/c++  -DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H -I/usr/include/eigen3 -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fvisibility=hidden   -DBOOST_TEST_DYN_LINK -o CMakeFiles/test-2dimage-filter-shaped_mean.dir/test_shaped_mean.cc.o -c /<<PKGBUILDDIR>>/mia/2d/filter/test_shaped_mean.cc
[ 30%] Linking CXX executable test-2dimage-filter-distance
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-2dimage-filter-distance.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fvisibility=hidden  -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -fvisibility=hidden -rdynamic CMakeFiles/test-2dimage-filter-distance.dir/test_distance.cc.o CMakeFiles/2dimage-filter-distance-common.dir/distance.cc.o  -o test-2dimage-filter-distance  -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/core -lboost_unit_test_framework ../libmia2dtest-2.4.so.6.0.0 ../libmia2d-2.4.so.6.0.0 ../../core/libmiacore-2.4.so.6.0.0 -lgsl -lgslcblas -lm -lboost_filesystem -lboost_system -lpthread -ldl -lfftw3f -lxml2 -lboost_unit_test_framework 
/usr/bin/ld: CMakeFiles/test-2dimage-filter-distance.dir/test_distance.cc.o: in function `test_distance_double::test_method()':
./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:263: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<float>(mia::T2DImage<float> const&) const'
/usr/bin/ld: CMakeFiles/test-2dimage-filter-distance.dir/test_distance.cc.o: in function `filter<distance_2d_filter::C2DDistance, mia::C2DImage>':
./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:255: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<signed char>(mia::T2DImage<signed char> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:256: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<unsigned char>(mia::T2DImage<unsigned char> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:257: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<short>(mia::T2DImage<short> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:258: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<unsigned short>(mia::T2DImage<unsigned short> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:259: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<int>(mia::T2DImage<int> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:260: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<unsigned int>(mia::T2DImage<unsigned int> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:261: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<long>(mia::T2DImage<long> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:262: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<unsigned long>(mia::T2DImage<unsigned long> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:264: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<double>(mia::T2DImage<double> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:254: undefined reference to `std::shared_ptr<mia::C2DImage> distance_2d_filter::C2DDistance::operator()<bool>(mia::T2DImage<bool> const&) const'
collect2: error: ld returned 1 exit status
make[4]: *** [mia/2d/filter/CMakeFiles/test-2dimage-filter-distance.dir/build.make:97: mia/2d/filter/test-2dimage-filter-distance] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:10579: mia/2d/filter/CMakeFiles/test-2dimage-filter-distance.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[ 30%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/similarity_profile.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++  -DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H -Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fvisibility=hidden -fPIC   -o CMakeFiles/mia3d.dir/similarity_profile.cc.o -c /<<PKGBUILDDIR>>/mia/3d/similarity_profile.cc
[ 30%] Linking CXX executable test-2dimage-filter-binarize
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[ 30%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/splinetransformpenalty.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++  -DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H -Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fvisibility=hidden -fPIC   -o CMakeFiles/mia3d.dir/splinetransformpenalty.cc.o -c /<<PKGBUILDDIR>>/mia/3d/splinetransformpenalty.cc
[ 30%] Linking CXX executable test-2dimage-filter-shaped_mean
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-2dimage-filter-shaped_mean.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fvisibility=hidden  -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -fvisibility=hidden -rdynamic CMakeFiles/test-2dimage-filter-shaped_mean.dir/test_shaped_mean.cc.o CMakeFiles/2dimage-filter-shaped_mean-common.dir/shaped_mean.cc.o  -o test-2dimage-filter-shaped_mean  -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/core -lboost_unit_test_framework ../libmia2dtest-2.4.so.6.0.0 ../libmia2d-2.4.so.6.0.0 ../../core/libmiacore-2.4.so.6.0.0 -lgsl -lgslcblas -lm -lboost_filesystem -lboost_system -lpthread -ldl -lfftw3f -lxml2 -lboost_unit_test_framework 
[ 30%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/stackdisttrans.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++  -DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H -Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fvisibility=hidden -fPIC   -o CMakeFiles/mia3d.dir/stackdisttrans.cc.o -c /<<PKGBUILDDIR>>/mia/3d/stackdisttrans.cc
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[ 30%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/timestep.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++  -DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H -Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fvisibility=hidden -fPIC   -o CMakeFiles/mia3d.dir/timestep.cc.o -c /<<PKGBUILDDIR>>/mia/3d/timestep.cc
[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/trackpoint.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++  -DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H -Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fvisibility=hidden -fPIC   -o CMakeFiles/mia3d.dir/trackpoint.cc.o -c /<<PKGBUILDDIR>>/mia/3d/trackpoint.cc
[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/transform.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++  -DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H -Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fvisibility=hidden -fPIC   -o CMakeFiles/mia3d.dir/transform.cc.o -c /<<PKGBUILDDIR>>/mia/3d/transform.cc
[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/transformfactory.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++  -DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H -Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -fvisibility=hidden -fPIC   -o CMakeFiles/mia3d.dir/transformfactory.cc.o -c /<<PKGBUILDDIR>>/mia/3d/transformfactory.cc
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[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/vectorfield.cc.o
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[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/vfregularizer.cc.o
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/cmake -E cmake_symlink_library libmia3d-2.4.so.6.0.0 libmia3d-2.4.so.6 libmia3d-2.4.so
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make[2]: *** [Makefile:144: all] Error 2
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dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
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