Bug#1133626: schroedinger-coordgenlibs: ftbfs with GCC-16

[Emanuele Rocca]

Package: src:schroedinger-coordgenlibs
Version: 3.0.2-3
Severity: important
Tags: sid forky ftbfs
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-16

Hi,

schroedinger-coordgenlibs fails to build in a test rebuild on at least amd64 and arm64 with
gcc-16/g++-16, but builds properly with gcc-15/g++-15. The severity of this
report will be raised before the forky release.

The full build log can be found at:
https://people.debian.org/~ema/gcc-16-rebuilds/output-1/schroedinger-coordgenlibs_arm64.build.xz

The last lines of the build log are at the end of this report.

To build with GCC 16, either set CC=gcc-16 CXX=g++-16 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures include unused (but set) variables, array subscripts
partly outside array bounds, and new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-16/porting_to.html

Please only close this issue after double-checking that the package can be
built correctly with GCC 16.

Please do not reassign this bug to another package. If a fix in another package
is required, then file a bug for the other package (or clone), and mark this
bug as blocked by the bug in the other package.

[...]


/usr/bin/c++ -DIN_COORDGEN -Dcoordgen_EXPORTS  -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fPIC -fvisibility=hidden   -Wall -Wextra -Werror -MD -MT CMakeFiles/coordgen.dir/sketcherMinimizerMarchingSquares.cpp.o -MF CMakeFiles/coordgen.dir/sketcherMinimizerMarchingSquares.cpp.o.d -o CMakeFiles/coordgen.dir/sketcherMinimizerMarchingSquares.cpp.o -c /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/sketcherMinimizerMarchingSquares.cpp
/usr/bin/c++ -DIN_COORDGEN -Dcoordgen_EXPORTS  -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fPIC -fvisibility=hidden   -Wall -Wextra -Werror -MD -MT CMakeFiles/coordgen.dir/sketcherMinimizerFragment.cpp.o -MF CMakeFiles/coordgen.dir/sketcherMinimizerFragment.cpp.o.d -o CMakeFiles/coordgen.dir/sketcherMinimizerFragment.cpp.o -c /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/sketcherMinimizerFragment.cpp
/usr/bin/c++ -DIN_COORDGEN -Dcoordgen_EXPORTS  -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fPIC -fvisibility=hidden   -Wall -Wextra -Werror -MD -MT CMakeFiles/coordgen.dir/sketcherMinimizerAtom.cpp.o -MF CMakeFiles/coordgen.dir/sketcherMinimizerAtom.cpp.o.d -o CMakeFiles/coordgen.dir/sketcherMinimizerAtom.cpp.o -c /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/sketcherMinimizerAtom.cpp
/usr/bin/c++ -DIN_COORDGEN -Dcoordgen_EXPORTS  -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fPIC -fvisibility=hidden   -Wall -Wextra -Werror -MD -MT CMakeFiles/coordgen.dir/sketcherMinimizerMolecule.cpp.o -MF CMakeFiles/coordgen.dir/sketcherMinimizerMolecule.cpp.o.d -o CMakeFiles/coordgen.dir/sketcherMinimizerMolecule.cpp.o -c /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/sketcherMinimizerMolecule.cpp
/usr/bin/c++ -DIN_COORDGEN -Dcoordgen_EXPORTS  -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fPIC -fvisibility=hidden   -Wall -Wextra -Werror -MD -MT CMakeFiles/coordgen.dir/sketcherMinimizerResidue.cpp.o -MF CMakeFiles/coordgen.dir/sketcherMinimizerResidue.cpp.o.d -o CMakeFiles/coordgen.dir/sketcherMinimizerResidue.cpp.o -c /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/sketcherMinimizerResidue.cpp
/usr/bin/c++ -DIN_COORDGEN -Dcoordgen_EXPORTS  -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fPIC -fvisibility=hidden   -Wall -Wextra -Werror -MD -MT CMakeFiles/coordgen.dir/sketcherMinimizerResidueInteraction.cpp.o -MF CMakeFiles/coordgen.dir/sketcherMinimizerResidueInteraction.cpp.o.d -o CMakeFiles/coordgen.dir/sketcherMinimizerResidueInteraction.cpp.o -c /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/sketcherMinimizerResidueInteraction.cpp
/usr/bin/c++ -DIN_COORDGEN -Dcoordgen_EXPORTS  -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fPIC -fvisibility=hidden   -Wall -Wextra -Werror -MD -MT CMakeFiles/coordgen.dir/sketcherMinimizerRing.cpp.o -MF CMakeFiles/coordgen.dir/sketcherMinimizerRing.cpp.o.d -o CMakeFiles/coordgen.dir/sketcherMinimizerRing.cpp.o -c /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/sketcherMinimizerRing.cpp
[ 71%] Linking CXX shared library libcoordgen.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/coordgen.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/coordgen.dir/link.d -Wl,-soname,libcoordgen.so.3 -o libcoordgen.so.3.0.2 CMakeFiles/coordgen.dir/CoordgenFragmentBuilder.cpp.o CMakeFiles/coordgen.dir/CoordgenFragmenter.cpp.o CMakeFiles/coordgen.dir/CoordgenMacrocycleBuilder.cpp.o CMakeFiles/coordgen.dir/CoordgenMinimizer.cpp.o CMakeFiles/coordgen.dir/CoordgenTemplates.cpp.o CMakeFiles/coordgen.dir/sketcherMinimizer.cpp.o CMakeFiles/coordgen.dir/sketcherMinimizerAtom.cpp.o CMakeFiles/coordgen.dir/sketcherMinimizerBond.cpp.o CMakeFiles/coordgen.dir/sketcherMinimizerFragment.cpp.o CMakeFiles/coordgen.dir/sketcherMinimizerMarchingSquares.cpp.o CMakeFiles/coordgen.dir/sketcherMinimizerMolecule.cpp.o CMakeFiles/coordgen.dir/sketcherMinimizerResidue.cpp.o CMakeFiles/coordgen.dir/sketcherMinimizerResidueInteraction.cpp.o CMakeFiles/coordgen.dir/sketcherMinimizerRing.cpp.o
/usr/bin/cmake -E cmake_symlink_library libcoordgen.so.3.0.2 libcoordgen.so.3 libcoordgen.so
make[3]: Leaving directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
[ 71%] Built target coordgen
make  -f example_dir/CMakeFiles/example.dir/build.make example_dir/CMakeFiles/example.dir/depend
make  -f test/CMakeFiles/test_coordgen.dir/build.make test/CMakeFiles/test_coordgen.dir/depend
make  -f test/CMakeFiles/test_smilesparser.dir/build.make test/CMakeFiles/test_smilesparser.dir/depend
make[3]: Entering directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
cd /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/schroedinger-coordgenlibs-3.0.2 /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/example_dir /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu/example_dir /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu/example_dir/CMakeFiles/example.dir/DependInfo.cmake "--color=" example
make[3]: Entering directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
cd /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/schroedinger-coordgenlibs-3.0.2 /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu/test /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu/test/CMakeFiles/test_coordgen.dir/DependInfo.cmake "--color=" test_coordgen
make[3]: Entering directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
cd /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/schroedinger-coordgenlibs-3.0.2 /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu/test /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu/test/CMakeFiles/test_smilesparser.dir/DependInfo.cmake "--color=" test_smilesparser
make[3]: Leaving directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
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make  -f example_dir/CMakeFiles/example.dir/build.make example_dir/CMakeFiles/example.dir/build
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make[3]: Entering directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
make[3]: Entering directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
make[3]: Entering directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
[ 85%] Building CXX object test/CMakeFiles/test_smilesparser.dir/test_smilesparser.cpp.o
[ 85%] Building CXX object test/CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o
[ 85%] Building CXX object example_dir/CMakeFiles/example.dir/example.cpp.o
cd /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu/example_dir && /usr/bin/c++ -DBOOST_ALL_DYN_LINK -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB  -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11   -Wall -Wextra -Werror -MD -MT example_dir/CMakeFiles/example.dir/example.cpp.o -MF CMakeFiles/example.dir/example.cpp.o.d -o CMakeFiles/example.dir/example.cpp.o -c /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/example_dir/example.cpp
cd /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DBOOST_ALL_DYN_LINK -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB  -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11   -Wall -Wextra -Werror -MD -MT test/CMakeFiles/test_smilesparser.dir/test_smilesparser.cpp.o -MF CMakeFiles/test_smilesparser.dir/test_smilesparser.cpp.o.d -o CMakeFiles/test_smilesparser.dir/test_smilesparser.cpp.o -c /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test/test_smilesparser.cpp
cd /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu/test && /usr/bin/c++ -DBOOST_ALL_DYN_LINK -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -DSOURCE_DIR=\"/build/reproducible-path/schroedinger-coordgenlibs-3.0.2\" -DTEST_SAMPLES_PATH=\"/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test\"  -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11   -Wall -Wextra -Werror -MD -MT test/CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o -MF CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o.d -o CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o -c /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test/test_coordgen.cpp
[ 90%] Linking CXX executable example
cd /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu/example_dir && /usr/bin/cmake -E cmake_link_script CMakeFiles/example.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/schroedinger-coordgenlibs-3.0.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/example.dir/link.d CMakeFiles/example.dir/example.cpp.o -o example  -Wl,-rpath,/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu ../libcoordgen.so.3.0.2 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.90.0 /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.90.0
make[3]: Leaving directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
[ 90%] Built target example
In file included from /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test/test_smilesparser.cpp:7:
/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test/coordgenBasicSMILES.h: In function ‘sketcherMinimizerMolecule* schrodinger::approxSmilesParse(const std::string&)’:
/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test/coordgenBasicSMILES.h:33:12: error: variable ‘idx’ set but not used [-Werror=unused-but-set-variable=]
   33 |     size_t idx = 0;
      |            ^~~
In file included from /build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test/test_coordgen.cpp:13:
/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test/coordgenBasicSMILES.h: In function ‘sketcherMinimizerMolecule* schrodinger::approxSmilesParse(const std::string&)’:
/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test/coordgenBasicSMILES.h:33:12: error: variable ‘idx’ set but not used [-Werror=unused-but-set-variable=]
   33 |     size_t idx = 0;
      |            ^~~
/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test/test_coordgen.cpp: In member function ‘void testMinimizedRingsShape::test_method()’:
/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/test/test_coordgen.cpp:313:9: error: variable ‘bondsN’ set but not used [-Werror=unused-but-set-variable=]
  313 |     int bondsN = 0;
      |         ^~~~~~
cc1plus: all warnings being treated as errors
make[3]: *** [test/CMakeFiles/test_smilesparser.dir/build.make:82: test/CMakeFiles/test_smilesparser.dir/test_smilesparser.cpp.o] Error 1
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make[2]: *** [CMakeFiles/Makefile2:1158: test/CMakeFiles/test_smilesparser.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
cc1plus: all warnings being treated as errors
make[3]: *** [test/CMakeFiles/test_coordgen.dir/build.make:82: test/CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o] Error 1
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make[2]: *** [CMakeFiles/Makefile2:1126: test/CMakeFiles/test_coordgen.dir/all] Error 2
make[2]: Leaving directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
make[1]: *** [Makefile:149: all] Error 2
make[1]: Leaving directory '/build/reproducible-path/schroedinger-coordgenlibs-3.0.2/obj-aarch64-linux-gnu'
dh_auto_build: error: cd obj-aarch64-linux-gnu && make -j128 INSTALL="install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:7: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2