[Debichem-devel] Bug#1037837: rdkit: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:30:42 BST 2023
Package: src:rdkit
Version: 202209.3-1
Severity: normal
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-13
[This bug is targeted to the upcoming trixie release]
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-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/rdkit_202209.3-1_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 13, either set CC=gcc-13 CXX=g++-13 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-13/porting_to.html
[...]
from /<<PKGBUILDDIR>>/Code/RDGeneral/types.h:27,
from /<<PKGBUILDDIR>>/Code/RDGeneral/types.cpp:12:
/<<PKGBUILDDIR>>/Code/RDGeneral/RDLog.h:131:8: error: ‘uint64_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’?
131 | std::uint64_t d_origState = 0;
| ^~~~~~~~
| wint_t
In file included from /<<PKGBUILDDIR>>/Code/RDGeneral/RDLog.cpp:10:
/<<PKGBUILDDIR>>/Code/RDGeneral/RDLog.h:131:8: error: ‘uint64_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’?
131 | std::uint64_t d_origState = 0;
| ^~~~~~~~
| wint_t
/<<PKGBUILDDIR>>/Code/RDGeneral/RDLog.cpp: In constructor ‘RDLog::LogStateSetter::LogStateSetter()’:
/<<PKGBUILDDIR>>/Code/RDGeneral/RDLog.cpp:36:7: error: ‘d_origState’ was not declared in this scope
36 | d_origState |= 1 << i;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/Code/RDGeneral/RDLog.cpp: In constructor ‘RDLog::LogStateSetter::LogStateSetter(RDLog::RDLoggerList)’:
/<<PKGBUILDDIR>>/Code/RDGeneral/RDLog.cpp:46:7: error: ‘d_origState’ was not declared in this scope
46 | d_origState ^= 1 << i;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/Code/RDGeneral/RDLog.cpp: In destructor ‘RDLog::LogStateSetter::~LogStateSetter()’:
/<<PKGBUILDDIR>>/Code/RDGeneral/RDLog.cpp:55:36: error: ‘d_origState’ was not declared in this scope
55 | (*allLogs[i])->df_enabled ^= d_origState >> i & 1;
| ^~~~~~~~~~~
[ 5%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/<<PKGBUILDDIR>>/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /<<PKGBUILDDIR>>/External/GA/util/RandomUtil.cpp
In file included from /<<PKGBUILDDIR>>/Code/RDGeneral/Invariant.h:22,
from /<<PKGBUILDDIR>>/Code/RDGeneral/types.h:27,
from /<<PKGBUILDDIR>>/Code/RDGeneral/utils.h:15,
from /<<PKGBUILDDIR>>/Code/RDGeneral/utils.cpp:10:
/<<PKGBUILDDIR>>/Code/RDGeneral/RDLog.h:131:8: error: ‘uint64_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’?
131 | std::uint64_t d_origState = 0;
| ^~~~~~~~
| wint_t
make[4]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make:135: Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o] Error 1
make[4]: *** Waiting for unfinished jobs....
[ 5%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/<<PKGBUILDDIR>>/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /<<PKGBUILDDIR>>/External/GA/util/Util.cpp
make[4]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make:79: Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o] Error 1
make[4]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make:93: Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o] Error 1
make[4]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make:107: Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:3480: Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[ 5%] Linking CXX shared library ../../lib/libRDKitga.so
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2022.09.3 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2022.09.3 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 5%] Built target ga
[ 5%] Linking CXX shared library ../../lib/libRDKitRDStreams.so
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2022.09.3 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 5%] Built target RDStreams
[ 5%] Linking CXX static library librdkitCatch.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1
/usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o
/usr/bin/ranlib librdkitCatch.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 5%] Built target rdkitCatch
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:92: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:40: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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