Your message dated Sun, 03 Sep 2023 19:46:08 +0000 with message-id <e1qct2u-0034dw...@fasolo.debian.org> and subject line Bug#1037837: fixed in rdkit 202303.3-1 has caused the Debian Bug report #1037837, regarding rdkit: ftbfs with GCC-13 to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1037837: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037837 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:rdkit Version: 202209.3-1 Severity: normal Tags: sid trixie User: debian-...@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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--- Begin Message ---Source: rdkit Source-Version: 202303.3-1 Done: Nicholas Breen <nbr...@debian.org> We believe that the bug you reported is fixed in the latest version of rdkit, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 1037...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Nicholas Breen <nbr...@debian.org> (supplier of updated rdkit package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sun, 03 Sep 2023 09:06:22 -0700 Source: rdkit Architecture: source Version: 202303.3-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr...@debian.org> Closes: 990653 1015650 1037837 Changes: rdkit (202303.3-1) unstable; urgency=medium . * Team upload. * New upstream release. - Builds with GCC-13. (Closes: #1037837) - Builds with LTO enabled. (Closes: #1015650) * debian/rules (override_dh_install): work around files going to a versioned /usr/lib/python3.XX/site-packages directory, instead of the desired /usr/lib/python3/dist-packages. * debian/rules (override_dh_auto_clean): Docs/Book/Cookbook.rst is shipped in the current upstream tarball, so don't remove it in the clean target. * debian/control, control.in: - rdkit-doc: add Depends on libjs-jquery, libjs-underscore. (Closes: #990653) - Add Build-Depends on python3-myst-parser. - Update B-Ds on transitional packages, libfreetype6-dev -> libfreetype-dev and libcairo-dev -> libcairo2-dev. - Bump Standards-Version to 4.6.2 and remove unused fields. * debian/upstream/metadata: Add Repository, Bug-Database URLs. * debian/rules: Remove obsolete --parallel option. * Rebase patches and update lintian overrides. Checksums-Sha1: b730ecd3e633c8ee3be9a3c4cf42b669b6361db1 2877 rdkit_202303.3-1.dsc cc5f8c17f253569a7f39a1136a920f44d463e213 62182116 rdkit_202303.3.orig.tar.xz 4b14ab7cd8c7ef290f90c3b8672af6f09e4a5db2 101432 rdkit_202303.3-1.debian.tar.xz 6dd0a899cc609984c9ba7eb9a93057b0380cd8c6 16370 rdkit_202303.3-1_source.buildinfo Checksums-Sha256: 707d24ae767c04c3cdefb2c6ed477ddcc272f0021990d82065e263ea9aa7982a 2877 rdkit_202303.3-1.dsc cf23c81b65c478784b8f43fcc3ce4f45aa2cb79b542d610c4b487333a1f1acfe 62182116 rdkit_202303.3.orig.tar.xz c4e5c2affe304b966d206baf4acef1bb8b774c68667d7392af1efebe91fcfbee 101432 rdkit_202303.3-1.debian.tar.xz 9d395467c69f4aff9354260641f19cc729ad7a651e5c6c900503ccfb411d1c62 16370 rdkit_202303.3-1_source.buildinfo Files: ee10ce72fc4a556fd8538bd0ff0c043f 2877 science optional rdkit_202303.3-1.dsc 49ee9ee3cc15199d9abd11eefd1ef9ae 62182116 science optional rdkit_202303.3.orig.tar.xz f0cd20091f078a4004180c4a9a088aca 101432 science optional rdkit_202303.3-1.debian.tar.xz c9924afb4d0442e89e301a269803a625 16370 science optional rdkit_202303.3-1_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEhD5fph5gYziYdtLl7kr9aexlEI8FAmT0upYSHG5icmVlbkBk ZWJpYW4ub3JnAAoJEO5K/WnsZRCPiG0P/jVwOTdAR0C9C9ZAJVCjfMEq/vFmNEip f3NvsFjxSvsKbFErE38VqXHU6mmFFz50m3j9Q7bhMxhUBEQgyZoiNBqs+Jd7+xEt xL9FQ4Tic/M4UJ4eHzTTHv4Gyj6d3o4FcKIsC+xDKv5GH+BJoAOc/XULwBNAEyf3 Z3GuPMTkUYIgpHWgcw/UGx+UQlX+MwBWKiqbSakctvdIUGGGIcfsCl575gpfWj59 Aci/43ElJsfOx99Ppcgy0S7RZ0CyIYVMYOBndWVky0+PGLoY0KPtACkzOchmG9W1 f8i+XY1rQVSnRYUbBR7Q4AubsKgi9M59owkn1tkl4lsnx4vVJJp9jsr1mcpT8s0E GkSqjvtfTVig4hRzRap1XvD112oJ84H0pmZMmpvHJ1YH9hASdSeanYk3mIgmh7tI sNbEI+4/fJYxYWhBkNIT4JJUTGCayiLQr/PyRypWWEWgWHdM2GJAQjd5A22JzbS0 3r0lhxkicCZRiBHLkkPUcB8aRrD4yyTSV6/Sj7mnFBiTWY2js4Qq/yuNxvcRPp6E UcK2YvOft3KFrvP/KQSqD68vOzXa+ZvdHpVGSDFJbdMFlY9II9+q/Yv1m+4yiG6h 7DeFxoFG1hM6n+b/H+mfiBsUwA7Lqj8m5bT6JCPfa8zXmJLvBC7fFwm4m55WV/A3 fccoHhjEseBO =UZYt -----END PGP SIGNATURE-----
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