Your message dated Sun, 03 Sep 2023 19:46:08 +0000
with message-id <[email protected]>
and subject line Bug#1015650: fixed in rdkit 202303.3-1
has caused the Debian Bug report #1015650,
regarding rdkit: ftbfs with LTO (link time optimization) enabled
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 [email protected]
immediately.)
--
1015650: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1015650
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:rdkit
Version: 202203.2-1
Severity: minor
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-lto
This package currently fails to build (at least on the amd64
architecture) with link time optimizations enabled. For a background
for LTO please see
https://wiki.debian.org/ToolChain/LTO
The goal is to enable this optimization by default in an upcoming
Debian release in dpkg-buildflags for 64bit architectures. The goal
is to get this package to build with link time optimizations, or to
explicitly disable link time optimizations for this package build.
To reproduce the build failure, enable the lto optimization in
testing/unstable by adding "optimize=+lto" to DEB_BUILD_MAINT_OPTIONS
in the debian/rules file, or if this macro is unset, just set it:
export DEB_BUILD_MAINT_OPTIONS = optimize=+lto
Please try to fix the build with lto enabled, fixing the packaging or
forwarding the issue upstream. If the issue cannot be fixed,
explicitly disallow building the package with lto by adding to your
rules file:
export DEB_BUILD_MAINT_OPTIONS = optimize=-lto
or adding that string to your existing setting of DEB_BUILD_MAINT_OPTIONS.
The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/dpkglto/rdkit_202203.2-1_unstable_dpkglto.log
The last lines of the build log are at the end of this report.
[...]
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto
-ffat-lto-objects -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 -flto=auto
-ffat-lto-objects -Wl,-z,relro -Wl,-z,now
CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o
-o testMultithreadedMolSupplier
../../../lib/libRDKitFileParsers.so.1.2022.03.2
../../../lib/libRDKitFingerprints.so.1.2022.03.2
../../../lib/libRDKitRDStreams.so.1.2022.03.2
../../../lib/libRDKitDepictor.so.1.2022.03.2
../../../lib/libRDKitMolAlign.so.1.2022.03.2
../../../lib/libRDKitAlignment.so.1.2022.03.2
/usr/lib/x86_64-linux-gnu/libcoordgen.so
../../../lib/libRDKitMolTransforms.so.1.2022.03.2
../../../lib/libRDKitEigenSolvers.so.1.2022.03.2
/usr/lib/x86_64-linux-gnu/libmaeparser.so
/usr/lib/x86_64-linux-gnu/libboost_system.so
/usr/lib/x86_64-linux-gnu/libboost_iostre
ams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so
/usr/lib/x86_64-linux-gnu/libboost_system.so
/usr/lib/x86_64-linux-gnu/libboost_iostreams.so
/usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so
../../../lib/libRDKitSmilesParse.so.1.2022.03.2
../../../lib/libRDKitSubgraphs.so.1.2022.03.2
../../../lib/libRDKitSubstructMatch.so.1.2022.03.2
../../../lib/libRDKitGenericGroups.so.1.2022.03.2
../../../lib/libRDKitGraphMol.so.1.2022.03.2
../../../lib/libRDKitRDGeometryLib.so.1.2022.03.2
../../../lib/libRDKitDataStructs.so.1.2022.03.2
../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -ldl -lpthread
/usr/lib/x86_64-linux-gnu/libboost_iostreams.so
/usr/lib/x86_64-linux-gnu/libboost_regex.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 54%] Built target testGeneralFileReader
make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make
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make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends
"Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/Code/GraphMol/FileParsers
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/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers
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[ 54%] Building CXX object
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers &&
/usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK
-DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT
-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3
-DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS
-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION
-I/<<PKGBUILDDIR>>/External -I/usr/include/python3.10
-I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/Code
-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-flto=auto -ffat-lto-objects -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 -std=gnu++14 -MD -MT
Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF
CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFil
es/testTplParser.dir/testTpls.cpp.o -c
/<<PKGBUILDDIR>>/Code/GraphMol/FileParsers/testTpls.cpp
/usr/bin/ld: /tmp/ccl1kHda.ltrans0.ltrans.o: in function
`PrintThread::~PrintThread()':
/usr/include/x86_64-linux-gnu/c++/11/bits/gthr-default.h:749: undefined
reference to `PrintThread::cout_mutex'
/usr/bin/ld: /usr/include/x86_64-linux-gnu/c++/11/bits/gthr-default.h:779:
undefined reference to `PrintThread::cout_mutex'
/usr/bin/ld: /tmp/ccl1kHda.ltrans0.ltrans.o: in function
`PrintThread::~PrintThread()':
/usr/include/x86_64-linux-gnu/c++/11/bits/gthr-default.h:749: undefined
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/usr/bin/ld: /usr/include/x86_64-linux-gnu/c++/11/bits/gthr-default.h:779:
undefined reference to `PrintThread::cout_mutex'
/usr/bin/ld: /tmp/ccl1kHda.ltrans0.ltrans.o: in function `virtual thunk to
PrintThread::~PrintThread()':
/usr/include/c++/11/bits/std_mutex.h:104: undefined reference to
`PrintThread::cout_mutex'
/usr/bin/ld:
/tmp/ccl1kHda.ltrans0.ltrans.o:/usr/include/c++/11/bits/std_mutex.h:104: more
undefined references to `PrintThread::cout_mutex' follow
collect2: error: ld returned 1 exit status
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/usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD
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/usr/lib/x86_64-linux-gnu/libboost_regex.so
/usr/lib/x86_64-linux-gnu/libboost_system.so
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/Depictor &&
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--verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto
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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -flto=auto
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CMakeFiles/depictorCatch.dir/catch_tests.cpp.o
CMakeFiles/depictorCatch.dir/__/catch_main.cpp.o -o depictorCatch
../../../lib/libRDKitFileParsers.so.1.2022.03.2
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/usr/lib/x86_64-linux-gnu/libcoordgen.so
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[ 54%] Linking CXX executable testTplParser
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/usr/lib/x86_64-linux-gnu/libcoordgen.so
../../../lib/libRDKitMolTransforms.so.1.2022.03.2
../../../lib/libRDKitEigenSolvers.so.1.2022.03.2
../../../lib/libRDKitSmilesParse.so.1.2022.03.2
../../../lib/libRDKitGraphMol.so.1.2022.03.2
../../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../../lib/libRDKitDataS
tructs.so.1.2022.03.2 ../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread
-ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so
/usr/lib/x86_64-linux-gnu/libboost_system.so
/usr/lib/x86_64-linux-gnu/libboost_iostreams.so
/usr/lib/x86_64-linux-gnu/libboost_regex.so
/usr/lib/x86_64-linux-gnu/libboost_system.so
/usr/lib/x86_64-linux-gnu/libboost_iostreams.so
/usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 56%] Built target fileParsersTest1
[ 56%] Linking CXX executable smiTestCatch
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse &&
/usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt
--verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto
-ffat-lto-objects -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 -flto=auto
-ffat-lto-objects -Wl,-z,relro -Wl,-z,now
CMakeFiles/smiTestCatch.dir/__/catch_main.cpp.o
CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch
../../../lib/libRDKitFileParsers.so.1.2022.03.2
../../../lib/libRDKitSmilesParse.so.1.2022.03.2
../../../lib/libRDKitDepictor.so.1.2022.03.2
../../../lib/libRDKitMolAlign.so.1.2022.03.2
../../../lib/libRDKitAlignment.so.1.2022.03.2
/usr/lib/x86_64-linux-gnu/libcoordgen.so
../../../lib/libRDKitSubstructMatch.so.1.2022.03.2
../../../lib/libRDKitGenericGroups.so.1.2022.03.2
../../../lib/libRDKitMolTransforms.so.1.2022.03.2
../../../lib/libRDKitEigenSolvers.so.1.2022.03.2
../../../lib/libRDKitGraphMol.so.1.2022.03.2 ../../../lib/libRDKitRDGeometr
yLib.so.1.2022.03.2 ../../../lib/libRDKitDataStructs.so.1.2022.03.2
../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl
/usr/lib/x86_64-linux-gnu/libmaeparser.so
/usr/lib/x86_64-linux-gnu/libboost_system.so
/usr/lib/x86_64-linux-gnu/libboost_iostreams.so
/usr/lib/x86_64-linux-gnu/libboost_regex.so
/usr/lib/x86_64-linux-gnu/libboost_system.so
/usr/lib/x86_64-linux-gnu/libboost_iostreams.so
/usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 56%] Built target smiTestCatch
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 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: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: rdkit
Source-Version: 202303.3-1
Done: Nicholas Breen <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nicholas Breen <[email protected]> (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 [email protected])
-----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 <[email protected]>
Changed-By: Nicholas Breen <[email protected]>
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.
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