New release based on latest rdkit #456

sharped-rsc · 2024-04-22T09:18:52Z

sharped-rsc
Apr 22, 2024

Hi,

First of all, thanks for the time that you've put in to creating and maintaining this package it is super useful.

I was just wondering if there is any timeline for releasing a new version of the RDKitJS packages based upon the latest RDKit (Release_2024.03.1)? As we were hoping to upgrade to make use of some of the features added in the latest release.

Thank you in advance,

Dave

lounsbrough · 2024-04-23T18:18:00Z

lounsbrough
Apr 23, 2024

My team also needs the latest rdkit code released. I have closed my related issue in favor of this thread.
#454

0 replies

lounsbrough · 2024-05-21T16:09:19Z

lounsbrough
May 21, 2024

@MichelML - It looks like you were the one who released last time. Are you able to release this for us?

0 replies

MichelML · 2024-06-06T13:19:00Z

MichelML
Jun 6, 2024
Maintainer

Hey guys, sorry for the delay here, last months have been hectic on my end, I blocked my whole day tomorrow to fix the build/release process (it's broken at the moment and I did not find time to fix it until then).

I will post progress here tomorrow!

cc @lounsbrough @sharped-rsc

0 replies

MichelML · 2024-06-16T12:07:46Z

MichelML
Jun 16, 2024
Maintainer

@greglandrum @ptosco I'm getting this when building the minimallib from the branch Release_2024_03_3 using the Dockerfile from its branch and I'm getting this:

...

303.7 In file included from /opt/boost/include/boost/dynamic_bitset/dynamic_bitset.hpp:30:
303.7 In file included from /opt/boost/include/boost/dynamic_bitset/config.hpp:15:
303.7 In file included from /opt/boost/include/boost/config.hpp:48:
303.7 /opt/boost/include/boost/config/stdlib/libcpp.hpp:176:9: warning: 'BOOST_NO_CXX98_FUNCTION_BASE' macro redefined [-Wmacro-redefined]
303.7   176 | #define BOOST_NO_CXX98_FUNCTION_BASE
303.7       |         ^
303.7 <command line>:3:9: note: previous definition is here
303.7     3 | #define BOOST_NO_CXX98_FUNCTION_BASE 1
303.7       |         ^
304.2 1 warning generated.
304.3 [ 55%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler_static.dir/rules/Rule2.cpp.o
304.4 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule2.cpp:12:
304.4 In file included from /src/rdkit/Code/GraphMol/PeriodicTable.h:10:
304.4 In file included from /src/rdkit/Code/RDGeneral/export.h:3:
304.4 In file included from /src/rdkit/Code/RDGeneral/RDExportMacros.h:19:
304.4 In file included from /opt/boost/include/boost/config.hpp:48:
304.4 /opt/boost/include/boost/config/stdlib/libcpp.hpp:176:9: warning: 'BOOST_NO_CXX98_FUNCTION_BASE' macro redefined [-Wmacro-redefined]
304.4   176 | #define BOOST_NO_CXX98_FUNCTION_BASE
304.4       |         ^
304.4 <command line>:3:9: note: previous definition is here
304.4     3 | #define BOOST_NO_CXX98_FUNCTION_BASE 1
304.4       |         ^
305.8 1 warning generated.
305.8 [ 55%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler_static.dir/rules/Rule3.cpp.o
306.8 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule3.cpp:12:
306.8 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule3.h:13:
306.8 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/SequenceRule.h:16:
306.8 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/../CIPLabeler.h:13:
306.8 In file included from /opt/boost/include/boost/dynamic_bitset.hpp:15:
306.8 In file included from /opt/boost/include/boost/dynamic_bitset/dynamic_bitset.hpp:30:
306.8 In file included from /opt/boost/include/boost/dynamic_bitset/config.hpp:15:
306.8 In file included from /opt/boost/include/boost/config.hpp:48:
306.8 /opt/boost/include/boost/config/stdlib/libcpp.hpp:176:9: warning: 'BOOST_NO_CXX98_FUNCTION_BASE' macro redefined [-Wmacro-redefined]
306.8   176 | #define BOOST_NO_CXX98_FUNCTION_BASE
306.8       |         ^
306.8 <command line>:3:9: note: previous definition is here
306.8     3 | #define BOOST_NO_CXX98_FUNCTION_BASE 1
306.8       |         ^
307.5 1 warning generated.
307.5 [ 55%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler_static.dir/rules/Rule4a.cpp.o
308.5 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp:12:
308.5 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule4a.h:13:
308.5 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/SequenceRule.h:16:
308.5 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/../CIPLabeler.h:13:
308.5 In file included from /opt/boost/include/boost/dynamic_bitset.hpp:15:
308.5 In file included from /opt/boost/include/boost/dynamic_bitset/dynamic_bitset.hpp:30:
308.5 In file included from /opt/boost/include/boost/dynamic_bitset/config.hpp:15:
308.5 In file included from /opt/boost/include/boost/config.hpp:48:
308.5 /opt/boost/include/boost/config/stdlib/libcpp.hpp:176:9: warning: 'BOOST_NO_CXX98_FUNCTION_BASE' macro redefined [-Wmacro-redefined]
308.5   176 | #define BOOST_NO_CXX98_FUNCTION_BASE
308.5       |         ^
308.5 <command line>:3:9: note: previous definition is here
308.5     3 | #define BOOST_NO_CXX98_FUNCTION_BASE 1
308.5       |         ^
309.0 1 warning generated.
309.1 [ 55%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler_static.dir/rules/Rule4b.cpp.o
309.1 1 warning generated.
309.2 [ 55%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler_static.dir/rules/Rule4c.cpp.o
310.2 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp:12:
310.2 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule4c.h:13:
310.2 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/SequenceRule.h:16:
310.2 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/../CIPLabeler.h:13:
310.2 In file included from /opt/boost/include/boost/dynamic_bitset.hpp:15:
310.2 In file included from /opt/boost/include/boost/dynamic_bitset/dynamic_bitset.hpp:30:
310.2 In file included from /opt/boost/include/boost/dynamic_bitset/config.hpp:15:
310.2 In file included from /opt/boost/include/boost/config.hpp:48:
310.2 /opt/boost/include/boost/config/stdlib/libcpp.hpp:176:9: warning: 'BOOST_NO_CXX98_FUNCTION_BASE' macro redefined [-Wmacro-redefined]
310.2   176 | #define BOOST_NO_CXX98_FUNCTION_BASE
310.2       |         ^
310.2 <command line>:3:9: note: previous definition is here
310.2     3 | #define BOOST_NO_CXX98_FUNCTION_BASE 1
310.2       |         ^
310.2 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp:15:
310.2 In file included from /src/rdkit/Code/RDGeneral/Invariant.h:12:
310.2 In file included from /src/rdkit/Code/RDGeneral/export.h:3:
310.2 In file included from /src/rdkit/Code/RDGeneral/RDExportMacros.h:19:
310.2 In file included from /opt/boost/include/boost/config.hpp:48:
310.2 /opt/boost/include/boost/config/stdlib/libcpp.hpp:176:9: warning: 'BOOST_NO_CXX98_FUNCTION_BASE' macro redefined [-Wmacro-redefined]
310.2   176 | #define BOOST_NO_CXX98_FUNCTION_BASE
310.2       |         ^
310.2 <command line>:3:9: note: previous definition is here
310.2     3 | #define BOOST_NO_CXX98_FUNCTION_BASE 1
310.2       |         ^
310.8 1 warning generated.
310.8 [ 55%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler_static.dir/rules/Rule5.cpp.o
311.8 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule5.cpp:12:
311.8 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule5.h:13:
311.8 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/SequenceRule.h:16:
311.8 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/../CIPLabeler.h:13:
311.8 In file included from /opt/boost/include/boost/dynamic_bitset.hpp:15:
311.8 In file included from /opt/boost/include/boost/dynamic_bitset/dynamic_bitset.hpp:30:
311.8 In file included from /opt/boost/include/boost/dynamic_bitset/config.hpp:15:
311.8 In file included from /opt/boost/include/boost/config.hpp:48:
311.8 /opt/boost/include/boost/config/stdlib/libcpp.hpp:176:9: warning: 'BOOST_NO_CXX98_FUNCTION_BASE' macro redefined [-Wmacro-redefined]
311.8   176 | #define BOOST_NO_CXX98_FUNCTION_BASE
311.8       |         ^
311.8 <command line>:3:9: note: previous definition is here
311.8     3 | #define BOOST_NO_CXX98_FUNCTION_BASE 1
311.8       |         ^
312.4 1 warning generated.
312.4 [ 55%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler_static.dir/rules/Rule5New.cpp.o
312.9 1 warning generated.
312.9 [ 57%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler_static.dir/rules/Rule6.cpp.o
313.5 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp:13:
313.5 In file included from /src/rdkit/Code/RDGeneral/Invariant.h:12:
313.5 In file included from /src/rdkit/Code/RDGeneral/export.h:3:
313.5 In file included from /src/rdkit/Code/RDGeneral/RDExportMacros.h:19:
313.5 In file included from /opt/boost/include/boost/config.hpp:48:
313.5 /opt/boost/include/boost/config/stdlib/libcpp.hpp:176:9: warning: 'BOOST_NO_CXX98_FUNCTION_BASE' macro redefined [-Wmacro-redefined]
313.5   176 | #define BOOST_NO_CXX98_FUNCTION_BASE
313.5       |         ^
313.5 <command line>:3:9: note: previous definition is here
313.5     3 | #define BOOST_NO_CXX98_FUNCTION_BASE 1
313.5       |         ^
313.9 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule6.cpp:12:
313.9 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/Rule6.h:13:
313.9 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/SequenceRule.h:16:
313.9 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/../CIPLabeler.h:13:
313.9 In file included from /opt/boost/include/boost/dynamic_bitset.hpp:15:
313.9 In file included from /opt/boost/include/boost/dynamic_bitset/dynamic_bitset.hpp:30:
313.9 In file included from /opt/boost/include/boost/dynamic_bitset/config.hpp:15:
313.9 In file included from /opt/boost/include/boost/config.hpp:48:
313.9 /opt/boost/include/boost/config/stdlib/libcpp.hpp:176:9: warning: 'BOOST_NO_CXX98_FUNCTION_BASE' macro redefined [-Wmacro-redefined]
313.9   176 | #define BOOST_NO_CXX98_FUNCTION_BASE
313.9       |         ^
313.9 <command line>:3:9: note: previous definition is here
313.9     3 | #define BOOST_NO_CXX98_FUNCTION_BASE 1
313.9       |         ^
314.5 1 warning generated.
314.5 [ 57%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler_static.dir/rules/SequenceRule.cpp.o
315.1 1 warning generated.
315.5 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp:12:
315.5 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/SequenceRule.h:16:
315.5 In file included from /src/rdkit/Code/GraphMol/CIPLabeler/rules/../CIPLabeler.h:13:
315.5 In file included from /opt/boost/include/boost/dynamic_bitset.hpp:15:
315.5 In file included from /opt/boost/include/boost/dynamic_bitset/dynamic_bitset.hpp:30:
315.5 In file included from /opt/boost/include/boost/dynamic_bitset/config.hpp:15:
315.5 In file included from /opt/boost/include/boost/config.hpp:48:
315.5 /opt/boost/include/boost/config/stdlib/libcpp.hpp:176:9: warning: 'BOOST_NO_CXX98_FUNCTION_BASE' macro redefined [-Wmacro-redefined]
315.5   176 | #define BOOST_NO_CXX98_FUNCTION_BASE
315.5       |         ^
315.5 <command line>:3:9: note: previous definition is here
315.5     3 | #define BOOST_NO_CXX98_FUNCTION_BASE 1
315.5       |         ^
319.4 1 warning generated.
319.4 [ 57%] Linking CXX static library libRDKitCIPLabeler_static.a
319.6 [ 57%] Built target CIPLabeler_static
319.6 make[1]: *** [CMakeFiles/Makefile2:7310: Code/MinimalLib/CMakeFiles/RDKit_minimal.dir/rule] Error 2
319.6 make: *** [Makefile:2231: RDKit_minimal] Error 2

Any idea on how to fix this?

0 replies

MichelML · 2024-06-16T17:53:57Z

MichelML
Jun 16, 2024
Maintainer

ref rdkit/rdkit#7530

0 replies

sharped-rsc · 2024-07-11T15:38:31Z

sharped-rsc
Jul 11, 2024
Author

Hi @MichelML, I just wanted to ask if you have any update on building the new package.
Thank you in advanced, Dave

2 replies

MichelML Jul 11, 2024
Maintainer

There was a fix upstream in the main rdkit repo, but the build is still breaking here, I will report when I have more updates but I'm very busy at the moment, this is why progress is really slow.

cc @ptosco

sharped-rsc Jul 11, 2024
Author

@MichelML I completely understand. Thanks for the update.

lounsbrough · 2024-08-21T15:59:39Z

lounsbrough
Aug 21, 2024

@MichelML - just checking in to see if this is still blocked. Is there anything I can do to help? I don't have access to the Azure deployment pipeline, but let me know if there's some way I can try and help troubleshoot.

2 replies

MichelML Aug 23, 2024
Maintainer

@lounsbrough it's back! Latest release is now 2024.3.5 👍

lounsbrough Aug 23, 2024

That's awesome, thank you!

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New release based on latest rdkit #456

sharped-rsc Apr 22, 2024

Replies: 7 comments · 4 replies

lounsbrough Apr 23, 2024

lounsbrough May 21, 2024

MichelML Jun 6, 2024 Maintainer

MichelML Jun 16, 2024 Maintainer

MichelML Jun 16, 2024 Maintainer

sharped-rsc Jul 11, 2024 Author

MichelML Jul 11, 2024 Maintainer

sharped-rsc Jul 11, 2024 Author

lounsbrough Aug 21, 2024

MichelML Aug 23, 2024 Maintainer

lounsbrough Aug 23, 2024

sharped-rsc
Apr 22, 2024

Replies: 7 comments 4 replies

lounsbrough
Apr 23, 2024

lounsbrough
May 21, 2024

MichelML
Jun 6, 2024
Maintainer

MichelML
Jun 16, 2024
Maintainer

MichelML
Jun 16, 2024
Maintainer

sharped-rsc
Jul 11, 2024
Author

MichelML Jul 11, 2024
Maintainer

sharped-rsc Jul 11, 2024
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lounsbrough
Aug 21, 2024

MichelML Aug 23, 2024
Maintainer