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* [bug#68790] [PATCH 0/9] Update rdkit and its dependencies
@ 2024-01-28 22:59 David Elsing
  2024-01-28 23:01 ` [bug#68790] [PATCH 1/9] gnu: tinydir: Update to 1.2.6 David Elsing
                   ` (9 more replies)
  0 siblings, 10 replies; 11+ messages in thread
From: David Elsing @ 2024-01-28 22:59 UTC (permalink / raw)
  To: 68790; +Cc: David Elsing

This patch series updates rdkit and some of its dependencies.

I incorporated the patch from [1], which was addressed upstream, but is
not in a new release yet.

It seems like RDKit is only tested on 64 bit systems upstream and
several tests fail on i686 (including one due to a known bug in
Boost.Python [2]), therefore I set supported-systems to
%64bit-supported-systems.

Avalon Toolkit moved to a new repository [3], which was forked for RDKit
[4]. As the changes in the fork are small and only fixes, I put them in
a patch and use [3] as upstream.

[1] https://issues.guix.gnu.org/64559
[2] https://github.com/boostorg/python/issues/312
[3] https://github.com/rohdebe1/ava-formake
[4] https://github.com/rdkit/ava-formake

David Elsing (9):
  gnu: tinydir: Update to 1.2.6.
  gnu: fast-float: Update to 6.0.0.
  gnu: gemmi: Update to 0.6.4.
  gnu: maeparser: Update to 1.3.1.
  gnu: coordgenlibs: Update to 3.0.2.
  gnu: yaehmop: Update to 2023.03.1.
  gnu: avalon-toolkit: Update to 2.0.5a.
  gnu: freesasa: Fix memerr tests.
  gnu: rdkit: Update to 2023.09.4.

 gnu/local.mk                                  |   2 +
 gnu/packages/c.scm                            |   6 +-
 gnu/packages/chemistry.scm                    | 175 +++++++--------
 gnu/packages/cpp.scm                          |  10 +-
 .../patches/avalon-toolkit-rdkit-fixes.patch  | 110 +++++++++
 ...rdkit-unbundle-external-dependencies.patch | 208 ++++++++++--------
 .../patches/tinydir-fix-cbehave-test.patch    |  16 +-
 7 files changed, 330 insertions(+), 197 deletions(-)
 create mode 100644 gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch

-- 
2.41.0





^ permalink raw reply	[flat|nested] 11+ messages in thread

end of thread, other threads:[~2024-02-13 12:20 UTC | newest]

Thread overview: 11+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2024-01-28 22:59 [bug#68790] [PATCH 0/9] Update rdkit and its dependencies David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 1/9] gnu: tinydir: Update to 1.2.6 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 2/9] gnu: fast-float: Update to 6.0.0 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 3/9] gnu: gemmi: Update to 0.6.4 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 4/9] gnu: maeparser: Update to 1.3.1 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 5/9] gnu: coordgenlibs: Update to 3.0.2 David Elsing
2024-01-28 23:01 ` [bug#68790] [PATCH 6/9] gnu: yaehmop: Update to 2023.03.1 David Elsing
2024-01-28 23:02 ` [bug#68790] [PATCH 7/9] gnu: avalon-toolkit: Update to 2.0.5a David Elsing
2024-01-28 23:02 ` [bug#68790] [PATCH 8/9] gnu: freesasa: Fix memerr tests David Elsing
2024-01-28 23:02 ` [bug#68790] [PATCH 9/9] gnu: rdkit: Update to 2023.09.4 David Elsing
2024-02-13 12:18 ` [bug#68790] [PATCH 0/9] Update rdkit and its dependencies Christopher Baines

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