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helo=mout02.posteo.de X-Spam_score_int: -53 X-Spam_score: -5.4 X-Spam_bar: ----- X-Spam_report: (-5.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H5=-1, RCVD_IN_MSPIKE_WL=-0.01, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Flow: FLOW_IN X-Migadu-Country: US X-Migadu-Spam-Score: 3.64 X-Spam-Score: 3.64 X-Migadu-Queue-Id: CB33E10C7F X-Migadu-Scanner: mx12.migadu.com X-TUID: qxmTwM+HCiD4 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