gnu: rdkit: Update to 2023.09.4....* gnu/packages/chemistry.scm (rdkit): Update to 2023.09.4.
[arguments]: Skip testConrec test in check phase.
[native-inputs]: Replace catch2 with catch2-3.
* gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust
patch.
[supported-systems]: New field.
Signed-off-by: Christopher Baines <mail@cbaines.net>
David Elsing
2024-02-13
gnu: freesasa: Fix memerr tests....* gnu/packages/chemistry.scm (freesasa)[arguments]: Add
"CFLAGS=-fno-builtin-malloc" to #:configure-flags.
Signed-off-by: Christopher Baines <mail@cbaines.net>
David Elsing
2024-02-13
gnu: avalon-toolkit: Update to 2.0.5a....The bug freeing static memory and the makefile have been improved upstream, so
we don't have to work around them anymore. Now, two static libraries are built
instead.
* gnu/packages/chemistry.scm (avalon-toolkit): Update to 2.0.5a.
[source]: Switch to git reference from GitHub. Adjust snippet. Add patch from
the RDKit fork.
[arguments]: Remove 'dont-free-static-memory phase. Use provided
makefile. Adjust 'install phase.
* gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Signed-off-by: Christopher Baines <mail@cbaines.net>
David Elsing
2024-02-13
gnu: yaehmop: Update to 2023.03.1....* gnu/packages/chemistry.scm (yaehmop): Update to 2023.03.1.
Signed-off-by: Christopher Baines <mail@cbaines.net>
David Elsing
2024-02-13
gnu: coordgenlibs: Update to 3.0.2....* gnu/packages/chemistry.scm (coordgenlibs): Update to 3.0.2.
Signed-off-by: Christopher Baines <mail@cbaines.net>
David Elsing
2024-02-13
gnu: maeparser: Update to 1.3.1....* gnu/packages/chemistry.scm (maeparser): Update to 1.3.1.
Signed-off-by: Christopher Baines <mail@cbaines.net>
David Elsing
2024-02-13
gnu: gemmi: Update to 0.6.4....* gnu/packages/chemistry.scm (gemmi): Update to 0.6.4.
[arguments]: Adjust include/gemmi/sprintf.hpp -> src/sprintf.cpp.
(freesasa)[arguments]: Link to gemmi_cpp explicitly.
Signed-off-by: Christopher Baines <mail@cbaines.net>
David Elsing
2024-01-09
gnu: msgpack: Deprecate with msgpack-c....* gnu/packages/serialization.scm (msgpack-c): New variable.
(msgpack-cxx): New variable.
(msgpack): Rename to...
(msgpack-3): ... this, and inherit from msgpack-c.
* gnu/packages/vim.scm (eovim) [arguments]: Add help-cmake-find-msgpack-c
phase.
[inputs]: Replace msgpack with msgpack-c.
* gnu/packages/terminals.scm (tmate)
[inputs]: Replace msgpack with msgpack-3.
* gnu/packages/networking.scm (opendht)
[propagated-inputs]: Replace msgpack with msgpack-cxx.
* gnu/packages/chemistry.scm (mmtf-cpp) [propagated-inputs]: Likewise.