cave show -f libghemical::gentoo * sci-libs/libghemical::gentoo ::gentoo 2.00 2.99.1 3.0.0(~)* {:0} sci-libs/libghemical-3.0.0:0::gentoo Description Chemical quantum mechanics and molecular mechanics Homepage http://bioinformatics.org/ghemical/ Herds sci-chemistry Long Description Ghemical supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models is included. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available. Use flags mopac7 mpqc -static-libs build_options: symbols=strip dwarf_compress -optional_tests -trace work=remove Overridden Masks Keywords ~amd64 ~ppc ~x86 pkg-config --libs --cflags blas -I//opt/acml5.3.0/gfortran64_mp/include -L//opt/acml5.3.0/gfortran64_mp/lib -lacml_mp There are a bunch of packages using blas / lapack that are not using pkg-config to get includes and library paths right. There's two ways to solve this: a) either fix all of the offending packages (like libghemical) to use pkg-config b) let blas / lapack variants install /usr/lib/lib{blas,lapack}.{so,a} symlinks to _current eselect profile ==================================================================================== I've used b) and solved the problem by putting links to the libraries into /etc/env.d/alternatives/{blas,lapack} like this (only blas shown as an example): # ls -l /etc/env.d/alternatives/blas/acml-gfortran64-openmp/usr/lib64/ insgesamt 4 lrwxrwxrwx 1 root root 39 16. Apr 05:13 libblas.a -> ../../opt/acml5.3.0/lib64/libacml_mp.so lrwxrwxrwx 1 root root 39 16. Apr 05:13 libblas.so -> ../../opt/acml5.3.0/lib64/libacml_mp.so drwxr-xr-x 2 root root 4096 24. Mär 14:13 pkgconfig # eselect blas list Available providers for blas: [1] acml-gfortran64 [2] acml-gfortran64-openmp * [3] eigen [4] openblas-threads # eselect blas set acml-gfortran64-openmp # ls -l /usr/lib64/libblas* lrwxrwxrwx 1 root root 62 16. Apr 16:29 /usr/lib64/libblas.a -> ../../etc/env.d/alternatives/blas/_current/usr/lib64/libblas.a lrwxrwxrwx 1 root root 63 16. Apr 16:29 /usr/lib64/libblas.so -> ../../etc/env.d/alternatives/blas/_current/usr/lib64/libblas.so Since this is a symbolic link to a link within a _current profile, it will properly switch with (or break) on an eselect change of blas, which is what we want. The links are updates by eselect itself on a library change. ==================================================================================== To use b) as a fix throughout the system every package installing a blas/lapack variant should install working symlinks within /etc/env.d/alternatives/{blas,lapack}/${variant}/usr/$(get-libdir) e.g. /etc/env.d/alternatives/blas/${variant}/usr/lib64/libblas.so /etc/env.d/alternatives/blas/${variant}/usr/lib64/libblas.a -> bugs should be filed for every package installing a blas/lapack variant that does not In case a) -> bugs should be filed for each package not using pkg-config to find libs and cflags when linking blas or lapack Greetings Reproducible: Always
Created attachment 345698 [details] 1366081008-install-sci-libs_libghemical-3.0.0:0::gentoo.out
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=daddde5e9f55ebf842ffc35660de9007810ffb39 commit daddde5e9f55ebf842ffc35660de9007810ffb39 Author: Arthur Zamarin <arthurzam@gentoo.org> AuthorDate: 2024-06-12 06:15:53 +0000 Commit: Arthur Zamarin <arthurzam@gentoo.org> CommitDate: 2024-06-12 06:15:53 +0000 sci-libs/libghemical: treeclean Closes: https://bugs.gentoo.org/931860 Bug: https://bugs.gentoo.org/891895 Bug: https://bugs.gentoo.org/850739 Bug: https://bugs.gentoo.org/831798 Bug: https://bugs.gentoo.org/514352 Bug: https://bugs.gentoo.org/466112 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org> profiles/package.mask | 5 --- sci-libs/libghemical/Manifest | 1 - .../libghemical/files/libghemical-2.98-gl.patch | 13 ------- sci-libs/libghemical/libghemical-3.0.0.ebuild | 40 ---------------------- sci-libs/libghemical/metadata.xml | 21 ------------ 5 files changed, 80 deletions(-)
