Created attachment 256808 [details] [PATCH] biology/mmseqs2: update 16-747c6 → 17-b804f MMseqs2 Release 17-b804f Latest MMseqs2 Release 17 is mostly a bug fix release. Highlights include usability improvements in MMseqs2-GPU and fix for a common crash in the prefilter that was affecting many clustering runs. New Features and Enhancements result2profile can print frequencies in TSV format (c2c3ad9) add a new masking mode --mask-n-repeat (c2c3ad9) Improve GPU clients in server mode to wait for databasess to be loaded (e095774) GPU server now takes CUDA_VISIBLE_DEVICES into account. (b804fbe) Reduced glibc requirements for precompiled MMseqs2-GPU binaries to 2.17 (i.e. CentOS 7; db8ad2d) Bug Fixes Segmentation fault in easy-cluster starting in #916 (dc7f8ad) GPU version generated corrupted sequence outputs #912 (e3b16fa) Sequences starting with * could break Sequence mapping #927 (492297b) Indexes without k-mer index are masked now (4766f92) Invalid taxids check in majoritylca does not abort the whole process (8d17137) Merged taxID larger than any taxid in nodes.dmp could corrupt memory #931 (fd37b37) Developer Notes Export NATIVE_ARCH in cmake (17cd5c0)
Do you have DEVELOPER=yes in your /etc/make.conf? Stage-QA is issuing a warning about libzstd.so not being needed. CMakeLists.txt has a comment stating that the static library must be used, so this should be a BUILD_DEPEND rather than a RUN_DEPEND. Otherwise, everything seems to be in order.
A commit in branch main references this bug: URL: https://cgit.FreeBSD.org/ports/commit/?id=2889989be020e1f7f0072226f2c87357c2fc15b5 commit 2889989be020e1f7f0072226f2c87357c2fc15b5 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2025-01-25 13:21:33 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2025-01-25 13:24:31 +0000 biology/mmseqs2: Update to 17.b804.f MMseqs2 Release 17 is mostly a bug fix release. Highlights include usability improvements in MMseqs2-GPU and fix for a common crash in the prefilter that was affecting many clustering runs. Changes: https://github.com/soedinglab/MMseqs2/releases PR: 284165 Reported by: alster@vinterdalen.se biology/mmseqs2/Makefile | 6 +++--- biology/mmseqs2/distinfo | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-)
Thanks!