git: bf93df2cef7f - main - biology/vsearch: Update to 2.32.0
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Date: Sun, 20 Sep 2026 13:26:00 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=bf93df2cef7fcb03a1d1b386b6987efec0690e2a
commit bf93df2cef7fcb03a1d1b386b6987efec0690e2a
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-09-20 13:22:42 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-09-20 13:25:58 +0000
biology/vsearch: Update to 2.32.0
Numererous bug fixes, new per-command man pages, and a few other
enhancements.
Changes: https://github.com/torognes/vsearch/releases
Normally I don't upgrade ports so close to the end of a quarter, but
this release has a lot of bug fixes, which I think outweigh the risk
of a regression slipping into the next quarterly branch.
Reported by: portscout
---
biology/vsearch/Makefile | 13 ++---
biology/vsearch/distinfo | 6 +-
.../vsearch/files/patch-src_core_searchcore.cpp | 18 ++++++
biology/vsearch/files/patch-src_searchcore.cc | 18 ------
biology/vsearch/files/patch-src_sintax.cc | 18 ------
biology/vsearch/files/patch-src_vsearch.h | 10 ----
biology/vsearch/pkg-plist | 67 ++++++++++++++++++++++
7 files changed, 94 insertions(+), 56 deletions(-)
diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile
index 89da4b6fea16..09a763aaffba 100644
--- a/biology/vsearch/Makefile
+++ b/biology/vsearch/Makefile
@@ -1,6 +1,6 @@
PORTNAME= vsearch
DISTVERSIONPREFIX= v
-DISTVERSION= 2.31.0
+DISTVERSION= 2.32.0
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
@@ -13,17 +13,16 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.txt
ONLY_FOR_ARCHS= aarch64 amd64 powerpc64le
ONLY_FOR_ARCHS_REASON= Explicitly enumerated by upstream developers
+BUILD_DEPENDS= hs-pandoc>0:textproc/hs-pandoc \
+ bash>0:shells/bash
+
USES= autoreconf ghostscript:build gmake localbase
USE_GITHUB= yes
GH_ACCOUNT= torognes
GNU_CONFIGURE= yes
-GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share
-
-PLIST_FILES= bin/vsearch share/man/man1/vsearch.1.gz
-PORTDOCS= *
-OPTIONS_DEFINE= DOCS
-OPTIONS_SUB= yes
+post-stage:
+ ${INSTALL_MAN} ${WRKSRC}/man/manpages/*.1 ${STAGEDIR}${PREFIX}/share/man/man1
.include <bsd.port.mk>
diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo
index e084e4c70095..eeb7894b7bc6 100644
--- a/biology/vsearch/distinfo
+++ b/biology/vsearch/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1777740585
-SHA256 (torognes-vsearch-v2.31.0_GH0.tar.gz) = fb6348fe38107cdcde6e3651913aa54eb8233fcd3379ab9e7fc936c090e05915
-SIZE (torognes-vsearch-v2.31.0_GH0.tar.gz) = 609494
+TIMESTAMP = 1789908958
+SHA256 (torognes-vsearch-v2.32.0_GH0.tar.gz) = aa6fecd099ba4970b2685e41e3a97e04f1317d12cb315870e3acdc1cd6b7fe5d
+SIZE (torognes-vsearch-v2.32.0_GH0.tar.gz) = 824198
diff --git a/biology/vsearch/files/patch-src_core_searchcore.cpp b/biology/vsearch/files/patch-src_core_searchcore.cpp
new file mode 100644
index 000000000000..a7c0855d89b1
--- /dev/null
+++ b/biology/vsearch/files/patch-src_core_searchcore.cpp
@@ -0,0 +1,18 @@
+--- src/core/searchcore.cpp.orig 2026-09-19 20:41:23 UTC
++++ src/core/searchcore.cpp
+@@ -309,9 +309,14 @@ auto accumulate_slice_counts(struct searchinfo_s const
+ auto const bits = View<unsigned char>{std::next(bitmap, first_byte),
+ slice_bitmap_bytes};
+ #ifdef __x86_64__
++ // Not sure how to enable ssse3 without enabling other
++ // non-portable features.
++ // This code is only used rarely, so disable ssse3 for now.
++ // It won't affect performance much on the whole.
++ // https://github.com/torognes/vsearch/pull/497
+ if (parameters.runtime.ssse3_present != 0)
+ {
+- increment_counters_from_bitmap_ssse3(slice, bits);
++ increment_counters_from_bitmap_sse2(slice, bits);
+ }
+ else
+ {
diff --git a/biology/vsearch/files/patch-src_searchcore.cc b/biology/vsearch/files/patch-src_searchcore.cc
deleted file mode 100644
index 85894cf869e5..000000000000
--- a/biology/vsearch/files/patch-src_searchcore.cc
+++ /dev/null
@@ -1,18 +0,0 @@
---- src/searchcore.cc.orig 2025-10-05 12:35:57 UTC
-+++ src/searchcore.cc
-@@ -285,9 +285,14 @@ auto search_topscores(struct searchinfo_s * searchinfo
- if (bitmap != nullptr)
- {
- #ifdef __x86_64__
-+ // Not sure how to enable ssse3 without enabling other
-+ // non-portable features.
-+ // This code is only used rarely, so disable ssse3 for now.
-+ // It won't affect performance much on the whole.
-+ // https://github.com/torognes/vsearch/pull/497
- if (ssse3_present != 0)
- {
-- increment_counters_from_bitmap_ssse3(searchinfo->kmers,
-+ increment_counters_from_bitmap_sse2(searchinfo->kmers,
- bitmap, indexed_count);
- }
- else
diff --git a/biology/vsearch/files/patch-src_sintax.cc b/biology/vsearch/files/patch-src_sintax.cc
deleted file mode 100644
index b5af8da42d6e..000000000000
--- a/biology/vsearch/files/patch-src_sintax.cc
+++ /dev/null
@@ -1,18 +0,0 @@
---- src/sintax.cc.orig 2025-10-05 12:34:38 UTC
-+++ src/sintax.cc
-@@ -295,9 +295,14 @@ auto sintax_search_topscores(struct searchinfo_s * sea
- if (bitmap != nullptr)
- {
- #ifdef __x86_64__
-+ // Not sure how to enable ssse3 without enabling other
-+ // non-portable features.
-+ // This code is only used rarely, so disable ssse3 for now.
-+ // It won't affect performance much on the whole.
-+ // https://github.com/torognes/vsearch/pull/497
- if (ssse3_present != 0)
- {
-- increment_counters_from_bitmap_ssse3(searchinfo->kmers,
-+ increment_counters_from_bitmap_sse2(searchinfo->kmers,
- bitmap, indexed_count);
- }
- else
diff --git a/biology/vsearch/files/patch-src_vsearch.h b/biology/vsearch/files/patch-src_vsearch.h
deleted file mode 100644
index 066f4488212d..000000000000
--- a/biology/vsearch/files/patch-src_vsearch.h
+++ /dev/null
@@ -1,10 +0,0 @@
---- src/vsearch.h.orig 2023-10-27 12:44:35 UTC
-+++ src/vsearch.h
-@@ -161,7 +161,6 @@
- #elif __FreeBSD__
-
- #define PROG_OS "freebsd"
--#include <sys/sysinfo.h>
- #include <sys/resource.h>
- #include <sys/endian.h>
- #define bswap_16(x) bswap16(x)
diff --git a/biology/vsearch/pkg-plist b/biology/vsearch/pkg-plist
new file mode 100644
index 000000000000..135eec879cf1
--- /dev/null
+++ b/biology/vsearch/pkg-plist
@@ -0,0 +1,67 @@
+bin/vsearch
+share/bash-completion/completions/vsearch
+share/fish/vendor_completions.d/vsearch.fish
+share/man/man1/vsearch-allpairs_global.1.gz
+share/man/man1/vsearch-chimeras_denovo.1.gz
+share/man/man1/vsearch-cluster_fast.1.gz
+share/man/man1/vsearch-cluster_size.1.gz
+share/man/man1/vsearch-cluster_smallmem.1.gz
+share/man/man1/vsearch-cluster_unoise.1.gz
+share/man/man1/vsearch-cut.1.gz
+share/man/man1/vsearch-derep_fulllength.1.gz
+share/man/man1/vsearch-derep_id.1.gz
+share/man/man1/vsearch-derep_prefix.1.gz
+share/man/man1/vsearch-derep_smallmem.1.gz
+share/man/man1/vsearch-fasta2fastq.1.gz
+share/man/man1/vsearch-fastq_chars.1.gz
+share/man/man1/vsearch-fastq_convert.1.gz
+share/man/man1/vsearch-fastq_eestats.1.gz
+share/man/man1/vsearch-fastq_eestats2.1.gz
+share/man/man1/vsearch-fastq_filter.1.gz
+share/man/man1/vsearch-fastq_join.1.gz
+share/man/man1/vsearch-fastq_mergepairs.1.gz
+share/man/man1/vsearch-fastq_stats.1.gz
+share/man/man1/vsearch-fastx_filter.1.gz
+share/man/man1/vsearch-fastx_getseq.1.gz
+share/man/man1/vsearch-fastx_getseqs.1.gz
+share/man/man1/vsearch-fastx_getsubseq.1.gz
+share/man/man1/vsearch-fastx_mask.1.gz
+share/man/man1/vsearch-fastx_revcomp.1.gz
+share/man/man1/vsearch-fastx_subsample.1.gz
+share/man/man1/vsearch-fastx_syncpairs.1.gz
+share/man/man1/vsearch-fastx_uniques.1.gz
+share/man/man1/vsearch-help.1.gz
+share/man/man1/vsearch-makeudb_usearch.1.gz
+share/man/man1/vsearch-maskfasta.1.gz
+share/man/man1/vsearch-orient.1.gz
+share/man/man1/vsearch-rereplicate.1.gz
+share/man/man1/vsearch-scramble.1.gz
+share/man/man1/vsearch-search_exact.1.gz
+share/man/man1/vsearch-sff_convert.1.gz
+share/man/man1/vsearch-shuffle.1.gz
+share/man/man1/vsearch-sintax.1.gz
+share/man/man1/vsearch-sortbylength.1.gz
+share/man/man1/vsearch-sortbysize.1.gz
+share/man/man1/vsearch-uchime2_denovo.1.gz
+share/man/man1/vsearch-uchime3_denovo.1.gz
+share/man/man1/vsearch-uchime_denovo.1.gz
+share/man/man1/vsearch-uchime_ref.1.gz
+share/man/man1/vsearch-udb2fasta.1.gz
+share/man/man1/vsearch-udbinfo.1.gz
+share/man/man1/vsearch-udbstats.1.gz
+share/man/man1/vsearch-usearch_global.1.gz
+share/man/man1/vsearch-version.1.gz
+share/man/man1/vsearch.1.gz
+share/man/man5/vsearch-cigar.5.gz
+share/man/man5/vsearch-fasta.5.gz
+share/man/man5/vsearch-fastq.5.gz
+share/man/man5/vsearch-sam.5.gz
+share/man/man5/vsearch-sff.5.gz
+share/man/man5/vsearch-udb.5.gz
+share/man/man7/vsearch-expected_error.7.gz
+share/man/man7/vsearch-history.7.gz
+share/man/man7/vsearch-nucleotides.7.gz
+share/man/man7/vsearch-pairwise_alignment_parameters.7.gz
+share/man/man7/vsearch-usearch.7.gz
+share/man/man7/vsearch-userfields.7.gz
+share/zsh/site-functions/_vsearch