diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile index 89da4b6fea16..09a763aaffba 100644 --- a/biology/vsearch/Makefile +++ b/biology/vsearch/Makefile @@ -1,29 +1,28 @@ PORTNAME= vsearch DISTVERSIONPREFIX= v -DISTVERSION= 2.31.0 +DISTVERSION= 2.32.0 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Versatile open-source tool for metagenomics WWW= https://github.com/torognes/vsearch LICENSE= GPLv3 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 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{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 - #include - #include - #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