diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/coverm/Makefile | 2 | ||||
| -rw-r--r-- | biology/vsearch/Makefile | 2 | ||||
| -rw-r--r-- | biology/vsearch/distinfo | 6 | ||||
| -rw-r--r-- | biology/vsearch/files/patch-src_searchcore.cc | 22 | ||||
| -rw-r--r-- | biology/vsearch/files/patch-src_sintax.cc | 12 |
5 files changed, 22 insertions, 22 deletions
diff --git a/biology/coverm/Makefile b/biology/coverm/Makefile index 9256b1dfe0c8..213b27d8d186 100644 --- a/biology/coverm/Makefile +++ b/biology/coverm/Makefile @@ -1,7 +1,7 @@ PORTNAME= coverm DISTVERSIONPREFIX= v DISTVERSION= 0.7.0 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile index d96e1c272462..897c01f7477d 100644 --- a/biology/vsearch/Makefile +++ b/biology/vsearch/Makefile @@ -1,6 +1,6 @@ PORTNAME= vsearch DISTVERSIONPREFIX= v -DISTVERSION= 2.30.0 +DISTVERSION= 2.30.1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo index 2e0dbf172a12..c124a6bce96e 100644 --- a/biology/vsearch/distinfo +++ b/biology/vsearch/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1740867400 -SHA256 (torognes-vsearch-v2.30.0_GH0.tar.gz) = 6d11ce960206ab64cf6d7907e539348d192a5b3f32f82d37c9bfbc4d789b576c -SIZE (torognes-vsearch-v2.30.0_GH0.tar.gz) = 285775 +TIMESTAMP = 1759667807 +SHA256 (torognes-vsearch-v2.30.1_GH0.tar.gz) = f65f03538a77cd1212bd04a52bb722114765329e64bd35e10ee2aefcd81137fe +SIZE (torognes-vsearch-v2.30.1_GH0.tar.gz) = 334663 diff --git a/biology/vsearch/files/patch-src_searchcore.cc b/biology/vsearch/files/patch-src_searchcore.cc index 84870932c9fd..85894cf869e5 100644 --- a/biology/vsearch/files/patch-src_searchcore.cc +++ b/biology/vsearch/files/patch-src_searchcore.cc @@ -1,18 +1,18 @@ ---- src/searchcore.cc.orig 2024-09-26 10:48:55 UTC +--- src/searchcore.cc.orig 2025-10-05 12:35:57 UTC +++ src/searchcore.cc -@@ -239,9 +239,14 @@ auto search_topscores(struct searchinfo_s * si) -> voi - if (bitmap) +@@ -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) ++ // 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(si->kmers, -+ increment_counters_from_bitmap_sse2(si->kmers, +- 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 index c6cd9ec46abb..b5af8da42d6e 100644 --- a/biology/vsearch/files/patch-src_sintax.cc +++ b/biology/vsearch/files/patch-src_sintax.cc @@ -1,7 +1,7 @@ ---- src/sintax.cc.orig 2024-09-26 10:48:55 UTC +--- src/sintax.cc.orig 2025-10-05 12:34:38 UTC +++ src/sintax.cc -@@ -289,9 +289,14 @@ auto sintax_search_topscores(struct searchinfo_s * si) - if (bitmap) +@@ -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 @@ -9,10 +9,10 @@ + // 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) + if (ssse3_present != 0) { -- increment_counters_from_bitmap_ssse3(si->kmers, -+ increment_counters_from_bitmap_sse2(si->kmers, +- increment_counters_from_bitmap_ssse3(searchinfo->kmers, ++ increment_counters_from_bitmap_sse2(searchinfo->kmers, bitmap, indexed_count); } else |