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Bacon" Subject: git: 9c84b1d1c88b - main - biology/vsearch: Update to 2.29.0 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 9c84b1d1c88b48d7c62cb51e0d6af53340ec46e4 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=9c84b1d1c88b48d7c62cb51e0d6af53340ec46e4 commit 9c84b1d1c88b48d7c62cb51e0d6af53340ec46e4 Author: Jason W. Bacon AuthorDate: 2024-10-21 20:15:58 +0000 Commit: Jason W. Bacon CommitDate: 2024-10-21 20:15:58 +0000 biology/vsearch: Update to 2.29.0 Several bug fixes Support for RISC-V Improved testing Changes: https://github.com/torognes/vsearch/releases Reported by: portscout --- biology/vsearch/Makefile | 2 +- biology/vsearch/distinfo | 6 +++--- biology/vsearch/files/patch-src_searchcore.cc | 18 ++++++++++++++++++ biology/vsearch/files/patch-src_sintax.cc | 18 ++++++++++++++++++ 4 files changed, 40 insertions(+), 4 deletions(-) diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile index 6d6ded03e517..4937c94ff19b 100644 --- a/biology/vsearch/Makefile +++ b/biology/vsearch/Makefile @@ -1,6 +1,6 @@ PORTNAME= vsearch DISTVERSIONPREFIX= v -DISTVERSION= 2.28.1 +DISTVERSION= 2.29.0 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo index f746cec601da..55cfb1fec6ff 100644 --- a/biology/vsearch/distinfo +++ b/biology/vsearch/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1714566699 -SHA256 (torognes-vsearch-v2.28.1_GH0.tar.gz) = 4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c -SIZE (torognes-vsearch-v2.28.1_GH0.tar.gz) = 272918 +TIMESTAMP = 1729339584 +SHA256 (torognes-vsearch-v2.29.0_GH0.tar.gz) = 2c5bd0d9b3c2ec8eecd1af06ae11611138d87fdfecfa423ae791d52dccd27e63 +SIZE (torognes-vsearch-v2.29.0_GH0.tar.gz) = 283459 diff --git a/biology/vsearch/files/patch-src_searchcore.cc b/biology/vsearch/files/patch-src_searchcore.cc new file mode 100644 index 000000000000..84870932c9fd --- /dev/null +++ b/biology/vsearch/files/patch-src_searchcore.cc @@ -0,0 +1,18 @@ +--- src/searchcore.cc.orig 2024-09-26 10:48:55 UTC ++++ src/searchcore.cc +@@ -239,9 +239,14 @@ auto search_topscores(struct searchinfo_s * si) -> voi + if (bitmap) + { + #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) + { +- increment_counters_from_bitmap_ssse3(si->kmers, ++ increment_counters_from_bitmap_sse2(si->kmers, + bitmap, indexed_count); + } + else diff --git a/biology/vsearch/files/patch-src_sintax.cc b/biology/vsearch/files/patch-src_sintax.cc new file mode 100644 index 000000000000..c6cd9ec46abb --- /dev/null +++ b/biology/vsearch/files/patch-src_sintax.cc @@ -0,0 +1,18 @@ +--- src/sintax.cc.orig 2024-09-26 10:48:55 UTC ++++ src/sintax.cc +@@ -289,9 +289,14 @@ auto sintax_search_topscores(struct searchinfo_s * si) + if (bitmap) + { + #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) + { +- increment_counters_from_bitmap_ssse3(si->kmers, ++ increment_counters_from_bitmap_sse2(si->kmers, + bitmap, indexed_count); + } + else