Date: Tue, 04 Aug 2026 04:52:55 +0000 From: Joseph Mingrone <jrm@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 9cd93f98a49e - main - biology/diamond: Update to 2.2.5 and fix deepclust crash Message-ID: <6a717027.19130.8a80691@gitrepo.freebsd.org>
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The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=9cd93f98a49e1e02b084e0f3ecf0cea028f2085d commit 9cd93f98a49e1e02b084e0f3ecf0cea028f2085d Author: Joseph Mingrone <jrm@FreeBSD.org> AuthorDate: 2026-08-04 04:11:09 +0000 Commit: Joseph Mingrone <jrm@FreeBSD.org> CommitDate: 2026-08-04 04:52:24 +0000 biology/diamond: Update to 2.2.5 and fix deepclust crash Initialize the seed_only member in the Hsp constructor that takes an ApproxHsp. deepclust builds Hsps through this constructor for its approximate alignments, so seed_only was left uninitialized. When it evaluated to true, the SEED_ONLY flag was set on an otherwise full-length intermediate output record. The multiblock join later parsed that record as seed-only, stopped four bytes short, and aborted with "Unexpected end of file", failing the deepclust-multiblock regression test. On Linux, the uninitialized member consistently evaluated to false, masking the bug. On FreeBSD, it evaluated to true, and triggered the crash. Release notes: https://github.com/bbuchfink/diamond/releases/tag/v2.2.5 Sponsored by: The FreeBSD Foundation --- biology/diamond/Makefile | 2 +- biology/diamond/distinfo | 6 +++--- biology/diamond/files/patch-src_basic_hssp.cpp | 10 ++++++++++ biology/diamond/files/patch-src_util_io_file.cpp | 11 ----------- 4 files changed, 14 insertions(+), 15 deletions(-) diff --git a/biology/diamond/Makefile b/biology/diamond/Makefile index c63fcb6e504d..62604d6f0e97 100644 --- a/biology/diamond/Makefile +++ b/biology/diamond/Makefile @@ -1,6 +1,6 @@ PORTNAME= diamond DISTVERSIONPREFIX= v -DISTVERSION= 2.2.4 +DISTVERSION= 2.2.5 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/diamond/distinfo b/biology/diamond/distinfo index 823bda4b4b8c..f80092a45ef9 100644 --- a/biology/diamond/distinfo +++ b/biology/diamond/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1785212282 -SHA256 (bbuchfink-diamond-v2.2.4_GH0.tar.gz) = 11c593677b67ef541095122c243eed384bb9933da12fffc676ad7b35a3e4dc44 -SIZE (bbuchfink-diamond-v2.2.4_GH0.tar.gz) = 15147435 +TIMESTAMP = 1785776010 +SHA256 (bbuchfink-diamond-v2.2.5_GH0.tar.gz) = ca58297af1c60e02a36363f11d161a27f5bd4fed8b172cc56fab65805f37056a +SIZE (bbuchfink-diamond-v2.2.5_GH0.tar.gz) = 15169124 diff --git a/biology/diamond/files/patch-src_basic_hssp.cpp b/biology/diamond/files/patch-src_basic_hssp.cpp new file mode 100644 index 000000000000..ed351593e4a6 --- /dev/null +++ b/biology/diamond/files/patch-src_basic_hssp.cpp @@ -0,0 +1,10 @@ +--- src/basic/hssp.cpp.orig 2026-08-04 03:42:17 UTC ++++ src/basic/hssp.cpp +@@ -356,6 +356,7 @@ Hsp::Hsp(const ApproxHsp& h, Loc qlen, Loc tlen) : + + Hsp::Hsp(const ApproxHsp& h, Loc qlen, Loc tlen) : + backtraced(true), ++ seed_only(false), + score(h.score), + frame(0), + length(h.query_range.length()), diff --git a/biology/diamond/files/patch-src_util_io_file.cpp b/biology/diamond/files/patch-src_util_io_file.cpp deleted file mode 100644 index 110aff8b7e35..000000000000 --- a/biology/diamond/files/patch-src_util_io_file.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- src/util/io/file.cpp.orig 2026-07-13 11:36:09 UTC -+++ src/util/io/file.cpp -@@ -21,6 +21,8 @@ along with this program. If not, see <http://www.gnu. - #ifdef _WIN32 - #include <io.h> - #include <fcntl.h> -+#else -+#include <unistd.h> // unlink - #endif - #include <string.h> // strerror - #include "file.h"home | help
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