From nobody Tue Aug 4 04:52:55 2026 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4hDh4Y3Jqyz6mMXY for ; Tue, 04 Aug 2026 04:53:01 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "YR1" (not verified)) by mx1.freebsd.org (Postfix) with ESMTPS id 4hDh4Y2Qs1z42lx for ; Tue, 04 Aug 2026 04:53:01 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1785819181; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=SlwVFGKHj/2218K892lm3Wl1kVCtg+f8rv/Fr/mWeDE=; b=SCA5E89wCLBoZnoeRHR3qKgVLc9Z0g7n0CBwfm5yZPPShe4W993KUlsfKX1K9XAZsnt0MX beODThmB1/PwUrGmXQrnEY4aqr8740BpZy9jiMiPI8BRcsJBnwoE+lpFmJ5sR5V92WMcFY D4QV8n5GqztwpbMXTsTchKeFaHewJp8BDX3EyAz4gRJcfNEzOK+rlUMMqmV9TVgIkc2h7Q 8xC112PJxHz8mIYF0YHw8E1pL7IummHh6xNNMlba6LwHwV1+Hsty9P8/UdU/NzU2tzEY0D cFIShiYRG1guOVBD3G+9yKhDRVJaJHrPJwt/L1WztRZiuqaWqp2M5k1RQAIulQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1785819181; a=rsa-sha256; cv=none; b=pCAKsW5TjvTONWgG5EcTSqDzHdQ/s80y5RhRSet6Gi8dOweSJCriiB8M4Uc9XzJ61xtAG/ Usshl5KmR0hLxJRZnN3ou+cnHG5goSBXnB+OIf3HXkD+6Cj7wi+jZI6+wRSVxQpym47MR8 4CoIrre3Cbu8zkVAxV8M/1/0hqKkLPlYo5/pwp2+48autw/TL1fNZ1kUABwBtNGDk1rwgq +mgxg/eMeb4g8utx00LCo3RYxwn3W+QcNJFWyW4UsBlifRszLYIqeQ6TVW5Q/wk28SN8yD JrdAUeoQg+v7/WZ84wCR6AEJhMOMfptv1DrcQrukxfQ4Jq7VaqT5jkLEBJTkUw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1785819181; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=SlwVFGKHj/2218K892lm3Wl1kVCtg+f8rv/Fr/mWeDE=; b=P2R9IpOMijfmKWc3YuAgrbXLsyfGgYDjBng7ktNaOA31DPU/gy/SmvjyM5Yde/Hh/fLuJ/ IF4mqoMkF85UEdbA8Vj9lwTvZJfW/QI+kSe5910xbeXaFoDFTWlKTADdNvUwUXYWoiLXbV yyEeXyp4fKqslZejwy8MBnrnQaNyLOzeqPTnxzQXEUJQPzJmfyuHJpCPAH+Qw9UkR8/aiS Ue6m3G7MI27NkYgLbbY+CY+aoOVSZ6gKSEEVqOkxQdc+ybKW7RG3rGzjLtFb7g3DfLNE4o o9S65OpW68vX4G3BPnUWur4XytvXUVCXVMRM/M4sxyGOkl34SqhEf98AQ3rRFw== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4hDh4Y14m9zYxh for ; Tue, 04 Aug 2026 04:53:01 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from git (uid 1279) (envelope-from git@FreeBSD.org) id 19130 by gitrepo.freebsd.org (DragonFly Mail Agent v0.13+ on gitrepo.freebsd.org); Tue, 04 Aug 2026 04:52:55 +0000 To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Joseph Mingrone Subject: git: 9cd93f98a49e - main - biology/diamond: Update to 2.2.5 and fix deepclust crash List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-dev-commits-ports-all@FreeBSD.org List-Id: List-Post: List-Help: List-Subscribe: List-Unsubscribe: List-Owner: Precedence: list MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jrm X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 9cd93f98a49e1e02b084e0f3ecf0cea028f2085d Auto-Submitted: auto-generated Date: Tue, 04 Aug 2026 04:52:55 +0000 Message-Id: <6a717027.19130.8a80691@gitrepo.freebsd.org> The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=9cd93f98a49e1e02b084e0f3ecf0cea028f2085d commit 9cd93f98a49e1e02b084e0f3ecf0cea028f2085d Author: Joseph Mingrone AuthorDate: 2026-08-04 04:11:09 +0000 Commit: Joseph Mingrone 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 - #include -+#else -+#include // unlink - #endif - #include // strerror - #include "file.h"