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Date:      Tue, 14 Apr 2026 07:12:44 +0000
From:      Yuri Victorovich <yuri@FreeBSD.org>
To:        ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org
Subject:   git: f1b5d87d18f6 - main - biology/seqan3: update 3.=?utf-8?Q?4.0 =E2=86=92?= 3.4.2
Message-ID:  <69dde8ec.41c7e.133a5e28@gitrepo.freebsd.org>
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The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=f1b5d87d18f6f78ea3948f45a1dda7865a8f1e75

commit f1b5d87d18f6f78ea3948f45a1dda7865a8f1e75
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-04-14 04:20:44 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-04-14 07:12:39 +0000

    biology/seqan3: update 3.4.0 → 3.4.2
---
 biology/seqan3/Makefile | 10 ++++++++--
 biology/seqan3/distinfo | 14 +++++++-------
 2 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/biology/seqan3/Makefile b/biology/seqan3/Makefile
index c1675008fd19..bdaa8f7f8e88 100644
--- a/biology/seqan3/Makefile
+++ b/biology/seqan3/Makefile
@@ -1,7 +1,7 @@
 PORTNAME=	seqan3
-DISTVERSION=	3.4.0
+DISTVERSION=	3.4.2
 CATEGORIES=	biology devel math
-MASTER_SITES=	https://github.com/cpm-cmake/CPM.cmake/releases/download/v0.42.0/:cpm
+MASTER_SITES=	https://github.com/cpm-cmake/CPM.cmake/releases/download/v0.42.1/:cpm
 DISTFILES=	CPM.cmake:cpm
 DIST_SUBDIR=	${PORTNAME}-${DISTVERSION}
 EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX} \
@@ -33,6 +33,10 @@ TEST_WRKSRC=	${WRKSRC}/.test
 
 NO_ARCH=	yes
 
+xpost-patch:
+	# remove CPM.cmake: it triggers undesirable logic in cmake scripts
+	@${RM} ${WRKSRC}/cmake/CPM.cmake
+
 post-install:
 	@${RM} -r ${STAGEDIR}${DOCSDIR}
 
@@ -42,4 +46,6 @@ do-test:
 		${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \
 		ctest
 
+# tests as of 3.4.2: 96% tests passed, 14 tests failed out of 315: some tests fail wuth SIGILL, see https://github.com/seqan/seqan3/issues/3415, other tests also fail, see https://github.com/seqan/seqan3/issues/3416
+
 .include <bsd.port.mk>
diff --git a/biology/seqan3/distinfo b/biology/seqan3/distinfo
index 9e9fe56de4ee..3d3ebb3710dc 100644
--- a/biology/seqan3/distinfo
+++ b/biology/seqan3/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1756395731
-SHA256 (seqan3-3.4.0/CPM.cmake) = 2020b4fc42dba44817983e06342e682ecfc3d2f484a581f11cc5731fbe4dce8a
-SIZE (seqan3-3.4.0/CPM.cmake) = 44969
-SHA256 (seqan3-3.4.0/seqan-seqan3-3.4.0_GH0.tar.gz) = 8e000e6788f1e2ada071b36f64231d56f18e2d687ab4122d86cd3aefc6c87743
-SIZE (seqan3-3.4.0/seqan-seqan3-3.4.0_GH0.tar.gz) = 1749810
-SHA256 (seqan3-3.4.0/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1
-SIZE (seqan3-3.4.0/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = 1183835
+TIMESTAMP = 1776139326
+SHA256 (seqan3-3.4.2/CPM.cmake) = f3a6dcc6a04ce9e7f51a127307fa4f699fb2bade357a8eb4c5b45df76e1dc6a5
+SIZE (seqan3-3.4.2/CPM.cmake) = 44969
+SHA256 (seqan3-3.4.2/seqan-seqan3-3.4.2_GH0.tar.gz) = bb7467f8e296279a89fa75909129e128d67195187fe066ed096e9fb6250e37e5
+SIZE (seqan3-3.4.2/seqan-seqan3-3.4.2_GH0.tar.gz) = 1752849
+SHA256 (seqan3-3.4.2/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1
+SIZE (seqan3-3.4.2/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = 1183835
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