MDee4dSiCE70iZ5MBzF4v5kaxqqztcPs9rIeceFjjy0KIq5IRtSjwW 4CH5kTLNzIm0seASy2RpuF9vOdz8q7vQpc0JuMkz3/LSqec0aT5q9DoUdqKTkw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1776802509; a=rsa-sha256; cv=none; b=E3Dyw1texkNU+0ueybMJrrWBDxPbjJ0dPAgy0nE7WuP4yvUUew0CTIRYWRmeQ+hIwBrXlo 7HwFozm+RIF1Zrte3/3IM8Wynw8ygc+GFVEMaH8NHofjLdzyPF4jUeR+3q08q4S+30SpqY Dk2ERh8D5WlOhqYFz0jqyheq/v0yvXBdc4ORoMtlUFVSPMgX0QztsULvtuVBIfHLJ4RhG2 KAzZWrFKRSqm/K28E+e+2Pd8NvNXD7OgYNZp4POgfLGzqK3kAuFbCSbeWbrk0yC/u08X0A WlUR5ardznnP9bAWjN7qyoGz25O+X90RqmO9A1VY9DxmtM326RdgLYm+PVnTmg== 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=1776802509; 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=ff2zo2ajCoEj4FEZDDUyieMbdDIxgTaaJqF+p8TpQ2c=; b=tqaEyQvRX13PNHLUI2tWZpY2WCfiZ9Ge7zetF08alrCS5mmPGCpsbMWd39ELCQH2hox9ha 8V5qWJQEOs6ipxnSWNd3y3AN3TGUVrf0eecXn/eUoBMWUgPdiFpfKVoAf/K938XatnFjYg q4NlM00l5hOxJr+3HzahR/rKDWjxXUXTgXjauwpPYhdnpTJpjgXMJberXIMYt5rQLXEKbK 1FzSQcsWuv2DQFfR2vmOX1t0gHBot7MB1+SpDRSKPf75Ec0LZvPZw6w+2DiXjxs/UpyRtC 7VvQVQYCV5HRVfsynd/GRiKSvXTVJh7nZD4U9qPrddYwx/YajjhOYJIfd7jFAw== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4g0YW06l7nzynF for ; Tue, 21 Apr 2026 20:15:08 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from git (uid 1279) (envelope-from git@FreeBSD.org) id 21662 by gitrepo.freebsd.org (DragonFly Mail Agent v0.13+ on gitrepo.freebsd.org); Tue, 21 Apr 2026 20:15:08 +0000 To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Robert Clausecker Subject: git: 372104dd71f6 - main - biology/ugene: fix build on aarch64 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: fuz X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 372104dd71f6e0b1d463713793510b0f7ca5f0a8 Auto-Submitted: auto-generated Date: Tue, 21 Apr 2026 20:15:08 +0000 Message-Id: <69e7dacc.21662.28363d10@gitrepo.freebsd.org> The branch main has been updated by fuz: URL: https://cgit.FreeBSD.org/ports/commit/?id=372104dd71f6e0b1d463713793510b0f7ca5f0a8 commit 372104dd71f6e0b1d463713793510b0f7ca5f0a8 Author: Robert Clausecker AuthorDate: 2026-04-19 19:39:38 +0000 Commit: Robert Clausecker CommitDate: 2026-04-21 20:14:30 +0000 biology/ugene: fix build on aarch64 The bundled copy of htslib is missing required assembly source files, causing build failure due to undefined symbols an aarch64. Unbundle htslib and use our working port biology/htslib instead. Approved by: makc (maintainer) MFH: 2026Q2 PR: 293379 --- biology/ugene/Makefile | 7 ++- ...atch-src_libs__3rdparty_samtools_CMakeLists.txt | 70 ++++++++++++++++++++++ 2 files changed, 74 insertions(+), 3 deletions(-) diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index 60d26dd34b52..ab0147da399c 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -1,5 +1,6 @@ PORTNAME= ugene PORTVERSION= 53.1 +PORTREVISION= 1 CATEGORIES= biology science MAINTAINER= makc@FreeBSD.org @@ -9,12 +10,12 @@ WWW= https://ugene.net/ LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE.txt -IGNORE_aarch64= fails to build: https://bugs.freebsd.org/293379 - +LIB_DEPENDS= libhts.so:biology/htslib RUN_DEPENDS= bash:shells/bash USES= cmake compiler:c++14-lang desktop-file-utils gl \ - localbase:ldflags qt:5 shared-mime-info shebangfix xorg + localbase:ldflags pkgconfig qt:5 shared-mime-info \ + shebangfix xorg USE_GL= gl glu USE_QT= buildtools:build linguisttools:build qmake:build \ core gui network networkauth printsupport \ diff --git a/biology/ugene/files/patch-src_libs__3rdparty_samtools_CMakeLists.txt b/biology/ugene/files/patch-src_libs__3rdparty_samtools_CMakeLists.txt new file mode 100644 index 000000000000..9e066dacc262 --- /dev/null +++ b/biology/ugene/files/patch-src_libs__3rdparty_samtools_CMakeLists.txt @@ -0,0 +1,70 @@ +--- src/libs_3rdparty/samtools/CMakeLists.txt.orig 2026-03-01 18:44:47 UTC ++++ src/libs_3rdparty/samtools/CMakeLists.txt +@@ -21,45 +21,6 @@ file(GLOB SRCS + #endif () + + file(GLOB SRCS +- src/samtools_core/htslib/cram/cram_codecs.c +- src/samtools_core/htslib/cram/cram_decode.c +- src/samtools_core/htslib/cram/cram_encode.c +- src/samtools_core/htslib/cram/cram_external.c +- src/samtools_core/htslib/cram/cram_index.c +- src/samtools_core/htslib/cram/cram_io.c +- src/samtools_core/htslib/cram/cram_stats.c +- src/samtools_core/htslib/cram/mFILE.c +- src/samtools_core/htslib/cram/open_trace_file.c +- src/samtools_core/htslib/cram/pooled_alloc.c +- src/samtools_core/htslib/cram/string_alloc.c +- src/samtools_core/htslib/htscodecs/htscodecs/arith_dynamic.c +- src/samtools_core/htslib/htscodecs/htscodecs/fqzcomp_qual.c +- src/samtools_core/htslib/htscodecs/htscodecs/htscodecs.c +- src/samtools_core/htslib/htscodecs/htscodecs/pack.c +- src/samtools_core/htslib/htscodecs/htscodecs/rANS_static.c +- src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c +- src/samtools_core/htslib/htscodecs/htscodecs/rANS_static32x16pr.c +- src/samtools_core/htslib/htscodecs/htscodecs/rle.c +- src/samtools_core/htslib/htscodecs/htscodecs/tokenise_name3.c +- src/samtools_core/htslib/htscodecs/htscodecs/utils.c +- src/samtools_core/htslib/bgzf.c +- src/samtools_core/htslib/errmod.c +- src/samtools_core/htslib/header.c +- src/samtools_core/htslib/hfile.c +- src/samtools_core/htslib/hts.c +- src/samtools_core/htslib/hts_expr.c +- src/samtools_core/htslib/hts_os.c +- src/samtools_core/htslib/kstring.c +- src/samtools_core/htslib/md5.c +- src/samtools_core/htslib/multipart.c +- src/samtools_core/htslib/probaln.c +- src/samtools_core/htslib/realn.c +- src/samtools_core/htslib/region.c +- src/samtools_core/htslib/sam.c +- src/samtools_core/htslib/sam_mods.c +- src/samtools_core/htslib/tbx.c +- src/samtools_core/htslib/textutils.c +- src/samtools_core/htslib/thread_pool.c + src/samtools_core/bam.c + src/samtools_core/bam_aux.c + src/samtools_core/bam_lpileup.c +@@ -233,13 +194,19 @@ endif () + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -w") + endif () + ++find_package(PkgConfig REQUIRED) ++pkg_check_modules(HTSLIB REQUIRED htslib) ++ + add_library(samtools STATIC ${SRCS}) + ++target_include_directories(samtools PRIVATE ${HTSLIB_INCLUDE_DIRS}) ++target_compile_options(samtools PRIVATE ${HTSLIB_CFLAGS_OTHER}) + target_link_libraries(samtools ++ ${HTSLIB_LIBRARIES} + Qt5::Core + # U2Core + zlib) + + #target_compile_options(samtools PRIVATE + # /we4013 # Treat implicit declarations as errors +-#) +\ No newline at end of file ++#)