Date: Tue, 21 Apr 2026 20:15:08 +0000 From: Robert Clausecker <fuz@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 372104dd71f6 - main - biology/ugene: fix build on aarch64 Message-ID: <69e7dacc.21662.28363d10@gitrepo.freebsd.org>
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The branch main has been updated by fuz: URL: https://cgit.FreeBSD.org/ports/commit/?id=372104dd71f6e0b1d463713793510b0f7ca5f0a8 commit 372104dd71f6e0b1d463713793510b0f7ca5f0a8 Author: Robert Clausecker <fuz@FreeBSD.org> AuthorDate: 2026-04-19 19:39:38 +0000 Commit: Robert Clausecker <fuz@FreeBSD.org> 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 ++#)home | help
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