Date: Sat, 18 Apr 2026 20:44:19 +0000 From: Max Brazhnikov <makc@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 7f73f34aa06d - main - biology/ugene: Update to 53.1 Message-ID: <69e3ed23.23617.79f8c432@gitrepo.freebsd.org>
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The branch main has been updated by makc: URL: https://cgit.FreeBSD.org/ports/commit/?id=7f73f34aa06d2c12fc03476b05ef8658c97b6989 commit 7f73f34aa06d2c12fc03476b05ef8658c97b6989 Author: Max Brazhnikov <makc@FreeBSD.org> AuthorDate: 2026-04-18 20:44:01 +0000 Commit: Max Brazhnikov <makc@FreeBSD.org> CommitDate: 2026-04-18 20:44:01 +0000 biology/ugene: Update to 53.1 Release Notes: https://ugene.net/changelist.html Port changes: - Fix build on non-x86, mark IGNORE for aarch64. - Switch to cmake, qmake is not supported anymore. - Drop unused sqlite, renew Qt components. - Convert to PORTDATA, use shebangfix. Special thanks to fuz@ for testing and fixing non-x86 build! PR: 293379 --- biology/ugene/Makefile | 85 +- biology/ugene/distinfo | 6 +- biology/ugene/files/patch-linux | 42 + biology/ugene/files/patch-qmutex | 64 ++ .../patch-src_corelibs_U2Private_U2Private.pro | 41 - ...rty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp | 21 - ...dparty_QSpec_src_drivers_GTMouseDriverLinux.cpp | 20 - .../ugene/files/patch-src_plugins__3rdparty_ball | 28 + .../files/patch-src_plugins__checker_src_Main.cpp | 31 - biology/ugene/files/patch-src_ugenecl_src_Main.cpp | 46 +- biology/ugene/files/patch-src_ugeneui_src_Main.cpp | 45 - biology/ugene/files/patch-sse2neon | 40 + biology/ugene/files/patch-ugene.pro | 10 - biology/ugene/files/patch-unix | 37 + biology/ugene/pkg-plist | 1208 +------------------- 15 files changed, 297 insertions(+), 1427 deletions(-) diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index 959569de56f9..60d26dd34b52 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -1,6 +1,5 @@ PORTNAME= ugene -PORTVERSION= 40.1 -PORTREVISION= 1 +PORTVERSION= 53.1 CATEGORIES= biology science MAINTAINER= makc@FreeBSD.org @@ -10,56 +9,72 @@ WWW= https://ugene.net/ LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE.txt -BROKEN_aarch64= fails to build: invokes x86 asm -BROKEN_armv7= fails to build: src/SendReportDialog.cpp:435:20: error: invalid output constraint '=a' in asm, see https://github.com/ugeneunipro/ugene/issues/919 -BROKEN_riscv64= fails to build: invokes x86 asm +IGNORE_aarch64= fails to build: https://bugs.freebsd.org/293379 RUN_DEPENDS= bash:shells/bash -USE_GITHUB= yes -GH_ACCOUNT= ugeneunipro - -USES= desktop-file-utils gl qmake qt:5 shared-mime-info sqlite xorg +USES= cmake compiler:c++14-lang desktop-file-utils gl \ + localbase:ldflags qt:5 shared-mime-info shebangfix xorg USE_GL= gl glu -USE_QT= buildtools:build linguisttools:build \ - core gui network opengl printsupport scripttools script \ - sql svg testlib widgets xml \ +USE_QT= buildtools:build linguisttools:build qmake:build \ + core gui network networkauth printsupport \ + svg testlib websockets widgets xml \ imageformats:run USE_XORG= x11 xtst +USE_LDCONFIG= ${UGENE_LIBDIR} -QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \ - INSTALL_MANDIR="${PREFIX}/share/man" \ - UGENE_LRELEASE="${LRELEASE}" UGENE_LUPDATE="${LUPDATE}" \ - UGENE_USE_BUNDLED_SQLITE=0 -ALL_TARGET= release -CXXFLAGS_i386= -msse2 +USE_GITHUB= yes +GH_ACCOUNT= ugeneunipro -OPTIONS_DEFINE= OPENCL +CXXFLAGS_i386= -msse2 +LDFLAGS+= -pthread +SHEBANG_FILES= etc/shared/ugene +PORTDATA= * -OPENCL_QMAKE_ON= UGENE_OPENCL_DETECTED=1 +UGENE_LIBDIR= ${PREFIX}/lib/ugene .include <bsd.port.pre.mk> -.if ${ARCH} == i386 -QMAKE_ARGS+= CONFIG+=x86 +.if empty(ARCH:Mamd64) && empty(ARCH:Mi386) +BUILD_DEPENDS+= ${LOCALBASE}/include/sse2neon.h:devel/sse2neon .endif post-patch: -# yes, bash is required, stuff will not execute with sh - @${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \ - ${WRKSRC}/src/gen_bin_script.cmd \ - ${WRKSRC}/etc/shared/ugene ${WRKSRC}/etc/shared/ugened @${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \ ${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp - @${REINPLACE_CMD} 's, -lbreakpad$$$$D,,' \ - ${WRKSRC}/src/corelibs/U2Private/U2Private.pri \ - ${WRKSRC}/src/plugins_checker/plugins_checker.pri \ - ${WRKSRC}/src/ugenecl/ugenecl.pri \ - ${WRKSRC}/src/ugeneui/ugeneui.pri - @${REINPLACE_CMD} -e '/ugene\.desktop/s,share,&d,' \ - ${WRKSRC}/ugene.pri + ${REINPLACE_CMD} 's,stdc++fs,,' \ + ${WRKSRC}/src/libs_3rdparty/QSpec/CMakeLists.txt + ${REINPLACE_CMD} 's,/usr/local/share/ugene,${DATADIR},' \ + ${WRKSRC}/src/ugenecl/src/Main.cpp +# breakpad is not aware of FreeBSD + ${REINPLACE_CMD} '/libs_3rdparty\/breakpad/d' \ + ${WRKSRC}/src/corelibs/U2Private/CMakeLists.txt \ + ${WRKSRC}/CMakeLists.txt + ${REINPLACE_CMD} 's,breakpad,,' \ + ${WRKSRC}/src/ugeneui/CMakeLists.txt \ + ${WRKSRC}/src/ugenecl/CMakeLists.txt \ + ${WRKSRC}/src/corelibs/U2Private/CMakeLists.txt +# Do not alter binary names for debug build + ${REINPLACE_CMD} '/DEBUG_POSTFIX/d' \ + ${WRKSRC}/src/plugins_checker/CMakeLists.txt \ + ${WRKSRC}/src/ugenecl/CMakeLists.txt \ + ${WRKSRC}/src/ugenem/CMakeLists.txt \ + ${WRKSRC}/src/ugeneui/CMakeLists.txt \ + ${WRKSRC}/CMakeLists.txt -post-stage: - @cd ${STAGEDIR}${PREFIX} && ${RM} bin/ecp.* lib/ugene/ecp.* +do-install: + ${MKDIR} ${STAGEDIR}/${UGENE_LIBDIR} + cd ${BUILD_WRKSRC}/dist && ${COPYTREE_SHARE} . ${STAGEDIR}/${UGENE_LIBDIR}/ +.for prog in ugene ugenecl ugenem ugeneui + ${RLN} ${STAGEDIR}${UGENE_LIBDIR}/${prog} ${STAGEDIR}/${PREFIX}/bin/${prog} +.endfor + ${MKDIR} ${STAGEDIR}/${DATADIR} + cd ${WRKSRC} && ${COPYTREE_SHARE} data ${STAGEDIR}/${DATADIR} + ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.desktop ${STAGEDIR}/${DESKTOPDIR} + ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.png ${STAGEDIR}/${PREFIX}/share/pixmaps/ + ${INSTALL_DATA} ${WRKSRC}/etc/shared/application-x-ugene-ext.png ${STAGEDIR}/${PREFIX}/share/pixmaps/ + ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.1.gz ${STAGEDIR}/${PREFIX}/share/man/man1/ + ${MKDIR} ${STAGEDIR}/${PREFIX}/share/mime/packages + ${INSTALL_DATA} ${WRKSRC}/etc/shared/application-x-ugene.xml ${STAGEDIR}/${PREFIX}/share/mime/packages/ .include <bsd.port.post.mk> diff --git a/biology/ugene/distinfo b/biology/ugene/distinfo index 5eff6f289b9d..3d5da3ede80d 100644 --- a/biology/ugene/distinfo +++ b/biology/ugene/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1633934483 -SHA256 (ugeneunipro-ugene-40.1_GH0.tar.gz) = 92b954449f697957c6b6b2da803ba6ae9ad546f44c584bbb2ab8600ac8b45a6e -SIZE (ugeneunipro-ugene-40.1_GH0.tar.gz) = 28791083 +TIMESTAMP = 1775033524 +SHA256 (ugeneunipro-ugene-53.1_GH0.tar.gz) = 3eca3bc97824d855b5dfe4844b7a5d46052f98279fa015c7e152e111f89c4673 +SIZE (ugeneunipro-ugene-53.1_GH0.tar.gz) = 27484438 diff --git a/biology/ugene/files/patch-linux b/biology/ugene/files/patch-linux new file mode 100644 index 000000000000..f334ee07eca0 --- /dev/null +++ b/biology/ugene/files/patch-linux @@ -0,0 +1,42 @@ +--- src/corelibs/U2Private/src/crash_handler/CrashHandler.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/corelibs/U2Private/src/crash_handler/CrashHandler.cpp +@@ -36,7 +36,7 @@ + + #if defined(Q_OS_DARWIN) + # include "CrashHandlerPrivateMac.h" +-#elif defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN) ++#elif defined(Q_OS_LINUX) + # include "CrashHandlerPrivateUnixNotMac.h" + #elif defined(Q_OS_WIN) + # include "CrashHandlerPrivateWin.h" +@@ -124,7 +124,7 @@ void CrashHandler::setupPrivateHandler() { + assert(crashHandlerPrivate == nullptr); + #if defined(Q_OS_DARWIN) + crashHandlerPrivate = new CrashHandlerPrivateMac; +-#elif defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN) ++#elif defined(Q_OS_LINUX) + crashHandlerPrivate = new CrashHandlerPrivateUnixNotMac; + #elif defined(Q_OS_WIN) + crashHandlerPrivate = new CrashHandlerPrivateWin; +--- src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp +@@ -20,7 +20,7 @@ + */ + + #include <qglobal.h> +-#if defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN) ++#if defined(Q_OS_LINUX) + + # include <execinfo.h> + +--- src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.h.orig 2026-03-01 18:44:47 UTC ++++ src/corelibs/U2Private/src/crash_handler/CrashHandlerPrivateUnixNotMac.h +@@ -22,7 +22,7 @@ + #pragma once + + #include <qglobal.h> +-#if defined(Q_OS_UNIX) && !defined(Q_OS_DARWIN) ++#if defined(Q_OS_LINUX) + + # include <client/linux/handler/exception_handler.h> + diff --git a/biology/ugene/files/patch-qmutex b/biology/ugene/files/patch-qmutex new file mode 100644 index 000000000000..a11b98d3fce2 --- /dev/null +++ b/biology/ugene/files/patch-qmutex @@ -0,0 +1,64 @@ +--- src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.cpp +@@ -30,7 +30,7 @@ SubstMatrixRegistry::SubstMatrixRegistry(QObject* pOwn + namespace U2 { + + SubstMatrixRegistry::SubstMatrixRegistry(QObject* pOwn) +- : QObject(pOwn), mutex(QMutex::Recursive) { ++ : QObject(pOwn), mutex() { + readMatrices(); + } + +--- src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.h.orig 2026-03-01 18:44:47 UTC ++++ src/corelibs/U2Algorithm/src/registry/SubstMatrixRegistry.h +@@ -53,7 +53,7 @@ class U2ALGORITHM_EXPORT SubstMatrixRegistry : public + void readMatrices(); + static SMatrix parseMatrix(const QString& name, const QByteArray& text, QString& error); + +- mutable QMutex mutex; ++ mutable QRecursiveMutex mutex; + QMap<QString, SMatrix> matrixByName; + }; + +--- src/plugins/annotator/src/CollocationsDialogController.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/plugins/annotator/src/CollocationsDialogController.cpp +@@ -313,7 +313,7 @@ CollocationSearchTask::CollocationSearchTask(const QLi + ////////////////////////////////////////////////////////////////////////// + // task + CollocationSearchTask::CollocationSearchTask(const QList<AnnotationTableObject*>& table, const QSet<QString>& names, const CollocationsAlgorithmSettings& cfg) +- : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(QMutex::Recursive), keepSourceAnns(false) { ++ : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(), keepSourceAnns(false) { + GCOUNTER(cvar, "CollocationSearchTask"); + assert(cfg.distance >= 0); + assert(!names.isEmpty()); +@@ -342,7 +342,7 @@ CollocationSearchTask::CollocationSearchTask(const QLi + } + + CollocationSearchTask::CollocationSearchTask(const QList<SharedAnnotationData>& table, const QSet<QString>& names, const CollocationsAlgorithmSettings& cfg, bool _keepSourceAnns) +- : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(QMutex::Recursive), keepSourceAnns(_keepSourceAnns) { ++ : Task(tr("Search for annotated regions"), TaskFlag_None), cfg(cfg), lock(), keepSourceAnns(_keepSourceAnns) { + assert(cfg.distance >= 0); + assert(!names.isEmpty()); + foreach (const QString& name, names) { +--- src/plugins/annotator/src/CollocationsDialogController.h.orig 2026-03-01 18:44:47 UTC ++++ src/plugins/annotator/src/CollocationsDialogController.h +@@ -105,7 +105,7 @@ class CollocationSearchTask : public Task, public Coll + QMap<QString, CollocationsAlgorithmItem> items; + CollocationsAlgorithmSettings cfg; + QVector<U2Region> results; +- QMutex lock; ++ QRecursiveMutex lock; + + const bool keepSourceAnns; + QList<SharedAnnotationData> sourceAnns; +--- src/plugins/dna_export/src/ExportSequenceTask.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/plugins/dna_export/src/ExportSequenceTask.cpp +@@ -46,7 +46,7 @@ static const qint64 MAX_CHUNK_LENGTH = 4194305; // (4 + + static const qint64 MAX_CHUNK_LENGTH = 4194305; // (4 MiB + 1) chunk. Remainder of the division by 3 is 2. + +-static QMutex seqRefGuard(QMutex::NonRecursive); ++static QMutex seqRefGuard; + + namespace U2 { + diff --git a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro deleted file mode 100644 index 73f2d4038887..000000000000 --- a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro +++ /dev/null @@ -1,41 +0,0 @@ ---- src/corelibs/U2Private/U2Private.pro.orig 2018-08-16 13:59:12 UTC -+++ src/corelibs/U2Private/U2Private.pro -@@ -12,12 +12,7 @@ HEADERS += src/AppContextImpl.h \ - src/PluginSupportImpl.h \ - src/ServiceRegistryImpl.h \ - src/SettingsImpl.h \ -- src/TaskSchedulerImpl.h \ -- src/crash_handler/CrashHandler.h \ -- src/crash_handler/CrashHandlerArgsHelper.h \ -- src/crash_handler/CrashHandlerPrivate.h \ -- src/crash_handler/CrashLogCache.h \ -- src/crash_handler/StackWalker.h -+ src/TaskSchedulerImpl.h - - SOURCES += src/AppContextImpl.cpp \ - src/AppSettingsImpl.cpp \ -@@ -30,23 +25,13 @@ SOURCES += src/AppContextImpl.cpp \ - src/PluginSupportImpl.cpp \ - src/ServiceRegistryImpl.cpp \ - src/SettingsImpl.cpp \ -- src/TaskSchedulerImpl.cpp \ -- src/crash_handler/CrashHandler.cpp \ -- src/crash_handler/CrashHandlerArgsHelper.cpp \ -- src/crash_handler/CrashHandlerPrivate.cpp \ -- src/crash_handler/CrashLogCache.cpp \ -- src/crash_handler/StackWalker.cpp -+ src/TaskSchedulerImpl.cpp - - TRANSLATIONS += transl/russian.ts - - win32 { - HEADERS += src/crash_handler/CrashHandlerPrivateWin.h - SOURCES += src/crash_handler/CrashHandlerPrivateWin.cpp --} -- --unix_not_mac() { -- HEADERS += src/crash_handler/CrashHandlerPrivateUnixNotMac.h -- SOURCES += src/crash_handler/CrashHandlerPrivateUnixNotMac.cpp - } - - mac { diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp deleted file mode 100644 index c6956606c3ed..000000000000 --- a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp +++ /dev/null @@ -1,21 +0,0 @@ -Use the Linux driver for FreeBSD as well. Fixes crash on startup. - ---- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig 2021-09-08 14:18:53 UTC -+++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp -@@ -21,14 +21,14 @@ - - #include "GTKeyboardDriver.h" - --#if defined __linux__ -+#if defined(__linux__) || defined(__FreeBSD__) - # include <X11/extensions/XTest.h> - # include <X11/keysym.h> - #endif - - namespace HI { - --#if defined __linux__ -+#if defined(__linux__) || defined(__FreeBSD__) - - bool GTKeyboardDriver::keyPress(char key, Qt::KeyboardModifiers modifiers) { - DRIVER_CHECK(key != 0, "key = 0"); diff --git a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp deleted file mode 100644 index eb0c977bf399..000000000000 --- a/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp +++ /dev/null @@ -1,20 +0,0 @@ -Use the Linux driver for FreeBSD as well. Fixes crash on startup. - ---- src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp.orig 2018-09-02 00:23:24 UTC -+++ src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp -@@ -23,13 +23,13 @@ - - #include "GTMouseDriver.h" - --#ifdef __linux__ -+#if defined(__linux__) || defined(__FreeBSD__) - # include <X11/extensions/XTest.h> - #endif - - namespace HI { - --#ifdef __linux__ -+#if defined(__linux__) || defined(__FreeBSD__) - - # define GT_CLASS_NAME "GTMouseDriver Linux" - QPoint GTMouseDriver::mousePos = QPoint(-1, -1); diff --git a/biology/ugene/files/patch-src_plugins__3rdparty_ball b/biology/ugene/files/patch-src_plugins__3rdparty_ball new file mode 100644 index 000000000000..762c43a53506 --- /dev/null +++ b/biology/ugene/files/patch-src_plugins__3rdparty_ball @@ -0,0 +1,28 @@ +Description: indicating we use signed char, so that we don't depend on the + default choice of the implementation +Author: Pierre Gruet <pgt@debian.org> +Forwarded: no +Last-Update: 2024-10-04 + +--- src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h ++++ src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h +@@ -37,7 +37,7 @@ + { + namespace __private + { +- extern const char BALL_EXPORT neighbour_table_[27][3]; ++ extern const signed char BALL_EXPORT neighbour_table_[27][3]; + } + + template <typename Item> class HashGrid3; +--- src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp ++++ src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp +@@ -9,7 +9,7 @@ + { + namespace __private + { +- const char neighbour_table_[27][3] = ++ const signed char neighbour_table_[27][3] = + { + { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 }, + { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 }, diff --git a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp deleted file mode 100644 index e893985f32c3..000000000000 --- a/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp +++ /dev/null @@ -1,31 +0,0 @@ ---- src/plugins_checker/src/Main.cpp.orig 2018-08-16 13:59:06 UTC -+++ src/plugins_checker/src/Main.cpp -@@ -39,7 +39,7 @@ - #include <ServiceRegistryImpl.h> - #include <SettingsImpl.h> - #include <TaskSchedulerImpl.h> --#include <crash_handler/CrashHandler.h> -+//#include <crash_handler/CrashHandler.h> - - #define TR_SETTINGS_ROOT QString("test_runner/") - -@@ -55,8 +55,10 @@ static void registerCoreServices() { - } - #endif - -+#if 0 - CrashHandler::setupHandler(); - CrashHandler::setSendCrashReports(false); -+#endif - - const char* build = QT_VERSION_STR, *runtime = qVersion(); - if (strcmp(build, runtime) > 0){ -@@ -141,7 +143,7 @@ int main(int argc, char **argv) - delete cmdLineRegistry; - appContext->setCMDLineRegistry(NULL); - -- CrashHandler::shutdown(); -+ //CrashHandler::shutdown(); - - return rc; - } diff --git a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp index 1e91ae0651d0..b14f4f39b5f1 100644 --- a/biology/ugene/files/patch-src_ugenecl_src_Main.cpp +++ b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp @@ -1,36 +1,20 @@ ---- src/ugenecl/src/Main.cpp.orig 2018-08-16 13:59:20 UTC +--- src/ugenecl/src/Main.cpp.orig 2026-03-01 18:44:47 UTC +++ src/ugenecl/src/Main.cpp -@@ -93,7 +93,7 @@ - #include <ServiceRegistryImpl.h> - #include <SettingsImpl.h> - #include <TaskSchedulerImpl.h> --#include <crash_handler/CrashHandler.h> -+//#include <crash_handler/CrashHandler.h> - - // local project imports - #include "DumpHelpTask.h" -@@ -191,6 +191,7 @@ static void setSearchPaths() { - } - - int main(int argc, char **argv) { -+#if 0 - if (CrashHandler::isEnabled()) { - CrashHandler::setupHandler(); +@@ -151,7 +151,7 @@ static void setScriptsSearchPath() { + scriptsSearchPath.push_back(appDirPath + RELATIVE_DEV_SCRIPTS_DIR); } -@@ -198,6 +199,7 @@ int main(int argc, char **argv) - if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") { - CrashHandler::setSendCrashReports(false); + if (scriptsSearchPath.empty()) { +- scriptsSearchPath.push_back("/"); ++ scriptsSearchPath.push_back("/usr/local/share/ugene/scripts"); + } + QDir::setSearchPaths(PATH_PREFIX_SCRIPTS, scriptsSearchPath); + } +@@ -178,7 +178,7 @@ static void setDataSearchPaths() { } -+#endif - - if (!Version::checkBuildAndRuntimeVersions()) { - return -1; -@@ -617,7 +619,7 @@ int main(int argc, char **argv) - delete pwr; - appContext->setAlignmentAlgorithmsRegistry(NULL); -- CrashHandler::shutdown(); -+ //CrashHandler::shutdown(); + if (dataSearchPaths.empty()) { +- dataSearchPaths.push_back("/"); ++ dataSearchPaths.push_back("/usr/local/share/ugene/data"); + } - return rc; - } + QDir::setSearchPaths(PATH_PREFIX_DATA, dataSearchPaths); diff --git a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp deleted file mode 100644 index 251f739fbf1e..000000000000 --- a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp +++ /dev/null @@ -1,45 +0,0 @@ ---- src/ugeneui/src/Main.cpp.orig 2020-06-17 15:14:26 UTC -+++ src/ugeneui/src/Main.cpp -@@ -151,7 +151,7 @@ - #include <ServiceRegistryImpl.h> - #include <SettingsImpl.h> - #include <TaskSchedulerImpl.h> --#include <crash_handler/CrashHandler.h> -+//#include <crash_handler/CrashHandler.h> - - #include "app_settings/AppSettingsGUIImpl.h" - #include "app_settings/logview_settings/LogSettingsGUIController.h" -@@ -403,6 +403,7 @@ void fixMacFonts() { - } // namespace - - int main(int argc, char **argv) { -+#if 0 - if (CrashHandler::isEnabled()) { - CrashHandler::setupHandler(); - } -@@ -410,6 +411,7 @@ int main(int argc, char **argv) { - if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") { - CrashHandler::setSendCrashReports(false); - } -+#endif - - QT_REQUIRE_VERSION(argc, argv, QT_VERSION_STR); - -@@ -422,7 +424,7 @@ int main(int argc, char **argv) { - //QApplication app(argc, argv); - GApplication app(argc, argv); - --#ifdef Q_OS_LINUX -+#ifdef Q_OS_UNIX - QPixmap pixmap(":/ugene/images/originals/ugene_128.png"); - app.setWindowIcon(pixmap); - #endif -@@ -1088,7 +1090,7 @@ int main(int argc, char **argv) { - } - - UgeneUpdater::onClose(); -- CrashHandler::shutdown(); -+ //CrashHandler::shutdown(); - - return rc; - } diff --git a/biology/ugene/files/patch-sse2neon b/biology/ugene/files/patch-sse2neon new file mode 100644 index 000000000000..145f1a34811e --- /dev/null +++ b/biology/ugene/files/patch-sse2neon @@ -0,0 +1,40 @@ +--- src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp +@@ -1,5 +1,9 @@ + #include <assert.h> ++#if defined(__i386__) || defined(__amd64__) + #include <emmintrin.h> ++#else ++#include <sse2neon.h> ++#endif + #include <hmmer2/funcs.h> + + #include <U2Core/SequenceWalkerTask.h> +--- src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp +@@ -23,7 +23,11 @@ U2_DISABLE_WARNINGS + * MA 02110-1301, USA. + */ + ++#if defined(__i386__) || defined(__amd64__) + #include <emmintrin.h> ++#else ++#include <sse2neon.h> ++#endif + #include <iostream> + + #include "SmithWatermanAlgorithmSSE2.h" +--- src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.orig 2026-03-01 18:44:47 UTC ++++ src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h +@@ -21,7 +21,11 @@ + + #pragma once + ++#if defined(__i386__) || defined(__amd64__) + #include <emmintrin.h> ++#else ++#include <sse2neon.h> ++#endif + + #include "SmithWatermanAlgorithm.h" + diff --git a/biology/ugene/files/patch-ugene.pro b/biology/ugene/files/patch-ugene.pro deleted file mode 100644 index 29854f16d39d..000000000000 --- a/biology/ugene/files/patch-ugene.pro +++ /dev/null @@ -1,10 +0,0 @@ ---- ugene.pro.orig 2018-08-16 13:58:51 UTC -+++ ugene.pro -@@ -20,7 +20,6 @@ use_bundled_zlib() { - } - - SUBDIRS += \ -- src/libs_3rdparty/breakpad \ - src/libs_3rdparty/qscore \ - src/libs_3rdparty/sqlite3 \ - src/libs_3rdparty/samtools \ diff --git a/biology/ugene/files/patch-unix b/biology/ugene/files/patch-unix new file mode 100644 index 000000000000..f230ec9ff5d5 --- /dev/null +++ b/biology/ugene/files/patch-unix @@ -0,0 +1,37 @@ +--- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp +@@ -21,14 +21,14 @@ + + #include "GTKeyboardDriver.h" + +-#if defined __linux__ ++#if defined(Q_OS_UNIX) + # include <X11/extensions/XTest.h> + # include <X11/keysym.h> + #endif + + namespace HI { + +-#if defined __linux__ ++#if defined(Q_OS_UNIX) + + void GTKeyboardDriver::releasePressedKeys() { + GTKeyboardDriver::keyRelease(Qt::Key_Control); +--- src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp.orig 2026-03-01 18:44:47 UTC ++++ src/libs_3rdparty/QSpec/src/drivers/GTMouseDriverLinux.cpp +@@ -24,13 +24,13 @@ + #include <QByteArray> + + #include "GTMouseDriver.h" +-#ifdef __linux__ ++#ifdef Q_OS_UNIX + # include <X11/extensions/XTest.h> + #endif + + namespace HI { + +-#ifdef __linux__ ++#ifdef Q_OS_UNIX + + # define DELAY_ON_EVERY_N_PX 16 + /** diff --git a/biology/ugene/pkg-plist b/biology/ugene/pkg-plist index 10133c926025..028dd4d78d49 100644 --- a/biology/ugene/pkg-plist +++ b/biology/ugene/pkg-plist @@ -1,4 +1,7 @@ bin/ugene +bin/ugenecl +bin/ugenem +bin/ugeneui lib/ugene/libQSpec.so lib/ugene/libU2Algorithm.so lib/ugene/libU2Core.so @@ -10,6 +13,11 @@ lib/ugene/libU2Private.so lib/ugene/libU2Script.so lib/ugene/libU2Test.so lib/ugene/libU2View.so +lib/ugene/libqscore.a +lib/ugene/libqtscript.so +lib/ugene/libsamtools.a +lib/ugene/libugenedb.so +lib/ugene/libzlib.a lib/ugene/plugins/CoreTests.license lib/ugene/plugins/CoreTests.plugin lib/ugene/plugins/GUITestBase.license @@ -26,12 +34,8 @@ lib/ugene/plugins/chroma_view.license lib/ugene/plugins/chroma_view.plugin lib/ugene/plugins/circular_view.license lib/ugene/plugins/circular_view.plugin -lib/ugene/plugins/clark_support.license -lib/ugene/plugins/clark_support.plugin lib/ugene/plugins/dbi_bam.license lib/ugene/plugins/dbi_bam.plugin -lib/ugene/plugins/diamond_support.license -lib/ugene/plugins/diamond_support.plugin lib/ugene/plugins/dna_export.license lib/ugene/plugins/dna_export.plugin lib/ugene/plugins/dna_flexibility.license @@ -46,16 +50,14 @@ lib/ugene/plugins/enzymes.license lib/ugene/plugins/enzymes.plugin lib/ugene/plugins/external_tool_support.license lib/ugene/plugins/external_tool_support.plugin +lib/ugene/plugins/genecut.license +lib/ugene/plugins/genecut.plugin lib/ugene/plugins/genome_aligner.license lib/ugene/plugins/genome_aligner.plugin lib/ugene/plugins/gor4.license lib/ugene/plugins/gor4.plugin lib/ugene/plugins/hmm2.license lib/ugene/plugins/hmm2.plugin -lib/ugene/plugins/kalign.license -lib/ugene/plugins/kalign.plugin -lib/ugene/plugins/kraken_support.license -lib/ugene/plugins/kraken_support.plugin lib/ugene/plugins/libCoreTests.so lib/ugene/plugins/libGUITestBase.so lib/ugene/plugins/libannotator.so @@ -64,9 +66,7 @@ lib/ugene/plugins/libball.so lib/ugene/plugins/libbiostruct3d_view.so lib/ugene/plugins/libchroma_view.so lib/ugene/plugins/libcircular_view.so -lib/ugene/plugins/libclark_support.so lib/ugene/plugins/libdbi_bam.so -lib/ugene/plugins/libdiamond_support.so lib/ugene/plugins/libdna_export.so lib/ugene/plugins/libdna_flexibility.so lib/ugene/plugins/libdna_graphpack.so @@ -74,15 +74,11 @@ lib/ugene/plugins/libdna_stat.so lib/ugene/plugins/libdotplot.so lib/ugene/plugins/libenzymes.so lib/ugene/plugins/libexternal_tool_support.so +lib/ugene/plugins/libgenecut.so lib/ugene/plugins/libgenome_aligner.so lib/ugene/plugins/libgor4.so lib/ugene/plugins/libhmm2.so -lib/ugene/plugins/libkalign.so -lib/ugene/plugins/libkraken_support.so lib/ugene/plugins/liblinkdata_support.so -lib/ugene/plugins/libmetaphlan2_support.so -lib/ugene/plugins/libngs_reads_classification.so -lib/ugene/plugins/libopencl_support.so lib/ugene/plugins/liborf_marker.so lib/ugene/plugins/libpcr.so lib/ugene/plugins/libperf_monitor.so @@ -99,16 +95,9 @@ lib/ugene/plugins/libtest_runner.so lib/ugene/plugins/libumuscle.so lib/ugene/plugins/libvariants.so lib/ugene/plugins/libweight_matrix.so -lib/ugene/plugins/libwevote_support.so lib/ugene/plugins/libworkflow_designer.so lib/ugene/plugins/linkdata_support.license lib/ugene/plugins/linkdata_support.plugin -lib/ugene/plugins/metaphlan2_support.license -lib/ugene/plugins/metaphlan2_support.plugin -lib/ugene/plugins/ngs_reads_classification.license -lib/ugene/plugins/ngs_reads_classification.plugin -lib/ugene/plugins/opencl_support.license -lib/ugene/plugins/opencl_support.plugin lib/ugene/plugins/orf_marker.license lib/ugene/plugins/orf_marker.plugin lib/ugene/plugins/pcr.license @@ -141,1178 +130,17 @@ lib/ugene/plugins/variants.license lib/ugene/plugins/variants.plugin lib/ugene/plugins/weight_matrix.license lib/ugene/plugins/weight_matrix.plugin -lib/ugene/plugins/wevote_support.license -lib/ugene/plugins/wevote_support.plugin lib/ugene/plugins/workflow_designer.license lib/ugene/plugins/workflow_designer.plugin -lib/ugene/plugins_checker +@(root,wheel,755) lib/ugene/plugins_checker lib/ugene/transl_ru.qm lib/ugene/transl_tr.qm -lib/ugene/ugene -lib/ugene/ugenecl -lib/ugene/ugenem -lib/ugene/ugeneui -share/man/man1/ugene.1.gz +@(root,wheel,755) lib/ugene/ugene +@(root,wheel,755) lib/ugene/ugenecl +@(root,wheel,755) lib/ugene/ugenem +@(root,wheel,755) lib/ugene/ugeneui share/applications/ugene.desktop -share/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png +share/man/man1/ugene.1.gz share/mime/packages/application-x-ugene.xml +share/pixmaps/application-x-ugene-ext.png share/pixmaps/ugene.png -share/pixmaps/ugene.xpm -%%DATADIR%%/DBXRefRegistry.txt -%%DATADIR%%/adapters/adapters.fasta -%%DATADIR%%/adapters/illumina/NexteraPE-PE.fa -%%DATADIR%%/adapters/illumina/TruSeq2-PE.fa -%%DATADIR%%/adapters/illumina/TruSeq2-SE.fa -%%DATADIR%%/adapters/illumina/TruSeq3-PE-2.fa -%%DATADIR%%/adapters/illumina/TruSeq3-PE.fa -%%DATADIR%%/adapters/illumina/TruSeq3-SE.fa -%%DATADIR%%/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut -%%DATADIR%%/back_translation/Bacteria/Bacillus_subtilis.cut -%%DATADIR%%/back_translation/Bacteria/Escherichia_coli.cut -%%DATADIR%%/back_translation/Bacteria/Haemophilus_influenzae.cut -%%DATADIR%%/back_translation/Bacteria/Helicobacter_pylori.cut -%%DATADIR%%/back_translation/Bacteria/Listeria_monocytogenes.cut -%%DATADIR%%/back_translation/Bacteria/Neisseria_meningitidis.cut -%%DATADIR%%/back_translation/Bacteria/Salmonella_typhimurium_LT2.cut -%%DATADIR%%/back_translation/Bacteria/Streptomyces_coelicolor_A3(2).cut -%%DATADIR%%/back_translation/Bacteria/Sulfolobus_solfataricus_P2.cut -%%DATADIR%%/back_translation/Invertebrates/Apis_mellifera_(honey_bee).cut -%%DATADIR%%/back_translation/Invertebrates/Caenorhabditis_elegans.cut -%%DATADIR%%/back_translation/Invertebrates/Drosophila_melanogaster_(fruit_fly).cut -%%DATADIR%%/back_translation/Invertebrates/Plasmodium_falciparum_(malaria_parasite_P._falciparum).cut -%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Caenorhabditis_elegans.cut -%%DATADIR%%/back_translation/Invertebrates/mitochondrion_Drosophila_melanogaster_(fruit_fly).cut -%%DATADIR%%/back_translation/Mammalia/Bos_taurus_(cow).cut -%%DATADIR%%/back_translation/Mammalia/Canis_familiaris_(dog).cut -%%DATADIR%%/back_translation/Mammalia/Sus_scrofa_(pig).cut -%%DATADIR%%/back_translation/Mammalia/mitochondrion_Bos_taurus_(cow).cut -%%DATADIR%%/back_translation/Mammalia/mitochondrion_Sus_scrofa_(pig).cut -%%DATADIR%%/back_translation/Plants/Arabidopsis_thaliana_(thale_cress).cut -%%DATADIR%%/back_translation/Plants/Oryza_sativa.cut -%%DATADIR%%/back_translation/Plants/Zea_mays.cut -%%DATADIR%%/back_translation/Primates/Homo_sapiens_(human).cut -%%DATADIR%%/back_translation/Primates/Pan_troglodytes_(chimpanzee).cut -%%DATADIR%%/back_translation/Primates/mitochondrion_Homo_sapiens_(human).cut -%%DATADIR%%/back_translation/Primates/mitochondrion_Pan_troglodytes_(chimpanzee).cut -%%DATADIR%%/back_translation/Rodents/Mus_musculus_(house_mouse).cut -%%DATADIR%%/back_translation/Rodents/Rattus_norvegicus_(Norway_rat).cut -%%DATADIR%%/back_translation/Vertebrates/Gallus_gallus_(chicken).cut -%%DATADIR%%/back_translation/Vertebrates/Takifugu_rubripes_(Fugu_rubripes).cut -%%DATADIR%%/back_translation/Vertebrates/Xenopus_laevis_(African_clawed_frog).cut -%%DATADIR%%/back_translation/Vertebrates/mitochondrion_Gallus_gallus_(chicken).cut -%%DATADIR%%/back_translation/Vertebrates/mitochondrion_Takifugu_rubripes_(Fugu_rubripes).cut -%%DATADIR%%/back_translation/Viruses/Human_immunodeficiency_virus_1_(HIV-1).cut -%%DATADIR%%/back_translation/Viruses/Influenza_A_virus.cut 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