Date: Thu, 14 Apr 2016 04:07:44 +0000 (UTC) From: Alexey Dokuchaev <danfe@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r413242 - in head/biology/ugene: . files Message-ID: <201604140407.u3E47iIw022825@repo.freebsd.org>
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Author: danfe Date: Thu Apr 14 04:07:44 2016 New Revision: 413242 URL: https://svnweb.freebsd.org/changeset/ports/413242 Log: Update to version 1.22.0, which now unfortunately requires Qt 5.x. Also since around v1.18.0, UGENE is using Google's Breakpad library for crash reporting, which is very system-specific and does not support FreeBSD at the moment. Due to lack of resources and interest in porting it, simply disable crash reporting code for the time being. Added: head/biology/ugene/files/ head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro (contents, props changed) head/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp (contents, props changed) head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp (contents, props changed) head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp (contents, props changed) head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp (contents, props changed) head/biology/ugene/files/patch-ugene.pro (contents, props changed) Modified: head/biology/ugene/Makefile head/biology/ugene/distinfo head/biology/ugene/pkg-plist Modified: head/biology/ugene/Makefile ============================================================================== --- head/biology/ugene/Makefile Thu Apr 14 04:06:24 2016 (r413241) +++ head/biology/ugene/Makefile Thu Apr 14 04:07:44 2016 (r413242) @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= ugene -DISTVERSION= 1.17.0 -PORTREVISION= 1 +DISTVERSION= 1.22.0 CATEGORIES= biology science MASTER_SITES= http://ugene.unipro.ru/downloads/ DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \ @@ -20,16 +19,13 @@ RUN_DEPENDS= bash:shells/bash USES= desktop-file-utils execinfo qmake USE_GL= glu -USE_QT4= corelib gui network script webkit xml \ - linguisttools_build moc_build qmake_build qtestlib_build \ - rcc_build scripttools_build uic_build \ +USE_QT5= buildtools_build linguisttools_build scripttools_build \ + gui network printsupport script sql svg webkit widgets xml \ imageformats_run -USE_XORG= xtst -USE_LDCONFIG= yes -INSTALLS_ICONS= yes QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \ - INSTALL_MANDIR="${MAN1PREFIX}/man" + INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \ + LUPDATE="${LUPDATE}" ALL_TARGET= release DOCSDIR= ${DATADIR}/manuals @@ -60,6 +56,7 @@ PLIST_SUB+= SSE2="@comment " .endif post-extract: + @${MKDIR} ${WRKSRC}/data/manuals ${CP} -p ${_DISTDIR}/*.pdf ${WRKSRC}/data/manuals post-patch: @@ -67,12 +64,14 @@ post-patch: @${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \ ${WRKSRC}/src/gen_bin_script.cmd \ ${WRKSRC}/installer/_common_data/ugene - @${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}|' \ + @${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \ ${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp @${REINPLACE_CMD} -e '/unix_not_mac/,+11d' \ ${WRKSRC}/src/corelibs/U2Core/U2Core.pri -.for x in ugenecl ugeneui plugins_checker - @${ECHO_CMD} 'LIBS += -lexecinfo' >> ${WRKSRC}/src/${x}/${x}.pro -.endfor + @${REINPLACE_CMD} 's, -lbreakpad,,' \ + ${WRKSRC}/src/corelibs/U2Private/U2Private.pri \ + ${WRKSRC}/src/plugins_checker/plugins_checker.pri \ + ${WRKSRC}/src/ugenecl/ugenecl.pri \ + ${WRKSRC}/src/ugeneui/ugeneui.pri .include <bsd.port.post.mk> Modified: head/biology/ugene/distinfo ============================================================================== --- head/biology/ugene/distinfo Thu Apr 14 04:06:24 2016 (r413241) +++ head/biology/ugene/distinfo Thu Apr 14 04:07:44 2016 (r413242) @@ -1,8 +1,8 @@ -SHA256 (ugene/ugene-1.17.0.tar.gz) = d265a8a7d066e6cac2eeaa89645eb0ce1c0debeb9b321d80cea4a5595c082e08 -SIZE (ugene/ugene-1.17.0.tar.gz) = 20706555 -SHA256 (ugene/QueryDesigner_UserManual.pdf) = 17d7a68fdc9fc7ca2538c0b99a98a1f53cf664dc6207f98d9e4318eb35920847 -SIZE (ugene/QueryDesigner_UserManual.pdf) = 855679 -SHA256 (ugene/UniproUGENE_UserManual.pdf) = feee2712f81d24a84deb2f91fc0b13d64f051ff9c8b0129e862f8daafa8065a9 -SIZE (ugene/UniproUGENE_UserManual.pdf) = 13358880 -SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = cc63575ccf85bf66ab8594c7209ee0628dd1a84165375f955eb5a191bbc5e233 -SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 29393258 +SHA256 (ugene/ugene-1.22.0.tar.gz) = ee46be799c9f02a9b6a89f13747a4918d5c96c01676dc2d4cc4a4c98278912b6 +SIZE (ugene/ugene-1.22.0.tar.gz) = 20986853 +SHA256 (ugene/QueryDesigner_UserManual.pdf) = 5d232c0de7e9d1fd32b8ee0a78f9f4abe1ab9d6536ec3958c47de29f3096faf4 +SIZE (ugene/QueryDesigner_UserManual.pdf) = 855662 +SHA256 (ugene/UniproUGENE_UserManual.pdf) = ae6aef32a6e92a30ba7c36cdd894a8caf634d678f15da7ad9eab52b6f40b9ed6 +SIZE (ugene/UniproUGENE_UserManual.pdf) = 13443754 +SHA256 (ugene/WorkflowDesigner_UserManual.pdf) = 8cc6630f62c82de42926c14c3d01ebc3c7d85ab7d9ec2a81e55a19740806735c +SIZE (ugene/WorkflowDesigner_UserManual.pdf) = 29474484 Added: head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro Thu Apr 14 04:07:44 2016 (r413242) @@ -0,0 +1,47 @@ +--- src/corelibs/U2Private/U2Private.pro.orig 2016-03-31 12:22:14 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 \ +@@ -30,29 +25,7 @@ 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/english.ts \ + 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 { +- HEADERS += src/crash_handler/CrashHandlerPrivateMac.h \ +- src/SleepPreventerMac.h +- SOURCES += src/crash_handler/CrashHandlerPrivateMac.cpp \ +- src/SleepPreventerMac.cpp +-} Added: head/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp Thu Apr 14 04:07:44 2016 (r413242) @@ -0,0 +1,14 @@ +--- src/plugins_3rdparty/umuscle/src/MuscleWorkPool.cpp.orig 2016-03-31 12:22:09 UTC ++++ src/plugins_3rdparty/umuscle/src/MuscleWorkPool.cpp +@@ -28,9 +28,10 @@ namespace U2 { + + MuscleWorkPool::MuscleWorkPool(MuscleContext *_ctx, const MuscleTaskSettings &_config, TaskStateInfo& _ti, int _nThreads, const MAlignment& _ma, MAlignment& _res, bool _mhack) + :ctx(_ctx), config(_config), ma(_ma), res(_res), mhack(_mhack), Weights(NULL), ProgNodes(NULL), ph(NULL), ti(_ti), +- treeNodeStatus(NULL), treeNodeIndexes(NULL), nThreads(_nThreads), uJoin(0), ptrbOscillating(false), bAnyAccepted(false), InternalNodeIndexes(NULL), uInternalNodeCount(0), ++ treeNodeStatus(NULL), treeNodeIndexes(NULL), nThreads(_nThreads), uJoin(0), bAnyAccepted(false), InternalNodeIndexes(NULL), uInternalNodeCount(0), + bReversed(false), bRight(false), History(NULL), bLockLeft(NULL), bLockRight(false), msaIn(NULL) + { ++ *ptrbOscillating = false; + refineConstructot(); + } + MuscleWorkPool::~MuscleWorkPool() { Added: head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp Thu Apr 14 04:07:44 2016 (r413242) @@ -0,0 +1,31 @@ +--- src/plugins_checker/src/Main.cpp.orig 2016-03-31 12:22:09 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() { + + int main(int argc, char **argv) + { ++#if 0 + CrashHandler::setupHandler(); + CrashHandler::setSendCrashReports(false); ++#endif + + const char* build = QT_VERSION_STR, *runtime = qVersion(); + if (strcmp(build, runtime) > 0){ +@@ -140,7 +142,7 @@ int main(int argc, char **argv) + delete cmdLineRegistry; + appContext->setCMDLineRegistry(NULL); + +- CrashHandler::shutdown(); ++ //CrashHandler::shutdown(); + + return rc; + } Added: head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src_ugenecl_src_Main.cpp Thu Apr 14 04:07:44 2016 (r413242) @@ -0,0 +1,32 @@ +--- src/ugenecl/src/Main.cpp.orig 2016-03-31 12:22:19 UTC ++++ src/ugenecl/src/Main.cpp +@@ -94,7 +94,7 @@ + #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" +@@ -192,9 +192,11 @@ static void setSearchPaths() { + + int main(int argc, char **argv) + { ++#if 0 + if (CrashHandler::isEnabled()) { + CrashHandler::setupHandler(); + } ++#endif + const char* build = QT_VERSION_STR, *runtime = qVersion(); + if (strcmp(build, runtime) > 0){ + printf("Installed Qt version must be %s or greater \r\n", QT_VERSION_STR); +@@ -617,7 +619,7 @@ int main(int argc, char **argv) + delete pwr; + appContext->setAlignmentAlgorithmsRegistry(NULL); + +- CrashHandler::shutdown(); ++ //CrashHandler::shutdown(); + + return rc; + } Added: head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src_ugeneui_src_Main.cpp Thu Apr 14 04:07:44 2016 (r413242) @@ -0,0 +1,32 @@ +--- src/ugeneui/src/Main.cpp.orig 2016-03-31 12:22:18 UTC ++++ src/ugeneui/src/Main.cpp +@@ -134,7 +134,7 @@ + #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" +@@ -343,9 +343,11 @@ void fixMacFonts() { + + int main(int argc, char **argv) + { ++#if 0 + if (CrashHandler::isEnabled()) { + CrashHandler::setupHandler(); + } ++#endif + + QT_REQUIRE_VERSION( argc, argv, QT_VERSION_STR ); + +@@ -966,7 +968,7 @@ int main(int argc, char **argv) + } + + UgeneUpdater::onClose(); +- CrashHandler::shutdown(); ++ //CrashHandler::shutdown(); + + return rc; + } Added: head/biology/ugene/files/patch-ugene.pro ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-ugene.pro Thu Apr 14 04:07:44 2016 (r413242) @@ -0,0 +1,28 @@ +--- ugene.pro.orig 2016-03-31 12:21:56 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/gtest \ +@@ -144,15 +143,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/s + win32 : UGENE_DEV_NULL = nul + unix : UGENE_DEV_NULL = /dev/null + +-UGENE_LRELEASE = +-UGENE_LUPDATE = +-system(lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) { +- UGENE_LRELEASE = lrelease-qt5 +- UGENE_LUPDATE = lupdate-qt5 +-} else : system(lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) { +- UGENE_LRELEASE = lrelease +- UGENE_LUPDATE = lupdate +-} ++UGENE_LRELEASE = $$LRELEASE ++UGENE_LUPDATE = $$LUPDATE + + #foreach 'language' + for( i, UGENE_TRANSL_IDX ) { Modified: head/biology/ugene/pkg-plist ============================================================================== --- head/biology/ugene/pkg-plist Thu Apr 14 04:06:24 2016 (r413241) +++ head/biology/ugene/pkg-plist Thu Apr 14 04:07:44 2016 (r413242) @@ -53,8 +53,6 @@ lib/ugene/libugenedb.so.1.0 lib/ugene/libugenedb.so.1.0.0 lib/ugene/plugins/CoreTests.license lib/ugene/plugins/CoreTests.plugin -lib/ugene/plugins/GUITestBase.license -lib/ugene/plugins/GUITestBase.plugin lib/ugene/plugins/annotator.license lib/ugene/plugins/annotator.plugin lib/ugene/plugins/api_tests.license @@ -83,8 +81,6 @@ lib/ugene/plugins/dotplot.license lib/ugene/plugins/dotplot.plugin lib/ugene/plugins/enzymes.license lib/ugene/plugins/enzymes.plugin -lib/ugene/plugins/expert_discovery.license -lib/ugene/plugins/expert_discovery.plugin lib/ugene/plugins/external_tool_support.license lib/ugene/plugins/external_tool_support.plugin lib/ugene/plugins/genome_aligner.license @@ -101,10 +97,6 @@ lib/ugene/plugins/libCoreTests.so lib/ugene/plugins/libCoreTests.so.1 lib/ugene/plugins/libCoreTests.so.1.0 lib/ugene/plugins/libCoreTests.so.1.0.0 -lib/ugene/plugins/libGUITestBase.so -lib/ugene/plugins/libGUITestBase.so.1 -lib/ugene/plugins/libGUITestBase.so.1.0 -lib/ugene/plugins/libGUITestBase.so.1.0.0 lib/ugene/plugins/libannotator.so lib/ugene/plugins/libannotator.so.1 lib/ugene/plugins/libannotator.so.1.0 @@ -161,10 +153,6 @@ lib/ugene/plugins/libenzymes.so lib/ugene/plugins/libenzymes.so.1 lib/ugene/plugins/libenzymes.so.1.0 lib/ugene/plugins/libenzymes.so.1.0.0 -lib/ugene/plugins/libexpert_discovery.so -lib/ugene/plugins/libexpert_discovery.so.1 -lib/ugene/plugins/libexpert_discovery.so.1.0 -lib/ugene/plugins/libexpert_discovery.so.1.0.0 lib/ugene/plugins/libexternal_tool_support.so lib/ugene/plugins/libexternal_tool_support.so.1 lib/ugene/plugins/libexternal_tool_support.so.1.0 @@ -310,10 +298,8 @@ lib/ugene/plugins/weight_matrix.plugin lib/ugene/plugins/workflow_designer.license lib/ugene/plugins/workflow_designer.plugin lib/ugene/plugins_checker -lib/ugene/transl_cs.qm lib/ugene/transl_en.qm lib/ugene/transl_ru.qm -lib/ugene/transl_zh.qm lib/ugene/ugene lib/ugene/ugenecl lib/ugene/ugenem @@ -374,7 +360,6 @@ share/pixmaps/ugene.xpm %%DATADIR%%/cmdline/align.uwl %%DATADIR%%/cmdline/convert-msa.uwl %%DATADIR%%/cmdline/convert-seq.uwl -%%DATADIR%%/cmdline/das_annotation.uwl %%DATADIR%%/cmdline/extract-sequence.uwl %%DATADIR%%/cmdline/extract_consensus_sequence.uwl %%DATADIR%%/cmdline/extract_consensus_string.uwl
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