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Update to version 1.22.0, which now unfortunately requires Qt 5.x. Also

Browse source 
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.
This commit is contained in:
Alexey Dokuchaev 2016-04-14 04:07:44 +00:00
parent c27d686994
commit 66ab33fca6
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=413242
9 changed files with 204 additions and 36 deletions
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25
biology/ugene/Makefile
View file

@ -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>

16
biology/ugene/distinfo
View file

@ -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

47
biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro Normal file
View file

@ -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
-}

14
biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp Normal file
View file

@ -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() {

31
biology/ugene/files/patch-src_plugins__checker_src_Main.cpp Normal file
View file

@ -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;
}

32
biology/ugene/files/patch-src_ugenecl_src_Main.cpp Normal file
View file

@ -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;
}

32
biology/ugene/files/patch-src_ugeneui_src_Main.cpp Normal file
View file

@ -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;
}

28
biology/ugene/files/patch-ugene.pro Normal file
View file

@ -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 ) {

15
biology/ugene/pkg-plist
View file

@ -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