- Resurrect and unbreak by updating to version 34.0

- Stop providing outdated offline PDF documentation,
  users are advised to use the online files instead

7 files changed, 215 insertions, 0 deletions

diff --git a/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
new file mode 100644
index 000000000000..73f2d4038887
--- /dev/null
+++ b/biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
@@ -0,0 +1,41 @@
+--- 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
new file mode 100644
index 000000000000..cc2164cb1db0
--- /dev/null
+++ b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
@@ -0,0 +1,22 @@
+Use the Linux driver for FreeBSD as well. Fixes crash on startup.
+
+--- src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp.orig	2018-09-02 00:22:54 UTC
++++ src/libs_3rdparty/QSpec/src/drivers/GTKeyboardDriverLinux.cpp
+@@ -22,7 +22,7 @@
+ #include <cctype>
+ #include "GTKeyboardDriver.h"
+ 
+-#if defined __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+     #define XK_LATIN1      // for latin symbol
+     #define XK_MISCELLANY  // for action keys
+     #include <X11/keysymdef.h>
+@@ -31,7 +31,7 @@
+ 
+ namespace HI {
+ 
+-#if defined __linux__
++#if defined(__linux__) || defined(__FreeBSD__)
+ 
+ #define GT_CLASS_NAME "GTKeyboardDriverLinux"
+ 
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
new file mode 100644
index 000000000000..8dfdd9b7d53f
--- /dev/null
+++ b/biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
@@ -0,0 +1,20 @@
+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
+@@ -22,13 +22,13 @@
+ #include "GTMouseDriver.h"
+ #include <QByteArray>
+ 
+-#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__checker_src_Main.cpp b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
new file mode 100644
index 000000000000..bd0d64942c01
--- /dev/null
+++ b/biology/ugene/files/patch-src_plugins__checker_src_Main.cpp
@@ -0,0 +1,31 @@
+--- 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() {
+ 
+ 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){
+@@ -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
new file mode 100644
index 000000000000..917fc096b4c4
--- /dev/null
+++ b/biology/ugene/files/patch-src_ugenecl_src_Main.cpp
@@ -0,0 +1,36 @@
+--- src/ugenecl/src/Main.cpp.orig	2018-08-16 13:59:20 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();
+     }
+@@ -198,6 +199,7 @@ int main(int argc, char **argv)
+     if (qgetenv(ENV_SEND_CRASH_REPORTS) == "0") {
+         CrashHandler::setSendCrashReports(false);
+     }
++#endif
+ 
+     const char* build = QT_VERSION_STR, *runtime = qVersion();
+     if (strcmp(build, runtime) > 0){
+@@ -617,7 +619,7 @@ int main(int argc, char **argv)
+     delete pwr;
+     appContext->setAlignmentAlgorithmsRegistry(NULL);
+ 
+-    CrashHandler::shutdown();
++    //CrashHandler::shutdown();
+ 
+     return rc;
+ }
diff --git a/biology/ugene/files/patch-src_ugeneui_src_Main.cpp b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
new file mode 100644
index 000000000000..e5dcadcdea21
--- /dev/null
+++ b/biology/ugene/files/patch-src_ugeneui_src_Main.cpp
@@ -0,0 +1,36 @@
+--- src/ugeneui/src/Main.cpp.orig	2018-08-16 13:59:19 UTC
++++ src/ugeneui/src/Main.cpp
+@@ -136,7 +136,7 @@
+ #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"
+@@ -353,6 +353,7 @@ void fixMacFonts() {
+ 
+ int main(int argc, char **argv)
+ {
++#if 0
+     if (CrashHandler::isEnabled()) {
+         CrashHandler::setupHandler();
+     }
+@@ -360,6 +361,7 @@ 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 );
+ 
+@@ -973,7 +975,7 @@ int main(int argc, char **argv)
+     }
+ 
+     UgeneUpdater::onClose();
+-    CrashHandler::shutdown();
++    //CrashHandler::shutdown();
+ 
+     return rc;
+ }
diff --git a/biology/ugene/files/patch-ugene.pro b/biology/ugene/files/patch-ugene.pro
new file mode 100644
index 000000000000..8962a9edc02e
--- /dev/null
+++ b/biology/ugene/files/patch-ugene.pro
@@ -0,0 +1,29 @@
+--- 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 \
+@@ -141,16 +140,8 @@ UGENE_TRANSL_QM_TARGET_DIR = $$OUT_PWD/src/_debug $$OU
+ win32 : UGENE_DEV_NULL = nul
+ unix : UGENE_DEV_NULL = /dev/null
+ 
+-UGENE_LRELEASE =
+-UGENE_LUPDATE =
+-message(Using QT from $$[QT_INSTALL_BINS])
+-system($$[QT_INSTALL_BINS]/lrelease-qt5 -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+-    UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease-qt5
+-    UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate-qt5
+-} else : system($$[QT_INSTALL_BINS]/lrelease -version > $$UGENE_DEV_NULL 2> $$UGENE_DEV_NULL) {
+-    UGENE_LRELEASE = $$[QT_INSTALL_BINS]/lrelease
+-    UGENE_LUPDATE = $$[QT_INSTALL_BINS]/lupdate
+-}
++UGENE_LRELEASE = $$LRELEASE
++UGENE_LUPDATE = $$LUPDATE
+ 
+ #foreach 'language'
+ for( i, UGENE_TRANSL_IDX ) {