branch rebuild (qt5)

sources

@@ -1 +1 @@
-SHA512 (ugene-1.30.0.tar.gz) = 333a9a2a98713b6fd72658aca5c3ad00f7bf8371f234ab0fdf4fb16031530edfbca66e55f3dd2b62f4acb804690a32597ce7abc2807a881a2c397c2dfdc77e7b
+SHA512 (ugene-1.31.0.tar.gz) = d8cef19ee07fbe94758dbcf33e080a981cefadb1a600898f569daf95b8e1bc69e9b913bd5b80e366596ea1a2db1a981446bdc82989a636a18aa8aea2559c8897

ugene-1.30.0-procps.patch

@@ -1,247 +0,0 @@
-diff --git a/src/plugins/repeat_finder/src/FindRepeatsDialog.h b/src/plugins/repeat_finder/src/FindRepeatsDialog.h
-index 3408680e5..779553ae3 100644
---- a/src/plugins/repeat_finder/src/FindRepeatsDialog.h
-+++ b/src/plugins/repeat_finder/src/FindRepeatsDialog.h
-@@ -23,7 +23,7 @@
- #define _U2_FIND_REPEATS_DIALOG_H_
- 
- #include <ui_FindRepeatsDialog.h>
--
-+#include <QAction>
- #include <U2Core/U2Region.h>
- 
- #include "FindRepeatsTask.h"
-diff --git a/src/corelibs/U2Designer/src/DelegateEditors.h b/src/corelibs/U2Designer/src/DelegateEditors.h
-index bbd86d884..cb2277adc 100644
---- a/src/corelibs/U2Designer/src/DelegateEditors.h
-+++ b/src/corelibs/U2Designer/src/DelegateEditors.h
-@@ -29,6 +29,7 @@
- #include <QComboBox>
- #include <QCoreApplication>
- #include <QDialog>
-+#include <QAction>
- #include <QHBoxLayout>
- #include <QKeyEvent>
- #include <QLineEdit>
-diff --git a/src/plugins/repeat_finder/src/RepeatQuery.h b/src/plugins/repeat_finder/src/RepeatQuery.h
-index 3dbd114f9..28317f7c6 100644
---- a/src/plugins/repeat_finder/src/RepeatQuery.h
-+++ b/src/plugins/repeat_finder/src/RepeatQuery.h
-@@ -22,6 +22,8 @@
- #ifndef _U2_REPEAT_QUERY_H_
- #define _U2_REPEAT_QUERY_H_
- 
-+#include <QAction>
-+
- #include "FindRepeatsTask.h"
- 
- #include "U2Lang/QDScheme.h"
-diff --git a/src/plugins/query_designer/src/QueryViewController.h b/src/plugins/query_designer/src/QueryViewController.h
-index 1f6b99119..afb4fc535 100644
---- a/src/plugins/query_designer/src/QueryViewController.h
-+++ b/src/plugins/query_designer/src/QueryViewController.h
-@@ -24,6 +24,8 @@
- 
- #include "ui_AddConstraintDialog.h"
- 
-+#include <QActionGroup>
-+
- #include <U2Lang/QDConstraint.h>
- 
- #include <U2Gui/MainWindow.h>
-diff --git a/src/plugins/query_designer/src/QueryViewController.cpp b/src/plugins/query_designer/src/QueryViewController.cpp
-index e4cbb2f13..31e9e8c7b 100644
---- a/src/plugins/query_designer/src/QueryViewController.cpp
-+++ b/src/plugins/query_designer/src/QueryViewController.cpp
-@@ -24,6 +24,7 @@
- #include <QSplitter>
- #include <QTabWidget>
- #include <QToolBar>
-+#include <QActionGroup>
- 
- #include <U2Core/AppContext.h>
- #include <U2Core/Counter.h>
-diff --git a/src/plugins/external_tool_support/src/hmmer/HmmerSearchDialog.h b/src/plugins/external_tool_support/src/hmmer/HmmerSearchDialog.h
-index df7f7e3ec..01f5770bd 100644
---- a/src/plugins/external_tool_support/src/hmmer/HmmerSearchDialog.h
-+++ b/src/plugins/external_tool_support/src/hmmer/HmmerSearchDialog.h
-@@ -22,6 +22,8 @@
- #ifndef _U2_HMMER_SEARCH_DIALOG_H_
- #define _U2_HMMER_SEARCH_DIALOG_H_
- 
-+#include <QButtonGroup>
-+
- #include <U2Gui/CreateAnnotationWidgetController.h>
- 
- #include "HmmerSearchTask.h"
-diff --git a/src/corelibs/U2Gui/src/util/HelpButton.h b/src/corelibs/U2Gui/src/util/HelpButton.h
-index a34b40759..2f4a83be4 100644
---- a/src/corelibs/U2Gui/src/util/HelpButton.h
-+++ b/src/corelibs/U2Gui/src/util/HelpButton.h
-@@ -25,6 +25,9 @@
- #include <QDialogButtonBox>
- #include <QMap>
- #include <QString>
-+#include <QPushButton>
-+#include <QButtonGroup>
-+
- #include <QWidget>
- 
- #include <U2Core/global.h>
-diff --git a/src/plugins/external_tool_support/src/hmmer/HmmerSearchDialog.cpp b/src/plugins/external_tool_support/src/hmmer/HmmerSearchDialog.cpp
-index 2fe191aa1..1fec25219 100644
---- a/src/plugins/external_tool_support/src/hmmer/HmmerSearchDialog.cpp
-+++ b/src/plugins/external_tool_support/src/hmmer/HmmerSearchDialog.cpp
-@@ -23,6 +23,7 @@
- 
- #include <QMessageBox>
- #include <QPushButton>
-+#include <QButtonGroup>
- 
- #include <U2Core/AppContext.h>
- #include <U2Core/DNAAlphabet.h>
-diff --git a/src/plugins/dotplot/src/DotPlotFilterDialog.cpp b/src/plugins/dotplot/src/DotPlotFilterDialog.cpp
-index 521d76338..9e0569a3e 100644
---- a/src/plugins/dotplot/src/DotPlotFilterDialog.cpp
-+++ b/src/plugins/dotplot/src/DotPlotFilterDialog.cpp
-@@ -20,6 +20,7 @@
-  */
- 
- #include <QMessageBox>
-+#include <QButtonGroup>
- 
- #include <U2Core/AnnotationSettings.h>
- #include <U2Core/AnnotationTableObject.h>
-diff --git a/src/ugeneui/src/project_support/DocumentProviderSelectorController.h b/src/ugeneui/src/project_support/DocumentProviderSelectorController.h
-index fc06833c7..c8330f069 100644
---- a/src/ugeneui/src/project_support/DocumentProviderSelectorController.h
-+++ b/src/ugeneui/src/project_support/DocumentProviderSelectorController.h
-@@ -22,6 +22,8 @@
- #ifndef _U2_DOCUMENT_PROVIDER_SELECTOR_CONTROLLER_H_
- #define _U2_DOCUMENT_PROVIDER_SELECTOR_CONTROLLER_H_
- 
-+#include <QButtonGroup>
-+
- #include <U2Core/DocumentUtils.h>
- 
- #include "ui_DocumentProviderSelectorDialog.h"
-diff --git a/src/ugeneui/src/project_support/DocumentProviderSelectorController.cpp b/src/ugeneui/src/project_support/DocumentProviderSelectorController.cpp
-index e93c8d32a..6aede08e4 100644
---- a/src/ugeneui/src/project_support/DocumentProviderSelectorController.cpp
-+++ b/src/ugeneui/src/project_support/DocumentProviderSelectorController.cpp
-@@ -23,6 +23,7 @@
- #include <QMessageBox>
- #include <QPushButton>
- #include <QRadioButton>
-+#include <QButtonGroup>
- #include <QToolButton>
- 
- #include <U2Core/AppContext.h>
-diff --git a/src/ugeneui/src/main_window/AboutDialogController.cpp b/src/ugeneui/src/main_window/AboutDialogController.cpp
-index da3dc5d73..e2aa5a853 100644
---- a/src/ugeneui/src/main_window/AboutDialogController.cpp
-+++ b/src/ugeneui/src/main_window/AboutDialogController.cpp
-@@ -27,6 +27,7 @@
- #include <U2Core/Settings.h>
- 
- #include <QPainter>
-+#include <QAction>
- #include <QBrush>
- #include <QStyle>
- #include <QHBoxLayout>
-@@ -47,7 +48,7 @@ AboutDialogController::AboutDialogController(QAction* visitWebAction, QWidget *p
-     frame->setLayout(l);
-     tWidget = NULL;
-     installAWidget();
--    connect(web_page_button, SIGNAL(clicked()), visitWebAction,  SLOT(trigger()));
-+    connect(web_page_button, SIGNAL(clicked(bool)), visitWebAction,  SLOT(trigger()));
-     
- #ifdef Q_OS_WIN
-     setWindowFlags(windowFlags() | Qt::MSWindowsFixedSizeDialogHint);
-diff --git a/src/corelibs/U2Gui/src/util/ProjectTreeItemSelectorDialog.cpp b/src/corelibs/U2Gui/src/util/ProjectTreeItemSelectorDialog.cpp
-index 0200ac7f4..62479a6d9 100644
---- a/src/corelibs/U2Gui/src/util/ProjectTreeItemSelectorDialog.cpp
-+++ b/src/corelibs/U2Gui/src/util/ProjectTreeItemSelectorDialog.cpp
-@@ -24,6 +24,7 @@
- #include <QSpacerItem>
- #include <QTreeView>
- #include <QVBoxLayout>
-+#include <QAction>
- 
- #include <U2Core/DocumentModel.h>
- #include <U2Core/U2SafePoints.h>
-diff --git a/src/corelibs/U2Core/U2Core.pri b/src/corelibs/U2Core/U2Core.pri
-index 7db5fdece..f7ea61510 100644
---- a/src/corelibs/U2Core/U2Core.pri
-+++ b/src/corelibs/U2Core/U2Core.pri
-@@ -50,15 +50,3 @@ unix {
-     target.path = $$UGENE_INSTALL_DIR/$$UGENE_RELATIVE_DESTDIR
-     INSTALLS += target
- }
--
--unix_not_mac(){
--    exists( /usr/lib/libproc.so* ) {
--      LIBS += -lproc
--    }else{
--        exists( /usr/local/lib/libproc.so* ){
--          LIBS += -lproc
--        }else{
--          LIBS += -lprocps
--        }
--    }
--}
-diff --git a/src/corelibs/U2Core/src/globals/AppResources.cpp b/src/corelibs/U2Core/src/globals/AppResources.cpp
-index 8c8159aaa..bc130c68a 100644
---- a/src/corelibs/U2Core/src/globals/AppResources.cpp
-+++ b/src/corelibs/U2Core/src/globals/AppResources.cpp
-@@ -35,7 +35,6 @@
- #include <unistd.h> //for sysconf(3)
- #endif
- #if defined(Q_OS_LINUX)
--#include <proc/readproc.h>
- #include <fstream>
- #endif
- 
-diff --git a/src/plugins/perf_monitor/src/PerfMonitorView.cpp b/src/plugins/perf_monitor/src/PerfMonitorView.cpp
-index 26f4ea2ce..3bad7b693 100644
---- a/src/plugins/perf_monitor/src/PerfMonitorView.cpp
-+++ b/src/plugins/perf_monitor/src/PerfMonitorView.cpp
-@@ -28,7 +28,7 @@
- 
- #ifdef Q_OS_LINUX
- #include <stdio.h>
--#include <proc/readproc.h>
-+#include <sys/sysinfo.h>
- #endif
- 
- #ifdef Q_OS_WIN32
-@@ -64,10 +64,10 @@ PerfMonitorView::PerfMonitorView() : MWMDIWindow(tr("Application counters")){
-     updateCounter.totalCount = 0;
- 
- #ifdef Q_OS_LINUX
--    struct proc_t usage;
--    look_up_our_self(&usage);
--    virtMemoryCounter.totalCount = usage.vsize;
--    rssMemoryCounter.totalCount = usage.rss;
-+    struct sysinfo usage;
-+    sysinfo(&usage);
-+    virtMemoryCounter.totalCount = usage.totalram;
-+    rssMemoryCounter.totalCount = 0; // not supported
- #endif
- #ifdef Q_OS_WIN32
-     PROCESS_MEMORY_COUNTERS memCounter;
-@@ -83,10 +83,10 @@ PerfMonitorView::PerfMonitorView() : MWMDIWindow(tr("Application counters")){
- void PerfMonitorView::timerEvent(QTimerEvent *) {
-     TimeCounter c(&updateCounter);
- #ifdef Q_OS_LINUX
--    struct proc_t usage;
--    look_up_our_self(&usage);
--    virtMemoryCounter.totalCount = usage.vsize;
--    rssMemoryCounter.totalCount = usage.rss;
-+    struct sysinfo usage;
-+    sysinfo(&usage);
-+    virtMemoryCounter.totalCount = usage.totalram;
-+    rssMemoryCounter.totalCount = 0; // not supported
- #endif
- #ifdef Q_OS_WIN32
-     PROCESS_MEMORY_COUNTERS memCounter;

ugene-1.31.0.patch

@@ -0,0 +1,24 @@
+diff --git a/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp b/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
+index a2541b880..f806afef7 100644
+--- a/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
++++ b/src/plugins/external_tool_support/src/trimmomatic/util/LengthSettingsWidget.cpp
+@@ -20,6 +20,7 @@
+  */
+ 
+ #include <U2Core/U2SafePoints.h>
++#include <QIntValidator>
+ 
+ #include "LengthSettingsWidget.h"
+ #include "LineEditHighlighter.h"
+diff --git a/src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp b/src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp
+index 00ecfef09..bce841083 100644
+--- a/src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp
++++ b/src/plugins/external_tool_support/src/trimmomatic/util/QualitySettingsWidget.cpp
+@@ -19,6 +19,7 @@
+  * MA 02110-1301, USA.
+  */
+ 
++#include <QIntValidator>
+ #include <U2Core/U2SafePoints.h>
+ 
+ #include "QualitySettingsWidget.h"

ugene.spec

@@ -1,7 +1,7 @@
 Name:    ugene
 Summary: Integrated bioinformatics toolkit
-Version: 1.30.0
-Release: 25%{?dist}
+Version: 1.31.0
+Release: 4%{?dist}
 #The entire source code is GPLv2+ except:
 #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2
 #files in src/plugins_3rdparty/script_debuger/src/qtscriptdebug/ which are GPLv2
@@ -9,7 +9,7 @@ License: GPLv2+ and GPLv2
 Group:   Applications/Engineering
 URL:     http://ugene.net
 Source0: http://ugene.net/downloads/%{name}-%{version}.tar.gz
-Patch0:  ugene-1.30.0-procps.patch
+Patch0:  ugene-1.31.0.patch
 
 BuildRequires: desktop-file-utils
 BuildRequires: mesa-libGLU-devel
@@ -43,7 +43,7 @@ is a designer for custom bioinformatics workflows.
 
 %prep
 %setup -q
-%patch0 -p1 -b .procps
+%patch0 -p1 -b .qt510
 
 %build
 %{qmake_qt5} -r \
@@ -67,7 +67,7 @@ desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop
 
 %files
 %{!?_licensedir:%global license %%doc}
-%license COPYRIGHT LICENSE.txt LICENSE.3rd_party.txt
+%license LICENSE.txt LICENSE.3rd_party.txt
 %{_bindir}/*
 %{_libdir}/%{name}/
 %{_datadir}/applications/%{name}.desktop
@@ -78,50 +78,9 @@ desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop
 %{_mandir}/man1/*
 
 %changelog
-* Sat Jul 14 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.30.0-25
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
+* Thu Dec 27 2018 Rex Dieter <rdieter@fedoraproject.org> - 1.31.0-4
+- branch rebuild (qt5)
 
-* Thu Jun 21 2018 Rex Dieter <rdieter@fedoraproject.org> - 1.30.0-24
-- rebuild (qt5)
-
-* Mon Jun 11 2018 Yuliya Algaer <yalgaer@fedoraproject.org> - 1.30.0-23
+* Fri Aug 24 2018 Yuliya Algaer <yalgaer@fedoraproject.org> - 1.31.0-3
 - New upstream release
 
-* Sun May 27 2018 Rex Dieter <rdieter@fedoraproject.org> - 1.29.0-7
-- rebuild (qt5)
-
-* Wed Feb 14 2018 Jan Grulich <jgrulich@redhat.com> - 1.29.0-6
-- rebuild (qt5)
-
-* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.29.0-5
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
-
-* Thu Jan 18 2018 Igor Gnatenko <ignatenkobrain@fedoraproject.org> - 1.29.0-4
-- Remove obsolete scriptlets
-
-* Tue Jan 02 2018 Kevin Kofler <Kevin@tigcc.ticalc.org> - 1.29.0-3
-- Fix FTBFS with Qt 5.10
-
-* Mon Jan 01 2018 Rex Dieter <rdieter@fedoraproject.org> - 1.29.0-2
-- rebuild (qt5)
-
-* Sun Dec 31 2017 Yuliya Algaer <yalgaer@fedoraproject.org> - 1.29.0-1
-- New upstream release.
-
-* Wed Dec 20 2017 Jan Grulich <jgrulich@redhat.com> - 1.28.1-3
-- rebuild (qt5)
-
-* Mon Nov 27 2017 Rex Dieter <rdieter@fedoraproject.org> - 1.28.1-2
-- rebuild (qt5)
-
-* Tue Nov 21 2017 Yuliya Algaer <yalgaer@fedoraproject.org> - 1.28.1-1
-- New upstream release.
-
-* Tue Oct 10 2017 Rex Dieter <rdieter@fedoraproject.org> - 1.27.0-8
-- rebuild (qt5)
-
-* Mon Aug 28 2017 Yuliya Algaer <yalgaer@fedoraproject.org> - 1.27.0-7
-- New upstream release
-
-* Thu Aug 03 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.26.3-4
-- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild