From 46de33e6cacb6841b5235c1d66f8be9a75d90812 Mon Sep 17 00:00:00 2001 From: Yuliya Algaer Date: Fri, 24 Aug 2018 22:37:19 +0700 Subject: [PATCH 1/5] Update to 1.31.0 --- ugene-1.30.0-procps.patch | 247 -------------------------------------- ugene.spec | 56 +-------- 2 files changed, 6 insertions(+), 297 deletions(-) delete mode 100644 ugene-1.30.0-procps.patch diff --git a/ugene-1.30.0-procps.patch b/ugene-1.30.0-procps.patch deleted file mode 100644 index d6498b4..0000000 --- a/ugene-1.30.0-procps.patch +++ /dev/null @@ -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 -- -+#include - #include - - #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 - #include - #include -+#include - #include - #include - #include -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 -+ - #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 -+ - #include - - #include -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 - #include - #include -+#include - - #include - #include -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 -+ - #include - - #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 - #include - #include -+#include -+#include -+ - #include - - #include -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 - #include -+#include - - #include - #include -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 -+#include - - #include - #include -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 -+ - #include - - #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 - #include - #include -+#include - #include - - #include -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 - - #include -+#include - #include - #include - #include -@@ -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 - #include - #include -+#include - - #include - #include -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 //for sysconf(3) - #endif - #if defined(Q_OS_LINUX) --#include - #include - #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 --#include -+#include - #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; diff --git a/ugene.spec b/ugene.spec index c463e97..5b14e50 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 1.30.0 -Release: 25%{?dist} +Version: 1.31.0 +Release: 1%{?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 +78,6 @@ desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog -* Sat Jul 14 2018 Fedora Release Engineering - 1.30.0-25 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild - -* Thu Jun 21 2018 Rex Dieter - 1.30.0-24 -- rebuild (qt5) - -* Mon Jun 11 2018 Yuliya Algaer - 1.30.0-23 +* Fri Aug 24 2018 Yuliya Algaer - 1.31.0-1 - New upstream release -* Sun May 27 2018 Rex Dieter - 1.29.0-7 -- rebuild (qt5) - -* Wed Feb 14 2018 Jan Grulich - 1.29.0-6 -- rebuild (qt5) - -* Fri Feb 09 2018 Fedora Release Engineering - 1.29.0-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild - -* Thu Jan 18 2018 Igor Gnatenko - 1.29.0-4 -- Remove obsolete scriptlets - -* Tue Jan 02 2018 Kevin Kofler - 1.29.0-3 -- Fix FTBFS with Qt 5.10 - -* Mon Jan 01 2018 Rex Dieter - 1.29.0-2 -- rebuild (qt5) - -* Sun Dec 31 2017 Yuliya Algaer - 1.29.0-1 -- New upstream release. - -* Wed Dec 20 2017 Jan Grulich - 1.28.1-3 -- rebuild (qt5) - -* Mon Nov 27 2017 Rex Dieter - 1.28.1-2 -- rebuild (qt5) - -* Tue Nov 21 2017 Yuliya Algaer - 1.28.1-1 -- New upstream release. - -* Tue Oct 10 2017 Rex Dieter - 1.27.0-8 -- rebuild (qt5) - -* Mon Aug 28 2017 Yuliya Algaer - 1.27.0-7 -- New upstream release - -* Thu Aug 03 2017 Fedora Release Engineering - 1.26.3-4 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild From 21dcca64431a02059831020f0f4eb0184c204813 Mon Sep 17 00:00:00 2001 From: Yuliya Algaer Date: Fri, 24 Aug 2018 23:01:12 +0700 Subject: [PATCH 2/5] Update to 1.31.0 --- sources | 2 +- ugene.spec | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/sources b/sources index 2d31cc2..547a645 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-1.30.0.tar.gz) = 333a9a2a98713b6fd72658aca5c3ad00f7bf8371f234ab0fdf4fb16031530edfbca66e55f3dd2b62f4acb804690a32597ce7abc2807a881a2c397c2dfdc77e7b +SHA512 (ugene-1.31.0.tar.gz) = d8cef19ee07fbe94758dbcf33e080a981cefadb1a600898f569daf95b8e1bc69e9b913bd5b80e366596ea1a2db1a981446bdc82989a636a18aa8aea2559c8897 diff --git a/ugene.spec b/ugene.spec index 5b14e50..54fb91a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 1.31.0 -Release: 1%{?dist} +Release: 2%{?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 @@ -78,6 +78,6 @@ desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog -* Fri Aug 24 2018 Yuliya Algaer - 1.31.0-1 +* Fri Aug 24 2018 Yuliya Algaer - 1.31.0-2 - New upstream release From ed635b00be659c26a515faed00471c25cac7da1b Mon Sep 17 00:00:00 2001 From: Yuliya Algaer Date: Fri, 24 Aug 2018 23:10:52 +0700 Subject: [PATCH 3/5] Update to 1.31.0 --- ugene.spec | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ugene.spec b/ugene.spec index 54fb91a..10930ca 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 1.31.0 -Release: 2%{?dist} +Release: 3%{?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 @@ -78,6 +78,6 @@ desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog -* Fri Aug 24 2018 Yuliya Algaer - 1.31.0-2 +* Fri Aug 24 2018 Yuliya Algaer - 1.31.0-3 - New upstream release From ac1cbe2ac8e9d301ebfcf9ff05e679e6257d5197 Mon Sep 17 00:00:00 2001 From: Yuliya Algaer Date: Fri, 24 Aug 2018 23:11:21 +0700 Subject: [PATCH 4/5] Update to 1.31.0 --- ugene-1.31.0.patch | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 ugene-1.31.0.patch diff --git a/ugene-1.31.0.patch b/ugene-1.31.0.patch new file mode 100644 index 0000000..a478a52 --- /dev/null +++ b/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 ++#include + + #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 + #include + + #include "QualitySettingsWidget.h" From 81cfd23ed422df1c90f86303e9c9313ea8ae58f8 Mon Sep 17 00:00:00 2001 From: Rex Dieter Date: Thu, 27 Dec 2018 10:19:56 -0600 Subject: [PATCH 5/5] branch rebuild (qt5) --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 10930ca..b0db5e6 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 1.31.0 -Release: 3%{?dist} +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 @@ -78,6 +78,9 @@ desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog +* Thu Dec 27 2018 Rex Dieter - 1.31.0-4 +- branch rebuild (qt5) + * Fri Aug 24 2018 Yuliya Algaer - 1.31.0-3 - New upstream release