From 0caa750728a5931b6182333516e54d7ab49a1713 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 31 Jan 2020 02:29:33 +0000 Subject: [PATCH 001/260] - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 6cd56f4..cddceac 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 33.0 -Release: 11%{?dist} +Release: 12%{?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 @@ -83,6 +83,9 @@ desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog +* Fri Jan 31 2020 Fedora Release Engineering - 33.0-12 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild + * Mon Dec 09 2019 Jan Grulich - 33.0-11 - rebuild (qt5) From 52598963ef137f1044bd005fb315d66d44f4099a Mon Sep 17 00:00:00 2001 From: Rex Dieter Date: Mon, 6 Apr 2020 11:59:16 -0500 Subject: [PATCH 002/260] rebuild (qt5) --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index cddceac..9491ec7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 33.0 -Release: 12%{?dist} +Release: 13%{?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 @@ -83,6 +83,9 @@ desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog +* Mon Apr 06 2020 Rex Dieter - 33.0-13 +- rebuild (qt5) + * Fri Jan 31 2020 Fedora Release Engineering - 33.0-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild From 416e8019abb34b825113663d28246d8f2966d61f Mon Sep 17 00:00:00 2001 From: Rex Dieter Date: Sat, 18 Apr 2020 08:51:05 -0500 Subject: [PATCH 003/260] ugene-34.0 update Source0 URL no longer uses qt5 private api (yay) use %check --- .gitignore | 1 + sources | 2 +- ugene.spec | 28 +++++++++++++--------------- 3 files changed, 15 insertions(+), 16 deletions(-) diff --git a/.gitignore b/.gitignore index 865ec36..ca3bd0f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ /ugene-1.*.tar.gz /ugene-33.0.tar.gz +/ugene-34.0.tar.gz diff --git a/sources b/sources index 5622a2a..cf25601 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-33.0.tar.gz) = 5e02a1845d7626c1287002a25bfa1551234fc94312963aef2981bdfe70af1959d5b1c4289af0138dfa9ba44846454ba2d4d9cd96f029bac1ab262ed2bc583d87 +SHA512 (ugene-34.0.tar.gz) = 70a0acbaae7d6e4184ff29841ad4f63d0f98dbf7ee14cdca278e8d5769cda3f9ab96ce376517f50920de034c7d67cb76d97b8f09fff61d6c95f1f5e8eaed90a7 diff --git a/ugene.spec b/ugene.spec index 9491ec7..a67d3be 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,18 +1,18 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 33.0 -Release: 13%{?dist} +Version: 34.0 +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 License: GPLv2+ and GPLv2 URL: http://ugene.net -Source0: http://ugene.net/downloads/%{name}-%{version}.tar.gz +Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz #Patch0: ugene-1.31.0.patch BuildRequires: desktop-file-utils BuildRequires: mesa-libGLU-devel -BuildRequires: qt5-qtbase-devel qt5-qtbase-private-devel +BuildRequires: qt5-qtbase-devel BuildRequires: qt5-qtbase-mysql BuildRequires: qt5-qtmultimedia-devel BuildRequires: qt5-qtscript-devel @@ -20,18 +20,12 @@ BuildRequires: qt5-qtsensors-devel BuildRequires: qt5-qtsvg-devel BuildRequires: qt5-qttools-devel BuildRequires: qt5-qtwebchannel-devel -BuildRequires: qt5-qtwebkit-devel BuildRequires: qt5-qtxmlpatterns-devel BuildRequires: qt5-qtwebengine-devel BuildRequires: qt5-qtwebsockets-devel BuildRequires: qt5-qtwebchannel-devel BuildRequires: zlib-devel -BuildConflicts: qt-devel - -#We need strict versions of qt for correct work of src/libs_3rdparty/qtbindings_* -%{?_qt5:Requires: %{_qt5}%{?_isa} = %{_qt5_version}} - Provides: bundled(sqlite) Provides: bundled(samtools) ExclusiveArch: %{ix86} x86_64 @@ -45,12 +39,8 @@ is a designer for custom bioinformatics workflows. %prep %setup -q -#%patch0 -p1 -b .qt510 %build -# workaround FTBFS (https://bugzilla.redhat.com/show_bug.cgi?id=1736931) -export CXXFLAGS="-fpermissive %{optflags}" - %{qmake_qt5} -r \ INSTALL_BINDIR=%{_bindir} \ INSTALL_LIBDIR=%{_libdir} \ @@ -68,7 +58,9 @@ make %{?_smp_mflags} %install make install INSTALL_ROOT=%{buildroot} -desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop + +%check +desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %files %{!?_licensedir:%global license %%doc} @@ -83,6 +75,12 @@ desktop-file-validate %{buildroot}/%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog +* Wed Apr 15 2020 Rex Dieter - 34.0-1 +- ugene-34.0 +- update Source0 URL +- no longer uses qt5 private api (yay) +- use %%check + * Mon Apr 06 2020 Rex Dieter - 33.0-13 - rebuild (qt5) From 0e36885d5bb6c048b4e56c42aa12193853dbf549 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 29 Jul 2020 13:12:38 +0000 Subject: [PATCH 004/260] - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index a67d3be..f52c536 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 34.0 -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 @@ -75,6 +75,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog +* Wed Jul 29 2020 Fedora Release Engineering - 34.0-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + * Wed Apr 15 2020 Rex Dieter - 34.0-1 - ugene-34.0 - update Source0 URL From efaee79225cb197c73b7b7e06aa8a87e3f56c9b9 Mon Sep 17 00:00:00 2001 From: Jan Grulich Date: Fri, 11 Sep 2020 11:29:46 +0200 Subject: [PATCH 005/260] rebuild (qt5) --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index f52c536..46c111b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 34.0 -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 @@ -75,6 +75,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog +* Fri Sep 11 2020 Jan Grulich - 34.0-3 +- rebuild (qt5) + * Wed Jul 29 2020 Fedora Release Engineering - 34.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild From 8e8ee8656a18c9b21a4704e466f97334dbf932c0 Mon Sep 17 00:00:00 2001 From: Jan Grulich Date: Fri, 11 Sep 2020 21:00:24 +0200 Subject: [PATCH 006/260] Fix build against Qt 5.15 --- ugene-fix-build-againt-qt-5.15.patch | 124 +++++++++++++++++++++++++++ ugene.spec | 6 +- 2 files changed, 129 insertions(+), 1 deletion(-) create mode 100644 ugene-fix-build-againt-qt-5.15.patch diff --git a/ugene-fix-build-againt-qt-5.15.patch b/ugene-fix-build-againt-qt-5.15.patch new file mode 100644 index 0000000..c79b1a8 --- /dev/null +++ b/ugene-fix-build-againt-qt-5.15.patch @@ -0,0 +1,124 @@ +diff --git a/src/corelibs/U2Designer/src/WorkflowGUIUtils.cpp b/src/corelibs/U2Designer/src/WorkflowGUIUtils.cpp +index 2e24754..e377cf0 100644 +--- a/src/corelibs/U2Designer/src/WorkflowGUIUtils.cpp ++++ b/src/corelibs/U2Designer/src/WorkflowGUIUtils.cpp +@@ -24,6 +24,7 @@ + #include + + #include ++#include + #include + #include + #include +diff --git a/src/corelibs/U2Gui/src/util/GUIUtils.cpp b/src/corelibs/U2Gui/src/util/GUIUtils.cpp +index 2848d21..d063a9d 100644 +--- a/src/corelibs/U2Gui/src/util/GUIUtils.cpp ++++ b/src/corelibs/U2Gui/src/util/GUIUtils.cpp +@@ -25,6 +25,7 @@ + #include + #include + #include ++#include + #include + #include + +diff --git a/src/corelibs/U2View/src/ov_phyltree/GraphicsCircularBranchItem.h b/src/corelibs/U2View/src/ov_phyltree/GraphicsCircularBranchItem.h +index ae5594b..abd6846 100644 +--- a/src/corelibs/U2View/src/ov_phyltree/GraphicsCircularBranchItem.h ++++ b/src/corelibs/U2View/src/ov_phyltree/GraphicsCircularBranchItem.h +@@ -25,6 +25,8 @@ + #include + #include "GraphicsBranchItem.h" + ++#include ++ + class QGraphicsItem; + + namespace U2 { +diff --git a/src/corelibs/U2View/src/ov_sequence/Overview.cpp b/src/corelibs/U2View/src/ov_sequence/Overview.cpp +index b2aa8c2..e8ef876 100644 +--- a/src/corelibs/U2View/src/ov_sequence/Overview.cpp ++++ b/src/corelibs/U2View/src/ov_sequence/Overview.cpp +@@ -38,7 +38,7 @@ + + #include + #include +- ++#include + + namespace U2 { + +diff --git a/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.cpp b/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.cpp +index aee6cfc..c4b73c4 100644 +--- a/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.cpp ++++ b/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.cpp +@@ -32,6 +32,7 @@ + #include + #include + ++#include + + namespace U2 { + +diff --git a/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.h b/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.h +index 2eee20d..ad91e9d 100644 +--- a/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.h ++++ b/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.h +@@ -28,7 +28,7 @@ + #include + + #include +- ++#include + + namespace U2 { + +diff --git a/src/plugins/circular_view/src/CircularView.h b/src/plugins/circular_view/src/CircularView.h +index e7d4ac5..899c30b 100644 +--- a/src/plugins/circular_view/src/CircularView.h ++++ b/src/plugins/circular_view/src/CircularView.h +@@ -41,7 +41,7 @@ + #include + #include + #include +- ++#include + + namespace U2 { + +diff --git a/src/plugins/query_designer/src/QueryViewItems.h b/src/plugins/query_designer/src/QueryViewItems.h +index 6470561..2525ffd 100644 +--- a/src/plugins/query_designer/src/QueryViewItems.h ++++ b/src/plugins/query_designer/src/QueryViewItems.h +@@ -33,6 +33,7 @@ + #include + #include + #include ++#include + + #define GRID_STEP 40 + +diff --git a/src/plugins/workflow_designer/src/ItemViewStyle.h b/src/plugins/workflow_designer/src/ItemViewStyle.h +index fb85cb1..8d7d0eb 100644 +--- a/src/plugins/workflow_designer/src/ItemViewStyle.h ++++ b/src/plugins/workflow_designer/src/ItemViewStyle.h +@@ -26,6 +26,7 @@ + #include + #include + #include ++#include + + class QDomElement; + +diff --git a/src/plugins/workflow_designer/src/WorkflowViewItems.h b/src/plugins/workflow_designer/src/WorkflowViewItems.h +index 058b625..0346f30 100644 +--- a/src/plugins/workflow_designer/src/WorkflowViewItems.h ++++ b/src/plugins/workflow_designer/src/WorkflowViewItems.h +@@ -29,6 +29,7 @@ + #include + #include + #include ++#include + + class QDomElement; + diff --git a/ugene.spec b/ugene.spec index 46c111b..3804f88 100644 --- a/ugene.spec +++ b/ugene.spec @@ -10,6 +10,8 @@ URL: http://ugene.net Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz #Patch0: ugene-1.31.0.patch +Patch1: ugene-fix-build-againt-qt-5.15.patch + BuildRequires: desktop-file-utils BuildRequires: mesa-libGLU-devel BuildRequires: qt5-qtbase-devel @@ -40,6 +42,8 @@ is a designer for custom bioinformatics workflows. %prep %setup -q +%patch1 -p1 -b .fix-build-againt-qt-5.15 + %build %{qmake_qt5} -r \ INSTALL_BINDIR=%{_bindir} \ @@ -121,7 +125,7 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop * Thu Oct 25 2018 Yuliya Algaer - 1.31.1-1 - New upstream release -* Thu Aug 24 2018 Yuliya Algaer - 1.31.0-6 +* Fri Aug 24 2018 Yuliya Algaer - 1.31.0-6 - New upstream release * Sat Jul 14 2018 Fedora Release Engineering - 1.30.0-25 From 8d8abec82de1de2423fa8eab280d354709f6b275 Mon Sep 17 00:00:00 2001 From: Jeff Law Date: Sun, 18 Oct 2020 10:15:10 -0600 Subject: [PATCH 007/260] Fix missing #includes for gcc-11 --- ugene-gcc11.patch | 36 ++++++++++++++++++++++++++++++++++++ ugene.spec | 7 ++++++- 2 files changed, 42 insertions(+), 1 deletion(-) create mode 100644 ugene-gcc11.patch diff --git a/ugene-gcc11.patch b/ugene-gcc11.patch new file mode 100644 index 0000000..a28e188 --- /dev/null +++ b/ugene-gcc11.patch @@ -0,0 +1,36 @@ +diff --git a/src/corelibs/U2Core/src/io/ZlibAdapter.cpp b/src/corelibs/U2Core/src/io/ZlibAdapter.cpp +index ce48ab3..93ea092 100644 +--- a/src/corelibs/U2Core/src/io/ZlibAdapter.cpp ++++ b/src/corelibs/U2Core/src/io/ZlibAdapter.cpp +@@ -19,6 +19,7 @@ + * MA 02110-1301, USA. + */ + ++#include + #include + + #include +diff --git a/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp b/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp +index 734a8f3..d8018fc 100644 +--- a/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp ++++ b/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp +@@ -19,6 +19,7 @@ + * MA 02110-1301, USA. + */ + ++#include + #include + #include + #include +diff --git a/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp b/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp +index 84fa723..4a0eaca 100644 +--- a/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp ++++ b/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp +@@ -19,6 +19,7 @@ + * MA 02110-1301, USA. + */ + ++#include + #include + #include + diff --git a/ugene.spec b/ugene.spec index 3804f88..e9867ab 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 34.0 -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 @@ -11,6 +11,7 @@ Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name #Patch0: ugene-1.31.0.patch Patch1: ugene-fix-build-againt-qt-5.15.patch +Patch2: %{name}-gcc11.patch BuildRequires: desktop-file-utils BuildRequires: mesa-libGLU-devel @@ -43,6 +44,7 @@ is a designer for custom bioinformatics workflows. %setup -q %patch1 -p1 -b .fix-build-againt-qt-5.15 +%patch2 -p1 -b .gcc11 %build %{qmake_qt5} -r \ @@ -79,6 +81,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog +* Sun Oct 18 2020 Jeff Law - 34.0-4 +- Fix missing #includes for gcc-11 + * Fri Sep 11 2020 Jan Grulich - 34.0-3 - rebuild (qt5) From 8944e803a970b92668d2a91149492ec97d96edfb Mon Sep 17 00:00:00 2001 From: Jan Grulich Date: Mon, 23 Nov 2020 07:55:33 +0100 Subject: [PATCH 008/260] rebuild (qt5) --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index e9867ab..7186b46 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 34.0 -Release: 4%{?dist} +Release: 5%{?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 @@ -81,6 +81,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog +* Mon Nov 23 07:55:33 CET 2020 Jan Grulich - 34.0-5 +- rebuild (qt5) + * Sun Oct 18 2020 Jeff Law - 34.0-4 - Fix missing #includes for gcc-11 From 553073af25a2b6342703f132dda90e5441320e28 Mon Sep 17 00:00:00 2001 From: Tom Stellard Date: Sat, 9 Jan 2021 00:20:54 +0000 Subject: [PATCH 009/260] Add BuildRequires: make https://fedoraproject.org/wiki/Changes/Remove_make_from_BuildRoot --- ugene.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/ugene.spec b/ugene.spec index 7186b46..16af0f5 100644 --- a/ugene.spec +++ b/ugene.spec @@ -13,6 +13,7 @@ Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name Patch1: ugene-fix-build-againt-qt-5.15.patch Patch2: %{name}-gcc11.patch +BuildRequires: make BuildRequires: desktop-file-utils BuildRequires: mesa-libGLU-devel BuildRequires: qt5-qtbase-devel From b451f9d67add2f0d1a56b52c608138710f850ebb Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 27 Jan 2021 22:36:08 +0000 Subject: [PATCH 010/260] - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 16af0f5..4b554df 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 34.0 -Release: 5%{?dist} +Release: 6%{?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 @@ -82,6 +82,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog +* Wed Jan 27 2021 Fedora Release Engineering - 34.0-6 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild + * Mon Nov 23 07:55:33 CET 2020 Jan Grulich - 34.0-5 - rebuild (qt5) From 9bdcbcba045fce3602fb1c909e05c53f55c53c3e Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 23 Jul 2021 19:57:48 +0000 Subject: [PATCH 011/260] - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 4b554df..f9282e9 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,7 +1,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 34.0 -Release: 6%{?dist} +Release: 7%{?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 @@ -82,6 +82,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/* %changelog +* Fri Jul 23 2021 Fedora Release Engineering - 34.0-7 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild + * Wed Jan 27 2021 Fedora Release Engineering - 34.0-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild From 524e7b25234c2f757eff8c8feff7a9246865d282 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 9 Nov 2021 21:15:06 +0900 Subject: [PATCH 012/260] 41.1 --- .gitignore | 1 + sources | 2 +- ugene-1.31.0.patch | 24 --- ugene-40.1-glibc-2_35.patch | 11 ++ ...0.1-libs_3rdparty-breakpad-arch-port.patch | 183 ++++++++++++++++++ ...ty-breakpad-sys_mmap_use_system_mmap.patch | 105 ++++++++++ ...ty-breakpad-unwind-nonsupported-arch.patch | 11 ++ ...1-plgins-smith_waterman-nonsse2-arch.patch | 103 ++++++++++ ...0.1-plugins_3rdparty-hmm2-nosse-arch.patch | 57 ++++++ ugene-40.1-qbswap-bigendian-workaround.patch | 45 +++++ ugene-40.1-ugenem-cpuid-supported-arch.patch | 20 ++ ugene-fix-build-againt-qt-5.15.patch | 124 ------------ ugene-gcc11.patch | 36 ---- ugene.spec | 133 ++++++++----- 14 files changed, 620 insertions(+), 235 deletions(-) delete mode 100644 ugene-1.31.0.patch create mode 100644 ugene-40.1-glibc-2_35.patch create mode 100644 ugene-40.1-libs_3rdparty-breakpad-arch-port.patch create mode 100644 ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch create mode 100644 ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch create mode 100644 ugene-40.1-plgins-smith_waterman-nonsse2-arch.patch create mode 100644 ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch create mode 100644 ugene-40.1-qbswap-bigendian-workaround.patch create mode 100644 ugene-40.1-ugenem-cpuid-supported-arch.patch delete mode 100644 ugene-fix-build-againt-qt-5.15.patch delete mode 100644 ugene-gcc11.patch diff --git a/.gitignore b/.gitignore index ca3bd0f..f3dfdb7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ /ugene-1.*.tar.gz /ugene-33.0.tar.gz /ugene-34.0.tar.gz +/ugene-40.1.tar.gz diff --git a/sources b/sources index cf25601..be82943 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-34.0.tar.gz) = 70a0acbaae7d6e4184ff29841ad4f63d0f98dbf7ee14cdca278e8d5769cda3f9ab96ce376517f50920de034c7d67cb76d97b8f09fff61d6c95f1f5e8eaed90a7 +SHA512 (ugene-40.1.tar.gz) = b2e056532a2ecf2a396d9bdd7a44f3af1e3e49d1ab2d95169be5583a4e59b43773d02224987b096fdd48f91568c65dc9fa575702a881b40fdabfdc776cd16af1 diff --git a/ugene-1.31.0.patch b/ugene-1.31.0.patch deleted file mode 100644 index a478a52..0000000 --- a/ugene-1.31.0.patch +++ /dev/null @@ -1,24 +0,0 @@ -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" diff --git a/ugene-40.1-glibc-2_35.patch b/ugene-40.1-glibc-2_35.patch new file mode 100644 index 0000000..e97b97c --- /dev/null +++ b/ugene-40.1-glibc-2_35.patch @@ -0,0 +1,11 @@ +--- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc.glibc 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc 2021-11-08 15:45:23.563723022 +0900 +@@ -141,7 +141,7 @@ void InstallAlternateStackLocked() { + // SIGSTKSZ may be too small to prevent the signal handlers from overrunning + // the alternative stack. Ensure that the size of the alternative stack is + // large enough. +- static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); ++ static const unsigned kSigStackSize = std::max(16384L, (long)SIGSTKSZ); + + // Only set an alternative stack if there isn't already one, or if the current + // one is too small. diff --git a/ugene-40.1-libs_3rdparty-breakpad-arch-port.patch b/ugene-40.1-libs_3rdparty-breakpad-arch-port.patch new file mode 100644 index 0000000..323159e --- /dev/null +++ b/ugene-40.1-libs_3rdparty-breakpad-arch-port.patch @@ -0,0 +1,183 @@ +--- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/thread_info.cc.port 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/thread_info.cc 2021-11-09 11:04:57.375470034 +0900 +@@ -270,9 +270,19 @@ void ThreadInfo::FillCPUContext(RawConte + out->float_save.fir = mcontext.fpc_eir; + #endif + } ++ ++#else ++uintptr_t ThreadInfo::GetInstructionPointer() const { ++ return 0; ++} ++ ++void ThreadInfo::FillCPUContext(RawContextCPU* out) const { ++} ++ + #endif // __mips__ + + void ThreadInfo::GetGeneralPurposeRegisters(void** gp_regs, size_t* size) { ++#if defined(__i386) || defined(__x86_64) || defined(__ARM_EABI__) || defined(__aarch64__) || defined(__mips__) + assert(gp_regs || size); + #if defined(__mips__) + if (gp_regs) +@@ -285,9 +295,11 @@ void ThreadInfo::GetGeneralPurposeRegist + if (size) + *size = sizeof(regs); + #endif ++#endif + } + + void ThreadInfo::GetFloatingPointRegisters(void** fp_regs, size_t* size) { ++#if defined(__i386) || defined(__x86_64) || defined(__ARM_EABI__) || defined(__aarch64__) || defined(__mips__) + assert(fp_regs || size); + #if defined(__mips__) + if (fp_regs) +@@ -300,6 +312,7 @@ void ThreadInfo::GetFloatingPointRegiste + if (size) + *size = sizeof(fpregs); + #endif ++#endif + } + + } // namespace google_breakpad +--- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/ucontext_reader.cc.port 2021-11-09 12:13:14.526068539 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/ucontext_reader.cc 2021-11-09 12:13:47.079160354 +0900 +@@ -254,6 +254,16 @@ void UContextReader::FillCPUContext(RawC + out->float_save.fir = uc->uc_mcontext.fpc_eir; // Unused. + #endif + } ++ ++#else ++uintptr_t UContextReader::GetStackPointer(const ucontext_t* uc) { ++ return 0; ++} ++uintptr_t UContextReader::GetInstructionPointer(const ucontext_t* uc) { ++ return 0; ++} ++void UContextReader::FillCPUContext(RawContextCPU* out, const ucontext_t* uc) { ++} + #endif + + } // namespace google_breakpad +--- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc.port 2021-11-09 11:04:57.135469882 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc 2021-11-09 12:06:47.875738562 +0900 +@@ -441,6 +441,7 @@ int ExceptionHandler::ThreadEntry(void* + // This function runs in a compromised context: see the top of the file. + // Runs on the crashing thread. + bool ExceptionHandler::HandleSignal(int /*sig*/, siginfo_t* info, void* uc) { ++#if defined(__i386) || defined(__x86_64) || defined(__ARM_EABI__) || defined(__aarch64__) || defined(__mips__) + if (filter_ && !filter_(callback_context_)) + return false; + +@@ -482,6 +483,9 @@ bool ExceptionHandler::HandleSignal(int + } + } + return GenerateDump(&g_crash_context_); ++#else ++ return false; ++#endif + } + + // This is a public interface to HandleSignal that allows the client to +@@ -660,6 +664,7 @@ bool ExceptionHandler::WriteMinidump(con + __attribute__((optimize("no-omit-frame-pointer"))) + #endif + bool ExceptionHandler::WriteMinidump() { ++#if defined(__i386) || defined(__x86_64) || defined(__ARM_EABI__) || defined(__aarch64__) || defined(__mips__) + if (!IsOutOfProcess() && !minidump_descriptor_.IsFD() && + !minidump_descriptor_.IsMicrodumpOnConsole()) { + // Update the path of the minidump so that this can be called multiple times +@@ -734,6 +739,9 @@ bool ExceptionHandler::WriteMinidump() { + #endif + + return GenerateDump(&context); ++#else ++ return false; ++#endif + } + + void ExceptionHandler::AddMappingInfo(const string& name, +--- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/microdump_writer/microdump_writer.cc.port 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/microdump_writer/microdump_writer.cc 2021-11-09 12:20:24.529281407 +0900 +@@ -338,7 +338,7 @@ class MicrodumpWriter { + # error "This mips ABI is currently not supported (n32)" + #endif + #else +-#error "This code has not been ported to your platform yet" ++ const char kArch[] = "unknown"; + #endif + + LogAppend("O "); +@@ -409,11 +409,15 @@ class MicrodumpWriter { + void DumpCPUState() { + RawContextCPU cpu; + my_memset(&cpu, 0, sizeof(RawContextCPU)); ++#if !defined(__i386__) && !defined(__x86_64) && !defined(__aarch64__) ++ UContextReader::FillCPUContext(&cpu, ucontext_); ++#else + #if !defined(__ARM_EABI__) && !defined(__mips__) + UContextReader::FillCPUContext(&cpu, ucontext_, float_state_); + #else + UContextReader::FillCPUContext(&cpu, ucontext_); + #endif ++#endif + LogAppend("C "); + LogAppend(&cpu, sizeof(cpu)); + LogCommitLine(); +--- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/linux_dumper.h.port 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/linux_dumper.h 2021-11-09 11:04:57.384470040 +0900 +@@ -63,6 +63,7 @@ namespace google_breakpad { + (defined(__mips__) && _MIPS_SIM == _ABIO32) + typedef Elf32_auxv_t elf_aux_entry; + #elif defined(__x86_64) || defined(__aarch64__) || \ ++ defined(__powerpc64__) || defined(__s390x__) || \ + (defined(__mips__) && _MIPS_SIM != _ABIO32) + typedef Elf64_auxv_t elf_aux_entry; + #endif +--- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/linux_ptrace_dumper.cc.port 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/linux_ptrace_dumper.cc 2021-11-09 11:04:57.384470040 +0900 +@@ -198,6 +198,7 @@ bool LinuxPtraceDumper::ReadRegisters(Th + // these members are set to -1. Returns true iff all three members are + // available. + bool LinuxPtraceDumper::GetThreadInfoByIndex(size_t index, ThreadInfo* info) { ++#if defined(__i386) || defined(__x86_64) || defined(__ARM_EABI__) || defined(__aarch64__) || defined(__mips__) + if (index >= threads_.size()) + return false; + +@@ -304,6 +305,9 @@ bool LinuxPtraceDumper::GetThreadInfoByI + info->stack_pointer = reinterpret_cast(stack_pointer); + + return true; ++#else ++ return false; ++#endif + } + + bool LinuxPtraceDumper::IsPostMortem() const { +--- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/minidump_writer.cc.port 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/minidump_writer/minidump_writer.cc 2021-11-09 12:20:06.954231835 +0900 +@@ -468,11 +468,15 @@ class MinidumpWriter { + if (!cpu.Allocate()) + return false; + my_memset(cpu.get(), 0, sizeof(RawContextCPU)); ++#if !defined(__i386__) && !defined(__x86_64) && !defined(__aarch64__) ++ UContextReader::FillCPUContext(cpu.get(), ucontext_); ++#else + #if !defined(__ARM_EABI__) && !defined(__mips__) + UContextReader::FillCPUContext(cpu.get(), ucontext_, float_state_); + #else + UContextReader::FillCPUContext(cpu.get(), ucontext_); + #endif ++#endif + thread.thread_context = cpu.location(); + crashing_thread_context_ = cpu.location(); + } else { +@@ -1206,7 +1210,7 @@ class MinidumpWriter { + return true; + } + #else +-# error "Unsupported CPU" ++ bool WriteCPUInformation(MDRawSystemInfo* sys_info) { return false; } + #endif + + bool WriteFile(MDLocationDescriptor* result, const char* filename) { diff --git a/ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch b/ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch new file mode 100644 index 0000000..5ca0423 --- /dev/null +++ b/ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch @@ -0,0 +1,105 @@ +--- ugene-40.1/src/libs_3rdparty/breakpad/src/common/memory_allocator.h.sys_mmap 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/common/memory_allocator.h 2021-11-08 22:21:13.962461668 +0900 +@@ -42,11 +42,14 @@ + #include + #endif + +-#ifdef __APPLE__ ++#if defined(__APPLE__) || defined(__linux__) + #define sys_mmap mmap + #define sys_munmap munmap ++#if !defined(__linux__) + #define MAP_ANONYMOUS MAP_ANON +-#else ++#endif ++#endif ++#if ! defined(__APPLE__) + #include "third_party/lss/linux_syscall_support.h" + #endif + +--- ugene-40.1/src/libs_3rdparty/breakpad/src/third_party/lss/linux_syscall_support.h.sys_mmap 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/third_party/lss/linux_syscall_support.h 2021-11-09 00:46:06.363362301 +0900 +@@ -85,10 +85,7 @@ + /* We currently only support x86-32, x86-64, ARM, MIPS, and PPC on Linux. + * Porting to other related platforms should not be difficult. + */ +-#if (defined(__i386__) || defined(__x86_64__) || defined(__ARM_ARCH_3__) || \ +- defined(__mips__) || defined(__PPC__) || defined(__ARM_EABI__) || \ +- defined(__aarch64__)) \ +- && (defined(__linux) || defined(__ANDROID__)) ++#if defined(__linux) || defined(__ANDROID__) + + #ifndef SYS_CPLUSPLUS + #ifdef __cplusplus +@@ -107,15 +104,21 @@ extern "C" { + #include + #include + #include +-#include + #include + #include + #include ++#include + #include ++#include + #include + #include ++#include + #include + ++#ifndef __linux__ ++#ifndef __linux__ ++#ifndef __linux__ ++ + #ifdef __mips__ + /* Include definitions of the ABI currently in use. */ + #include +@@ -4021,6 +4024,48 @@ struct kernel_statfs { + # pragma pop_macro("lstat64") + #endif + ++#endif ++#endif ++#endif ++#ifdef __linux__ ++#define sys_open open ++#define sys_close close ++#define sys_lseek lseek ++#define sys_write ::write ++#define sys_read read ++#define sys_pipe pipe ++#define sys_tgkill tgkill ++#define sys_gettid gettid ++#define sys_prctl prctl ++#define sys_clone clone ++#define sys_waitpid waitpid ++#define sys_sigaltstack sigaltstack ++#define sys_getpid getpid ++#define sys_ptrace(a,b,c,d) ptrace((enum __ptrace_request)a,b,c,d) ++#define sys_stat stat ++#define sys_sendmsg sendmsg ++#define sys_getdents getdents64 ++#define sys_readlink readlink ++#define sys_fstat fstat ++#define sys_fstat64 fstat64 ++#define sys_mmap mmap ++#define sys_munmap munmap ++#define kernel_iovec iovec ++#define kernel_msghdr msghdr ++#define kernel_stat stat ++#define kernel_stat64 stat64 ++#define kernel_dirent linux_dirent64 ++ ++struct linux_dirent64 { ++ ino64_t d_ino; /* 64-bit inode number */ ++ off64_t d_off; /* 64-bit offset to next structure */ ++ unsigned short d_reclen; /* Size of this dirent */ ++ unsigned char d_type; /* File type */ ++ char d_name[]; /* Filename (null-terminated) */ ++}; ++ ++#endif ++ + #if defined(__cplusplus) && !defined(SYS_CPLUSPLUS) + } + #endif diff --git a/ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch b/ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch new file mode 100644 index 0000000..10bcf83 --- /dev/null +++ b/ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch @@ -0,0 +1,11 @@ +--- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/raw_context_cpu.h.unwind 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/dump_writer_common/raw_context_cpu.h 2021-11-08 20:15:01.057998601 +0900 +@@ -45,7 +45,7 @@ typedef MDRawContextARM64_Old RawContext + #elif defined(__mips__) + typedef MDRawContextMIPS RawContextCPU; + #else +-#error "This code has not been ported to your platform yet." ++typedef unsigned long RawContextCPU; + #endif + + } // namespace google_breakpad diff --git a/ugene-40.1-plgins-smith_waterman-nonsse2-arch.patch b/ugene-40.1-plgins-smith_waterman-nonsse2-arch.patch new file mode 100644 index 0000000..47e48e6 --- /dev/null +++ b/ugene-40.1-plgins-smith_waterman-nonsse2-arch.patch @@ -0,0 +1,103 @@ +--- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp.sse_2 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp 2021-11-09 10:46:44.925720099 +0900 +@@ -99,9 +99,11 @@ + par->registerAlgorithm(new SWPairwiseAlignmentAlgorithm()); + regDependedIMPLFromOtherPlugins(); + ++#if defined (__SSE2__) + coreLog.trace("Registering SSE2 SW implementation"); + swar->registerFactory(new SWTaskFactory(SW_sse2), QString("SSE2")); + par->getAlgorithm("Smith-Waterman")->addAlgorithmRealization(new PairwiseAlignmentSmithWatermanTaskFactory(SW_sse2), new PairwiseAlignmentSmithWatermanGUIExtensionFactory(SW_sse2), "SSE2"); ++#endif + + this->connect(AppContext::getPluginSupport(), SIGNAL(si_allStartUpPluginsLoaded()), SLOT(regDependedIMPLFromOtherPlugins())); + } +--- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp.sse_2 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp 2021-11-09 12:00:58.015843958 +0900 +@@ -184,6 +184,7 @@ + sWatermanConfig.resultView), + true)); + break; ++#ifdef __SSE2__ + case SW_sse2: + addTaskResource(TaskResourceUsage(RESOURCE_MEMORY, + SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(sWatermanConfig.ptrn, +@@ -194,6 +195,7 @@ + maxScore, + sWatermanConfig.resultView), + true)); ++#endif + break; + default: + assert(0); +@@ -268,7 +270,12 @@ + + SmithWatermanAlgorithm *sw = nullptr; + if (algType == SW_sse2) { ++#if defined(__SSE2__) + sw = new SmithWatermanAlgorithmSSE2; ++#else ++ coreLog.error("SSE2 was not enabled in this build"); ++ return; ++#endif + } else if (algType == SW_cuda) { + #ifdef SW2_BUILD_WITH_CUDA + sw = new SmithWatermanAlgorithmCUDA; +@@ -579,7 +586,11 @@ + + SmithWatermanAlgorithm *sw = nullptr; + if (algType == SW_sse2) { ++#if defined(__SSE2__) + sw = new SmithWatermanAlgorithmSSE2; ++#else ++ coreLog.error("SSE2 was not enabled in this build"); ++#endif + } else if (algType == SW_cuda) { + #ifdef SW2_BUILD_WITH_CUDA + sw = new SmithWatermanAlgorithmCUDA; +@@ -734,6 +745,7 @@ + true)); + break; + case SW_sse2: ++#if defined(__SSE2__) + addTaskResource(TaskResourceUsage(RESOURCE_MEMORY, + SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(*ptrn, + sqnc->left(c.chunkSize * c.nThreads), +@@ -743,6 +755,7 @@ + maxScore, + SmithWatermanSettings::MULTIPLE_ALIGNMENT), + true)); ++#endif + break; + default: + assert(0); +--- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.sse_2 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp 2021-11-09 10:46:44.926720099 +0900 +@@ -19,6 +19,7 @@ + * MA 02110-1301, USA. + */ + ++#if defined(__SSE2__) + #include "SmithWatermanAlgorithmSSE2.h" + #include + #include +@@ -1192,3 +1193,4 @@ + } + + } // namespace U2 ++#endif +--- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h 2021-11-09 10:46:44.926720099 +0900 +@@ -22,6 +22,7 @@ + #ifndef _SMITHWATERMANALGORITHM_SSE2_H + #define _SMITHWATERMANALGORITHM_SSE2_H + ++#if defined(__SSE2__) + #include + + #include "SmithWatermanAlgorithm.h" +@@ -55,3 +56,4 @@ + } // namespace U2 + + #endif ++#endif diff --git a/ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch b/ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch new file mode 100644 index 0000000..b163a98 --- /dev/null +++ b/ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch @@ -0,0 +1,57 @@ +--- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/HMMSearchDialogController.cpp.sse 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/HMMSearchDialogController.cpp 2021-11-09 01:34:30.052988784 +0900 +@@ -81,7 +81,9 @@ + QWidget *w = createController->getWidget(); + QVBoxLayout *l = qobject_cast(layout()); + l->insertWidget(1, w); ++#if defined (__SSE2__) + algoCombo->addItem(tr("SSE optimized"), HMMSearchAlgo_SSEOptimized); ++#endif + algoCombo->addItem(tr("Conservative"), HMMSearchAlgo_Conservative); + + okButton = buttonBox->button(QDialogButtonBox::Ok); +--- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp.sse 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp 2021-11-09 01:34:30.052988784 +0900 +@@ -56,9 +56,15 @@ + tophit_s *dhit = AllocTophits(200); // domain hits: 200=lumpsize + + int nseq = 0; // number of sequences searched ++#if defined(__SSE2__) + if (s.alg == HMMSearchAlgo_SSEOptimized) { + main_loop_opt(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si, sseScoring); +- } else if (s.alg == HMMSearchAlgo_Conservative) { ++ } ++#else ++ if (0) { ++ } ++#endif ++ else if (s.alg == HMMSearchAlgo_Conservative) { + main_loop_serial(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si); + } else { + assert(false && "bad hmmsearch algorithm selected"); +--- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp.sse 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp 2021-11-09 01:41:17.023845328 +0900 +@@ -6,6 +6,7 @@ + #include + + #include ++#if defined (__SSE2__) + #include + + using namespace U2; +@@ -490,3 +491,4 @@ + + return results; + } ++#endif +--- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.h.sse 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.h 2021-11-09 01:34:30.052988784 +0900 +@@ -1,6 +1,8 @@ + #ifndef __HMMSEARCH_SSE_H__ + #define __HMMSEARCH_SSE_H__ + ++#if defined(__SSE2__) + QList sseScoring( unsigned char * dsq, int seqlen, plan7_s* hmm, HMMSeqGranulation * gr, U2::TaskStateInfo& ti ); ++#endif + + #endif // __HMMSEARCH_SSE_H__ diff --git a/ugene-40.1-qbswap-bigendian-workaround.patch b/ugene-40.1-qbswap-bigendian-workaround.patch new file mode 100644 index 0000000..7733aef --- /dev/null +++ b/ugene-40.1-qbswap-bigendian-workaround.patch @@ -0,0 +1,45 @@ +--- ugene-40.1/src/corelibs/U2Core/src/io/ZlibAdapter.cpp.char_bigen 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/corelibs/U2Core/src/io/ZlibAdapter.cpp 2021-11-09 16:41:07.802412220 +0900 +@@ -29,6 +29,12 @@ + + #include "LocalFileAdapter.h" + ++QT_BEGIN_NAMESPACE ++#if defined(Q_BYTE_ORDER) && Q_BYTE_ORDER == Q_BIG_ENDIAN ++template <> inline Q_DECL_CONSTEXPR char qbswap(char source) { return source; } ++#endif ++QT_END_NAMESPACE ++ + namespace U2 { + + class GzipUtil { +--- ugene-40.1/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp.char_bigen 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp 2021-11-09 14:55:12.703372481 +0900 +@@ -31,6 +31,12 @@ + #include + #include + ++QT_BEGIN_NAMESPACE ++#if defined(Q_BYTE_ORDER) && Q_BYTE_ORDER == Q_BIG_ENDIAN ++template <> inline Q_DECL_CONSTEXPR char qbswap(char source) { return source; } ++#endif ++QT_END_NAMESPACE ++ + namespace U2 { + + const QString DNAChromatogramSerializer::ID = "chroma_1.14"; +--- ugene-40.1/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp.char_bigen 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp 2021-11-09 16:40:41.872455587 +0900 +@@ -27,6 +27,12 @@ + #include + #include + ++QT_BEGIN_NAMESPACE ++#if defined(Q_BYTE_ORDER) && Q_BYTE_ORDER == Q_BIG_ENDIAN ++template <> inline Q_DECL_CONSTEXPR char qbswap(char source) { return source; } ++#endif ++QT_END_NAMESPACE ++ + namespace U2 { + + static quint8 cigarOp2samtools(U2CigarOp op, U2OpStatus &os) { diff --git a/ugene-40.1-ugenem-cpuid-supported-arch.patch b/ugene-40.1-ugenem-cpuid-supported-arch.patch new file mode 100644 index 0000000..878a7ff --- /dev/null +++ b/ugene-40.1-ugenem-cpuid-supported-arch.patch @@ -0,0 +1,20 @@ +--- ugene-40.1/src/ugenem/src/SendReportDialog.cpp.cpuid 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-40.1/src/ugenem/src/SendReportDialog.cpp 2021-11-08 19:56:32.468424643 +0900 +@@ -425,7 +425,7 @@ + return (int)(getMemorySize() / (1024 * 1024)); + } + +-#ifndef Q_OS_DARWIN ++#if defined(__x86_64__) || defined (__i386__) + void cpuID(unsigned i, unsigned regs[4]) { + # ifdef _WIN32 + __cpuid((int *)regs, (int)i); +@@ -441,7 +441,7 @@ + + QString ReportSender::getCPUInfo() { + QString result; +-#ifndef Q_OS_DARWIN ++#if defined(__x86_64__) || defined (__i386__) + unsigned regs[4]; + + // Get vendor diff --git a/ugene-fix-build-againt-qt-5.15.patch b/ugene-fix-build-againt-qt-5.15.patch deleted file mode 100644 index c79b1a8..0000000 --- a/ugene-fix-build-againt-qt-5.15.patch +++ /dev/null @@ -1,124 +0,0 @@ -diff --git a/src/corelibs/U2Designer/src/WorkflowGUIUtils.cpp b/src/corelibs/U2Designer/src/WorkflowGUIUtils.cpp -index 2e24754..e377cf0 100644 ---- a/src/corelibs/U2Designer/src/WorkflowGUIUtils.cpp -+++ b/src/corelibs/U2Designer/src/WorkflowGUIUtils.cpp -@@ -24,6 +24,7 @@ - #include - - #include -+#include - #include - #include - #include -diff --git a/src/corelibs/U2Gui/src/util/GUIUtils.cpp b/src/corelibs/U2Gui/src/util/GUIUtils.cpp -index 2848d21..d063a9d 100644 ---- a/src/corelibs/U2Gui/src/util/GUIUtils.cpp -+++ b/src/corelibs/U2Gui/src/util/GUIUtils.cpp -@@ -25,6 +25,7 @@ - #include - #include - #include -+#include - #include - #include - -diff --git a/src/corelibs/U2View/src/ov_phyltree/GraphicsCircularBranchItem.h b/src/corelibs/U2View/src/ov_phyltree/GraphicsCircularBranchItem.h -index ae5594b..abd6846 100644 ---- a/src/corelibs/U2View/src/ov_phyltree/GraphicsCircularBranchItem.h -+++ b/src/corelibs/U2View/src/ov_phyltree/GraphicsCircularBranchItem.h -@@ -25,6 +25,8 @@ - #include - #include "GraphicsBranchItem.h" - -+#include -+ - class QGraphicsItem; - - namespace U2 { -diff --git a/src/corelibs/U2View/src/ov_sequence/Overview.cpp b/src/corelibs/U2View/src/ov_sequence/Overview.cpp -index b2aa8c2..e8ef876 100644 ---- a/src/corelibs/U2View/src/ov_sequence/Overview.cpp -+++ b/src/corelibs/U2View/src/ov_sequence/Overview.cpp -@@ -38,7 +38,7 @@ - - #include - #include -- -+#include - - namespace U2 { - -diff --git a/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.cpp b/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.cpp -index aee6cfc..c4b73c4 100644 ---- a/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.cpp -+++ b/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.cpp -@@ -32,6 +32,7 @@ - #include - #include - -+#include - - namespace U2 { - -diff --git a/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.h b/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.h -index 2eee20d..ad91e9d 100644 ---- a/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.h -+++ b/src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.h -@@ -28,7 +28,7 @@ - #include - - #include -- -+#include - - namespace U2 { - -diff --git a/src/plugins/circular_view/src/CircularView.h b/src/plugins/circular_view/src/CircularView.h -index e7d4ac5..899c30b 100644 ---- a/src/plugins/circular_view/src/CircularView.h -+++ b/src/plugins/circular_view/src/CircularView.h -@@ -41,7 +41,7 @@ - #include - #include - #include -- -+#include - - namespace U2 { - -diff --git a/src/plugins/query_designer/src/QueryViewItems.h b/src/plugins/query_designer/src/QueryViewItems.h -index 6470561..2525ffd 100644 ---- a/src/plugins/query_designer/src/QueryViewItems.h -+++ b/src/plugins/query_designer/src/QueryViewItems.h -@@ -33,6 +33,7 @@ - #include - #include - #include -+#include - - #define GRID_STEP 40 - -diff --git a/src/plugins/workflow_designer/src/ItemViewStyle.h b/src/plugins/workflow_designer/src/ItemViewStyle.h -index fb85cb1..8d7d0eb 100644 ---- a/src/plugins/workflow_designer/src/ItemViewStyle.h -+++ b/src/plugins/workflow_designer/src/ItemViewStyle.h -@@ -26,6 +26,7 @@ - #include - #include - #include -+#include - - class QDomElement; - -diff --git a/src/plugins/workflow_designer/src/WorkflowViewItems.h b/src/plugins/workflow_designer/src/WorkflowViewItems.h -index 058b625..0346f30 100644 ---- a/src/plugins/workflow_designer/src/WorkflowViewItems.h -+++ b/src/plugins/workflow_designer/src/WorkflowViewItems.h -@@ -29,6 +29,7 @@ - #include - #include - #include -+#include - - class QDomElement; - diff --git a/ugene-gcc11.patch b/ugene-gcc11.patch deleted file mode 100644 index a28e188..0000000 --- a/ugene-gcc11.patch +++ /dev/null @@ -1,36 +0,0 @@ -diff --git a/src/corelibs/U2Core/src/io/ZlibAdapter.cpp b/src/corelibs/U2Core/src/io/ZlibAdapter.cpp -index ce48ab3..93ea092 100644 ---- a/src/corelibs/U2Core/src/io/ZlibAdapter.cpp -+++ b/src/corelibs/U2Core/src/io/ZlibAdapter.cpp -@@ -19,6 +19,7 @@ - * MA 02110-1301, USA. - */ - -+#include - #include - - #include -diff --git a/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp b/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp -index 734a8f3..d8018fc 100644 ---- a/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp -+++ b/src/corelibs/U2Core/src/util/DatatypeSerializeUtils.cpp -@@ -19,6 +19,7 @@ - * MA 02110-1301, USA. - */ - -+#include - #include - #include - #include -diff --git a/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp b/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp -index 84fa723..4a0eaca 100644 ---- a/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp -+++ b/src/libs_3rdparty/samtools/src/SamtoolsAdapter.cpp -@@ -19,6 +19,7 @@ - * MA 02110-1301, USA. - */ - -+#include - #include - #include - diff --git a/ugene.spec b/ugene.spec index f9282e9..8a30fb5 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,38 +1,49 @@ -Name: ugene -Summary: Integrated bioinformatics toolkit -Version: 34.0 -Release: 7%{?dist} +Name: ugene +Summary: Integrated bioinformatics toolkit + +Version: 40.1 +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 -License: GPLv2+ and GPLv2 -URL: http://ugene.net -Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz -#Patch0: ugene-1.31.0.patch +License: GPLv2+ and GPLv2 +URL: http://ugene.net +Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz +# Should be sent to be upstream +Patch1: ugene-40.1-glibc-2_35.patch +# Currently distro-specific +Patch101: ugene-40.1-ugenem-cpuid-supported-arch.patch +Patch102: ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch +Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch +Patch104: ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch +Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch +Patch106: ugene-40.1-plgins-smith_waterman-nonsse2-arch.patch +Patch107: ugene-40.1-qbswap-bigendian-workaround.patch -Patch1: ugene-fix-build-againt-qt-5.15.patch -Patch2: %{name}-gcc11.patch +BuildRequires: make +BuildRequires: gcc-c++ +BuildRequires: desktop-file-utils -BuildRequires: make -BuildRequires: desktop-file-utils -BuildRequires: mesa-libGLU-devel -BuildRequires: qt5-qtbase-devel -BuildRequires: qt5-qtbase-mysql -BuildRequires: qt5-qtmultimedia-devel -BuildRequires: qt5-qtscript-devel -BuildRequires: qt5-qtsensors-devel -BuildRequires: qt5-qtsvg-devel -BuildRequires: qt5-qttools-devel -BuildRequires: qt5-qtwebchannel-devel -BuildRequires: qt5-qtxmlpatterns-devel -BuildRequires: qt5-qtwebengine-devel -BuildRequires: qt5-qtwebsockets-devel -BuildRequires: qt5-qtwebchannel-devel -BuildRequires: zlib-devel +BuildRequires: cmake(Qt5Core) +BuildRequires: cmake(Qt5Gui) +BuildRequires: cmake(Qt5Network) +BuildRequires: cmake(Qt5PrintSupport) +BuildRequires: cmake(Qt5Script) +BuildRequires: cmake(Qt5ScriptTools) +BuildRequires: cmake(Qt5Sql) +BuildRequires: cmake(Qt5Svg) +BuildRequires: cmake(Qt5Test) +BuildRequires: cmake(Qt5Widgets) +BuildRequires: cmake(Qt5Xml) -Provides: bundled(sqlite) -Provides: bundled(samtools) -ExclusiveArch: %{ix86} x86_64 +BuildRequires: pkgconfig(gl) +BuildRequires: pkgconfig(glu) +BuildRequires: pkgconfig(sqlite3) +BuildRequires: pkgconfig(xtst) +BuildRequires: pkgconfig(zlib) + +Provides: bundled(samtools) = 0.1.18 %description Unipro UGENE is a cross-platform visual environment for DNA and protein @@ -43,45 +54,67 @@ is a designer for custom bioinformatics workflows. %prep %setup -q +%patch1 -p1 -b .glibc_2_35 +%patch101 -p1 -b .cpuid +%patch102 -p1 -b .sys_mmap +%patch103 -p1 -b .unwind +%patch104 -p1 -b .sse +%patch105 -p1 -b .port +%patch106 -p1 -b .sse_2 +%patch107 -p1 -b .char_bigen -%patch1 -p1 -b .fix-build-againt-qt-5.15 -%patch2 -p1 -b .gcc11 +# Umm... +sed -i.desktop ugene.pri -e '\@desktop@s|etc/share/|etc/shared/|' %build %{qmake_qt5} -r \ - INSTALL_BINDIR=%{_bindir} \ - INSTALL_LIBDIR=%{_libdir} \ - INSTALL_DATADIR=%{_datadir} \ - INSTALL_MANDIR=%{_mandir} \ -%if 0%{?_ugene_with_non_free} - UGENE_WITHOUT_NON_FREE=0 \ -%else - UGENE_WITHOUT_NON_FREE=1 \ -%endif - UGENE_EXCLUDE_LIST_ENABLED=1 + INSTALL_BINDIR=%{_bindir} \ + INSTALL_DATADIR=%{_datadir} \ + INSTALL_LIBDIR=%{_libdir} \ + INSTALL_MANDIR=%{_mandir} \ + UGENE_EXCLUDE_LIST_ENABLED=1 \ + UGENE_USE_BUNDLED_SQLITE=0 \ + UGENE_USE_BUNDLED_ZLIB=0 \ + UGENE_WITHOUT_NON_FREE=1 \ + %{nil} - -make %{?_smp_mflags} +%make_build -k %install -make install INSTALL_ROOT=%{buildroot} +make install \ + INSTALL_ROOT=%{buildroot} \ + INSTALL="install -p" \ + %{nil} %check desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %files -%{!?_licensedir:%global license %%doc} -%license LICENSE.txt LICENSE.3rd_party.txt -%{_bindir}/* -%{_libdir}/%{name}/ +%license LICENSE.txt +%license LICENSE.3rd_party.txt + +%{_bindir}/%{name} + +%dir %{_libdir}/%{name}/ +%{_libdir}/%{name}/lib*.so +%{_libdir}/%{name}/plugins/ +%{_libdir}/%{name}/%{name}* +%{_libdir}/%{name}/plugins_checker + +%dir %{_datadir}/%{name}/ +%{_datadir}/%{name}/data/ + %{_datadir}/applications/%{name}.desktop %{_datadir}/pixmaps/ugene.* %{_datadir}/icons/hicolor/*/*/* + %{_datadir}/mime/packages/*.xml -%{_datadir}/%{name}/ -%{_mandir}/man1/* +%{_mandir}/man1/%{name}.1* %changelog +* Tue Nov 9 2021 Mamoru TASAKA - 41.1-1 +- 41.1 + * Fri Jul 23 2021 Fedora Release Engineering - 34.0-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild From 08375d511de915bfb1961d8c7b19f4b0b80655fe Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 11 Nov 2021 20:50:55 +0900 Subject: [PATCH 013/260] try the latest git --- .gitignore | 2 + create-ugene-git-bare-tarball.sh | 33 ++++ sources | 2 +- ...t-plgins-smith_waterman-nonsse2-arch.patch | 60 +++---- ugene.spec | 157 +++++++++++++++--- ugene.wrapper | 4 + 6 files changed, 208 insertions(+), 50 deletions(-) create mode 100644 create-ugene-git-bare-tarball.sh rename ugene-40.1-plgins-smith_waterman-nonsse2-arch.patch => ugene-40.1-git-plgins-smith_waterman-nonsse2-arch.patch (64%) create mode 100644 ugene.wrapper diff --git a/.gitignore b/.gitignore index f3dfdb7..25727b9 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,5 @@ /ugene-33.0.tar.gz /ugene-34.0.tar.gz /ugene-40.1.tar.gz +/ugene-20211111T1455.tar.gz +/ugene-20211111T2046.tar.gz diff --git a/create-ugene-git-bare-tarball.sh b/create-ugene-git-bare-tarball.sh new file mode 100644 index 0000000..bd4262e --- /dev/null +++ b/create-ugene-git-bare-tarball.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +set -x +set -e + +REPONAME=ugene +GITURL=https://github.com/ugeneunipro/${REPONAME}.git + +DATE=$(date '+%Y%m%d') +TIME=$(date '+%H%M') + +TARNAME=${REPONAME}-${DATE}T${TIME}.tar.gz + +PWDDIR=$(pwd) +TMPDIR=$(mktemp -d /var/tmp/${REPONAME}-XXXXXX) +pushd $TMPDIR + +git clone --depth 30 --mirror $GITURL + +mkdir TMP +pushd TMP +git clone ../${REPONAME}.git +cd ${REPONAME} +git log 2>&1 | head -n 5 +#grep version README.md +echo +popd + +tar czf ${TARNAME} ${REPONAME}.git/ + +cp -p ${TARNAME} $PWDDIR +popd +rm -rf $TMPDIR diff --git a/sources b/sources index be82943..50f362e 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-40.1.tar.gz) = b2e056532a2ecf2a396d9bdd7a44f3af1e3e49d1ab2d95169be5583a4e59b43773d02224987b096fdd48f91568c65dc9fa575702a881b40fdabfdc776cd16af1 +SHA512 (ugene-20211111T2046.tar.gz) = 46368c569c1caf11fdb55a5a14e1e6817ae1fc29596f1e18a3b8853948ac2cea661d1576ba359cf8b5ebcb2eb014a5f925685b4c6de3ea79310cb4f12becbd9e diff --git a/ugene-40.1-plgins-smith_waterman-nonsse2-arch.patch b/ugene-40.1-git-plgins-smith_waterman-nonsse2-arch.patch similarity index 64% rename from ugene-40.1-plgins-smith_waterman-nonsse2-arch.patch rename to ugene-40.1-git-plgins-smith_waterman-nonsse2-arch.patch index 47e48e6..c7d8e27 100644 --- a/ugene-40.1-plgins-smith_waterman-nonsse2-arch.patch +++ b/ugene-40.1-git-plgins-smith_waterman-nonsse2-arch.patch @@ -1,5 +1,5 @@ ---- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp.sse_2 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp 2021-11-09 10:46:44.925720099 +0900 +--- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp.sse_2 2021-11-11 15:42:19.590500062 +0900 ++++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp 2021-11-11 15:42:26.384496818 +0900 @@ -99,9 +99,11 @@ par->registerAlgorithm(new SWPairwiseAlignmentAlgorithm()); regDependedIMPLFromOtherPlugins(); @@ -12,25 +12,25 @@ this->connect(AppContext::getPluginSupport(), SIGNAL(si_allStartUpPluginsLoaded()), SLOT(regDependedIMPLFromOtherPlugins())); } ---- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp.sse_2 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp 2021-11-09 12:00:58.015843958 +0900 -@@ -184,6 +184,7 @@ - sWatermanConfig.resultView), - true)); +--- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp.sse_2 2021-11-11 15:42:19.590500062 +0900 ++++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp 2021-11-11 15:46:26.960369309 +0900 +@@ -181,6 +181,7 @@ + sWatermanConfig.sqnc.left(c.chunkSize * c.nThreads), + sWatermanConfig.resultView); break; +#ifdef __SSE2__ case SW_sse2: - addTaskResource(TaskResourceUsage(RESOURCE_MEMORY, - SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(sWatermanConfig.ptrn, -@@ -194,6 +195,7 @@ - maxScore, - sWatermanConfig.resultView), - true)); + neededRam = SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(sWatermanConfig.ptrn, + sWatermanConfig.sqnc.left(c.chunkSize * c.nThreads), +@@ -189,6 +190,7 @@ + minScore, + maxScore, + sWatermanConfig.resultView); +#endif break; default: assert(0); -@@ -268,7 +270,12 @@ +@@ -267,7 +269,12 @@ SmithWatermanAlgorithm *sw = nullptr; if (algType == SW_sse2) { @@ -43,7 +43,7 @@ } else if (algType == SW_cuda) { #ifdef SW2_BUILD_WITH_CUDA sw = new SmithWatermanAlgorithmCUDA; -@@ -579,7 +586,11 @@ +@@ -581,7 +588,11 @@ SmithWatermanAlgorithm *sw = nullptr; if (algType == SW_sse2) { @@ -55,24 +55,24 @@ } else if (algType == SW_cuda) { #ifdef SW2_BUILD_WITH_CUDA sw = new SmithWatermanAlgorithmCUDA; -@@ -734,6 +745,7 @@ - true)); +@@ -745,6 +756,7 @@ + sqnc->left(c.chunkSize * c.nThreads), + SmithWatermanSettings::MULTIPLE_ALIGNMENT); break; ++#ifdef __SSE2__ case SW_sse2: -+#if defined(__SSE2__) - addTaskResource(TaskResourceUsage(RESOURCE_MEMORY, - SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(*ptrn, - sqnc->left(c.chunkSize * c.nThreads), -@@ -743,6 +755,7 @@ - maxScore, - SmithWatermanSettings::MULTIPLE_ALIGNMENT), - true)); + neededRam = SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(*ptrn, + sqnc->left(c.chunkSize * c.nThreads), +@@ -753,6 +765,7 @@ + minScore, + maxScore, + SmithWatermanSettings::MULTIPLE_ALIGNMENT); +#endif break; default: assert(0); ---- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.sse_2 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp 2021-11-09 10:46:44.926720099 +0900 +--- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.sse_2 2021-11-11 15:42:19.591500062 +0900 ++++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp 2021-11-11 15:42:26.385496818 +0900 @@ -19,6 +19,7 @@ * MA 02110-1301, USA. */ @@ -81,13 +81,13 @@ #include "SmithWatermanAlgorithmSSE2.h" #include #include -@@ -1192,3 +1193,4 @@ +@@ -1210,3 +1211,4 @@ } } // namespace U2 +#endif ---- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h 2021-11-09 10:46:44.926720099 +0900 +--- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2 2021-11-11 15:42:19.592500061 +0900 ++++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h 2021-11-11 15:42:26.385496818 +0900 @@ -22,6 +22,7 @@ #ifndef _SMITHWATERMANALGORITHM_SSE2_H #define _SMITHWATERMANALGORITHM_SSE2_H diff --git a/ugene.spec b/ugene.spec index 8a30fb5..838bc57 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,15 +1,56 @@ +%global gitdate 20211110 +%global gitcommit 2c40af7779f076c6a5e25a72f40842cbe88eb48b +%global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) +%global git_version D%{gitdate}git%{shortcommit} + +%global tarballdate 20211111 +%global tarballtime 2046 + +%global use_release 0 +%global use_gitbare 1 + +%if 0%{?use_gitbare} < 1 +# force +%global use_release 1 +%endif + +%if 0%{?use_release} >= 1 +%global GIT true +%else +%global GIT git +%endif + +%global mainrel 1.1 +%undefine prever + +%if 0%{?use_release} >= 1 +%global fedorarel %{?prever:0.}%{mainrel}%{?prever:.%{prerpmver}} +%endif +%if 0%{?use_gitbare} >= 1 +%global fedorarel %{mainrel}.%{git_version} +%endif + + Name: ugene Summary: Integrated bioinformatics toolkit Version: 40.1 -Release: 1%{?dist} +Release: %{fedorarel}%{?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 License: GPLv2+ and GPLv2 URL: http://ugene.net +%if 0%{?use_release} >= 1 Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz +%endif +%if 0%{?use_gitbare} >= 1 +Source0: %{name}-%{tarballdate}T%{tarballtime}.tar.gz +%endif +Source1: create-%{name}-git-bare-tarball.sh +# This is not installed +Source2: ugene.wrapper # Should be sent to be upstream Patch1: ugene-40.1-glibc-2_35.patch # Currently distro-specific @@ -18,13 +59,17 @@ Patch102: ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch Patch104: ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch -Patch106: ugene-40.1-plgins-smith_waterman-nonsse2-arch.patch +Patch106: ugene-40.1-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch BuildRequires: make BuildRequires: gcc-c++ BuildRequires: desktop-file-utils +%if 0%{?use_gitbare} >= 1 +BuildRequires: %{_bindir}/git +%endif + BuildRequires: cmake(Qt5Core) BuildRequires: cmake(Qt5Gui) BuildRequires: cmake(Qt5Network) @@ -53,27 +98,48 @@ complex analysis of the genomic data. One of the main features of UGENE is a designer for custom bioinformatics workflows. %prep +%if 0%{?use_release} >= 1 %setup -q -%patch1 -p1 -b .glibc_2_35 -%patch101 -p1 -b .cpuid -%patch102 -p1 -b .sys_mmap -%patch103 -p1 -b .unwind -%patch104 -p1 -b .sse -%patch105 -p1 -b .port -%patch106 -p1 -b .sse_2 -%patch107 -p1 -b .char_bigen - # Umm... sed -i.desktop ugene.pri -e '\@desktop@s|etc/share/|etc/shared/|' +%endif + +%if 0%{?use_gitbare} >= 1 +%setup -q -c -T -a 0 +git clone ./%{name}.git/ +cd %{name} +cp -a [A-Z]* .. + +git checkout -b %{version}-fedora %{gitcommit} +git config user.name "%{name} Fedora maintainer" +git config user.email "%{name}-maintainers@fedoraproject.org" +%endif + +%patch1 -p1 -b .glibc_2_35 + %GIT commit -m "Build fix for glibc 2.35 change" -a +%patch101 -p1 -b .cpuid + %GIT commit -m "ugenem: support architecture not supporting cpuid" -a +%patch102 -p1 -b .sys_mmap + %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a +%patch103 -p1 -b .unwind + %GIT commit -m "libs_3rdparty/breakpad: workaround for arch not supporting unwind" -a +%patch104 -p1 -b .sse + %GIT commit -m "plugins_3rdparty/hmm2: support architecture not supporting SSE2" -a +%patch105 -p1 -b .port + %GIT commit -m "libs_3rdparty/breakpad: workaround for arch not ported by the upstream" -a +%patch106 -p1 -b .sse_2 + %GIT commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a +%patch107 -p1 -b .char_bigen + %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a %build +%if 0%{?use_gitbare} >= 1 +cd %{name} +%endif %{qmake_qt5} -r \ - INSTALL_BINDIR=%{_bindir} \ - INSTALL_DATADIR=%{_datadir} \ - INSTALL_LIBDIR=%{_libdir} \ - INSTALL_MANDIR=%{_mandir} \ + PREFIX=%{_libdir}/%{name} \ UGENE_EXCLUDE_LIST_ENABLED=1 \ - UGENE_USE_BUNDLED_SQLITE=0 \ + UGENE_USE_SYSTEM_SQLITE=1 \ UGENE_USE_BUNDLED_ZLIB=0 \ UGENE_WITHOUT_NON_FREE=1 \ %{nil} @@ -81,11 +147,55 @@ sed -i.desktop ugene.pri -e '\@desktop@s|etc/share/|etc/shared/|' %make_build -k %install +LIBAPPDIR=%{_libdir}/%{name} + +%if 0%{?use_gitbare} >= 1 +cd %{name} +%endif make install \ INSTALL_ROOT=%{buildroot} \ INSTALL="install -p" \ %{nil} +# Some needed files are not installed..... +mkdir -p %{buildroot}$LIBAPPDIR +cp -a src/_release/* %{buildroot}$LIBAPPDIR +rm -f %{buildroot}$LIBAPPDIR/*.a + +# 1. manually move files... +pushd %{buildroot} +rm -f ./$LIBAPPDIR/LICENSE* + +# 1-0 bindir +mkdir -p ./%{_bindir} +install -cpm 0755 %{SOURCE2} ./%{_bindir}/%{name} + +# 1-1 data files +mkdir -p ./%{_datadir}/%{name}/ +mv ./$LIBAPPDIR/data ./%{_datadir}/%{name} +ln -sf ../../../%{_datadir}/%{name} ./$LIBAPPDIR/data + +# 1-11 hicolor +mkdir -p ./%{_datadir}/hicolor/32x32/mimetypes/ +mv ./$LIBAPPDIR/application-x-ugene-ext.png ./%{_datadir}/hicolor/32x32/mimetypes/ + +# 1-12 mime +mkdir -p ./%{_datadir}/mime/packages +mv ./$LIBAPPDIR/application-x-ugene.xml ./%{_datadir}/mime/packages + +# 1-13 man file +mkdir -p ./%{_mandir}/man1 +mv ./$LIBAPPDIR/%{name}.1* ./%{_mandir}/man1 + +# 1-14 desktop files +mkdir -p ./%{_datadir}/applications/ +mv ./$LIBAPPDIR/%{name}.desktop ./%{_datadir}/applications/ + +# 1-15 icons +mkdir -p ./%{_datadir}/pixmaps +mv ./$LIBAPPDIR/%{name}.{png,xpm} ./%{_datadir}/pixmaps +popd + %check desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop @@ -97,16 +207,25 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %dir %{_libdir}/%{name}/ %{_libdir}/%{name}/lib*.so -%{_libdir}/%{name}/plugins/ -%{_libdir}/%{name}/%{name}* + +%dir %{_libdir}/%{name}/plugins/ +%{_libdir}/%{name}/plugins/*.license +%{_libdir}/%{name}/plugins/*.plugin +%{_libdir}/%{name}/plugins/lib*.so + +%{_libdir}/%{name}/%{name} +%{_libdir}/%{name}/%{name}cl +%{_libdir}/%{name}/%{name}m +%{_libdir}/%{name}/%{name}ui %{_libdir}/%{name}/plugins_checker %dir %{_datadir}/%{name}/ %{_datadir}/%{name}/data/ +%{_libdir}/%{name}/data %{_datadir}/applications/%{name}.desktop %{_datadir}/pixmaps/ugene.* -%{_datadir}/icons/hicolor/*/*/* +%{_datadir}/hicolor/32x32/mimetypes/application-x-ugene-ext.png %{_datadir}/mime/packages/*.xml %{_mandir}/man1/%{name}.1* diff --git a/ugene.wrapper b/ugene.wrapper new file mode 100644 index 0000000..00f8788 --- /dev/null +++ b/ugene.wrapper @@ -0,0 +1,4 @@ +#!/usr/bin/bash +LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/ugene +export LD_LIBRARY_PATH +/usr/lib64/ugene/ugene "$@" From 1ec64ca57f3184fd38715b9387b15cb52e52c9ac Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 13 Nov 2021 20:06:15 +0900 Subject: [PATCH 014/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 8 ++++---- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index 25727b9..d69d851 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ /ugene-40.1.tar.gz /ugene-20211111T1455.tar.gz /ugene-20211111T2046.tar.gz +/ugene-20211113T2002.tar.gz diff --git a/sources b/sources index 50f362e..a5a8b78 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-20211111T2046.tar.gz) = 46368c569c1caf11fdb55a5a14e1e6817ae1fc29596f1e18a3b8853948ac2cea661d1576ba359cf8b5ebcb2eb014a5f925685b4c6de3ea79310cb4f12becbd9e +SHA512 (ugene-20211113T2002.tar.gz) = 3819479abd3a1686496d0740705a8763cbb27c96af4bb817ecdbc71c1f3752bf718d504d13670f5511cd5a6038369299db466153183b00b899fcbc305168af38 diff --git a/ugene.spec b/ugene.spec index 838bc57..f6fac53 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,10 +1,10 @@ -%global gitdate 20211110 -%global gitcommit 2c40af7779f076c6a5e25a72f40842cbe88eb48b +%global gitdate 20211113 +%global gitcommit 2b64290e485a85c5c3f7fcfa5275a2f51d1d507b %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211111 -%global tarballtime 2046 +%global tarballdate 20211113 +%global tarballtime 2002 %global use_release 0 %global use_gitbare 1 From 24b3104d3c93af9e3d4e9d61b419b345811568b8 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 14 Nov 2021 01:12:53 +0900 Subject: [PATCH 015/260] fix path --- ugene.spec | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ugene.spec b/ugene.spec index f6fac53..2d81c1b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -176,8 +176,8 @@ mv ./$LIBAPPDIR/data ./%{_datadir}/%{name} ln -sf ../../../%{_datadir}/%{name} ./$LIBAPPDIR/data # 1-11 hicolor -mkdir -p ./%{_datadir}/hicolor/32x32/mimetypes/ -mv ./$LIBAPPDIR/application-x-ugene-ext.png ./%{_datadir}/hicolor/32x32/mimetypes/ +mkdir -p ./%{_datadir}/icons/hicolor/32x32/mimetypes/ +mv ./$LIBAPPDIR/application-x-ugene-ext.png ./%{_datadir}/icons/hicolor/32x32/mimetypes/ # 1-12 mime mkdir -p ./%{_datadir}/mime/packages @@ -225,7 +225,7 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_datadir}/applications/%{name}.desktop %{_datadir}/pixmaps/ugene.* -%{_datadir}/hicolor/32x32/mimetypes/application-x-ugene-ext.png +%{_datadir}/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png %{_datadir}/mime/packages/*.xml %{_mandir}/man1/%{name}.1* From 07ffe0ec20a39fb3c066284f48a8c33e2e6e3c2c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 14 Nov 2021 21:26:46 +0900 Subject: [PATCH 016/260] remove nonfree code from git history of source code --- .gitignore | 1 + create-ugene-git-bare-tarball.sh | 20 ++++++++++++++++---- sources | 2 +- ugene.spec | 14 ++++++++++---- 4 files changed, 28 insertions(+), 9 deletions(-) diff --git a/.gitignore b/.gitignore index d69d851..5060444 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ /ugene-20211111T1455.tar.gz /ugene-20211111T2046.tar.gz /ugene-20211113T2002.tar.gz +/ugene-20211114T2118.tar.gz diff --git a/create-ugene-git-bare-tarball.sh b/create-ugene-git-bare-tarball.sh index bd4262e..3429be4 100644 --- a/create-ugene-git-bare-tarball.sh +++ b/create-ugene-git-bare-tarball.sh @@ -17,13 +17,25 @@ pushd $TMPDIR git clone --depth 30 --mirror $GITURL -mkdir TMP -pushd TMP -git clone ../${REPONAME}.git -cd ${REPONAME} +pushd ${REPONAME}.git + git log 2>&1 | head -n 5 #grep version README.md echo + +# remove non-free part +for NONFREE in \ + src/plugins_3rdparty/psipred +do + env FILTER_BRANCH_SQUELCH_WARNING=1 \ + git filter-branch --index-filter "git rm -r --cached --ignore-unmatch $NONFREE" HEAD +done + +# And again show git head info +git log 2>&1 | head -n 5 +#grep version README.md +echo + popd tar czf ${TARNAME} ${REPONAME}.git/ diff --git a/sources b/sources index a5a8b78..5a55920 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-20211113T2002.tar.gz) = 3819479abd3a1686496d0740705a8763cbb27c96af4bb817ecdbc71c1f3752bf718d504d13670f5511cd5a6038369299db466153183b00b899fcbc305168af38 +SHA512 (ugene-20211114T2118.tar.gz) = d69021ef9fb8b12cbb7e3274ce1e23095d621e748ef50ba6d4ff6c08ff55c7449f884650ed259cfddf52c8429125002562e028930e3fecc7d50dbf1e8b69cad5 diff --git a/ugene.spec b/ugene.spec index 2d81c1b..c06b2aa 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,10 +1,12 @@ %global gitdate 20211113 %global gitcommit 2b64290e485a85c5c3f7fcfa5275a2f51d1d507b +# New git commit with non-free part using "git filter-branch" +%global gitcommit_free f5456f8c1719d9873c4eb9b86582e818bcc15905 %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211113 -%global tarballtime 2002 +%global tarballdate 20211114 +%global tarballtime 2118 %global use_release 0 %global use_gitbare 1 @@ -20,7 +22,7 @@ %global GIT git %endif -%global mainrel 1.1 +%global mainrel 1.2 %undefine prever %if 0%{?use_release} >= 1 @@ -110,7 +112,7 @@ git clone ./%{name}.git/ cd %{name} cp -a [A-Z]* .. -git checkout -b %{version}-fedora %{gitcommit} +git checkout -b %{version}-fedora %{gitcommit_free} git config user.name "%{name} Fedora maintainer" git config user.email "%{name}-maintainers@fedoraproject.org" %endif @@ -132,6 +134,10 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %patch107 -p1 -b .char_bigen %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a +sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' +sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d' + %GIT commit -m "remove nonfree code" -a + %build %if 0%{?use_gitbare} >= 1 cd %{name} From db4cd409b8877fba7b4256b947a01c99db37e865 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 15 Nov 2021 08:26:46 +0900 Subject: [PATCH 017/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 5060444..915adbe 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ /ugene-20211111T2046.tar.gz /ugene-20211113T2002.tar.gz /ugene-20211114T2118.tar.gz +/ugene-20211115T0821.tar.gz diff --git a/sources b/sources index 5a55920..8085605 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-20211114T2118.tar.gz) = d69021ef9fb8b12cbb7e3274ce1e23095d621e748ef50ba6d4ff6c08ff55c7449f884650ed259cfddf52c8429125002562e028930e3fecc7d50dbf1e8b69cad5 +SHA512 (ugene-20211115T0821.tar.gz) = bf3911e85168252bb215a0543a831f09a5d28bfc36a6775858dc887800e98f44df3a077ccd15761f3f4174a50cfe6d7655427cf2f03597691810b5075da2f77a diff --git a/ugene.spec b/ugene.spec index c06b2aa..1e33250 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,12 +1,12 @@ -%global gitdate 20211113 -%global gitcommit 2b64290e485a85c5c3f7fcfa5275a2f51d1d507b +%global gitdate 20211114 +%global gitcommit 5e36f2c719850a2bcc0fb5c8bc79cf72f082c337 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free f5456f8c1719d9873c4eb9b86582e818bcc15905 +%global gitcommit_free 852060b860cf2c9ad6c9a702c3cd77b1da2af446 %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211114 -%global tarballtime 2118 +%global tarballdate 20211115 +%global tarballtime 0821 %global use_release 0 %global use_gitbare 1 From 61bfff4d1ad8c8db594699be2e5ca98bb07723a1 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 15 Nov 2021 19:45:18 +0900 Subject: [PATCH 018/260] update to the latest git --- .gitignore | 1 + create-ugene-git-bare-tarball.sh | 8 ++++++-- sources | 2 +- ugene.spec | 8 ++++---- 4 files changed, 12 insertions(+), 7 deletions(-) diff --git a/.gitignore b/.gitignore index 915adbe..8bd35f9 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ /ugene-20211113T2002.tar.gz /ugene-20211114T2118.tar.gz /ugene-20211115T0821.tar.gz +/ugene-20211115T1940.tar.gz diff --git a/create-ugene-git-bare-tarball.sh b/create-ugene-git-bare-tarball.sh index 3429be4..551b1fd 100644 --- a/create-ugene-git-bare-tarball.sh +++ b/create-ugene-git-bare-tarball.sh @@ -19,9 +19,8 @@ git clone --depth 30 --mirror $GITURL pushd ${REPONAME}.git -git log 2>&1 | head -n 5 +git log 2>&1 | head -n 5 > git-log-orig.txt #grep version README.md -echo # remove non-free part for NONFREE in \ @@ -36,6 +35,11 @@ git log 2>&1 | head -n 5 #grep version README.md echo +# Here again show original git head info +cat git-log-orig.txt +echo +rm -f git-log-orig.txt + popd tar czf ${TARNAME} ${REPONAME}.git/ diff --git a/sources b/sources index 8085605..ccedb77 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-20211115T0821.tar.gz) = bf3911e85168252bb215a0543a831f09a5d28bfc36a6775858dc887800e98f44df3a077ccd15761f3f4174a50cfe6d7655427cf2f03597691810b5075da2f77a +SHA512 (ugene-20211115T1940.tar.gz) = f3e13251a9a6c4d7866e8607b30bd7c0ae0aee8447ca6c39e9869e8ccc01a065b78dbdd5c422ecb1a4fcd4f67bf1a95b574812193884a1ed5715d542d4aeb95f diff --git a/ugene.spec b/ugene.spec index 1e33250..0e94588 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,12 +1,12 @@ -%global gitdate 20211114 -%global gitcommit 5e36f2c719850a2bcc0fb5c8bc79cf72f082c337 +%global gitdate 20211115 +%global gitcommit fdce3d0f8ade86c91f5bf136dc199f01daf3d642 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 852060b860cf2c9ad6c9a702c3cd77b1da2af446 +%global gitcommit_free ea1169286cdd8a90eea84acf6a1ebd28a5d31db5 %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} %global tarballdate 20211115 -%global tarballtime 0821 +%global tarballtime 1940 %global use_release 0 %global use_gitbare 1 From 864386bfbb0693c2c298b98289553fa5b6d079f0 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 16 Nov 2021 08:39:46 +0900 Subject: [PATCH 019/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 8bd35f9..0129447 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ /ugene-20211114T2118.tar.gz /ugene-20211115T0821.tar.gz /ugene-20211115T1940.tar.gz +/ugene-20211116T0835.tar.gz diff --git a/sources b/sources index ccedb77..420deaf 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-20211115T1940.tar.gz) = f3e13251a9a6c4d7866e8607b30bd7c0ae0aee8447ca6c39e9869e8ccc01a065b78dbdd5c422ecb1a4fcd4f67bf1a95b574812193884a1ed5715d542d4aeb95f +SHA512 (ugene-20211116T0835.tar.gz) = ed3e779c65b2383e22309624b1fca998d3e22cb989f76e1f4019f73329cff76e056a5394ef7a00bcf81b0917efa12e3ee8077ac0e6a82f55ccd0fae830e04782 diff --git a/ugene.spec b/ugene.spec index 0e94588..7512866 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,12 +1,12 @@ %global gitdate 20211115 -%global gitcommit fdce3d0f8ade86c91f5bf136dc199f01daf3d642 +%global gitcommit 0dd16f77a865d4b241b95a5ed003e6acea0d0f80 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free ea1169286cdd8a90eea84acf6a1ebd28a5d31db5 +%global gitcommit_free 6eb5fb1a05492f231d3ac07c8bea20f062297e73 %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211115 -%global tarballtime 1940 +%global tarballdate 20211116 +%global tarballtime 0835 %global use_release 0 %global use_gitbare 1 @@ -22,7 +22,7 @@ %global GIT git %endif -%global mainrel 1.2 +%global mainrel 1.3 %undefine prever %if 0%{?use_release} >= 1 From 91506d38cccf971659f1c174315b86d2b1e0b0c9 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 17 Nov 2021 08:46:55 +0900 Subject: [PATCH 020/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 0129447..588fdef 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,4 @@ /ugene-20211115T0821.tar.gz /ugene-20211115T1940.tar.gz /ugene-20211116T0835.tar.gz +/ugene-20211117T0834.tar.gz diff --git a/sources b/sources index 420deaf..7ba09b6 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-20211116T0835.tar.gz) = ed3e779c65b2383e22309624b1fca998d3e22cb989f76e1f4019f73329cff76e056a5394ef7a00bcf81b0917efa12e3ee8077ac0e6a82f55ccd0fae830e04782 +SHA512 (ugene-20211117T0834.tar.gz) = c74a36fb8c23fb3cc3e1bd7a574334591d2e7bfac3d017557d44538250b5ef6de3dac7d519b57800f7693921c2267bd0eca4ad5dad41174d30c2ce025aeb63ff diff --git a/ugene.spec b/ugene.spec index 7512866..672702f 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,12 +1,12 @@ -%global gitdate 20211115 -%global gitcommit 0dd16f77a865d4b241b95a5ed003e6acea0d0f80 +%global gitdate 20211117 +%global gitcommit 3056f18b678421555a7d27b8f1a0ef7c0abab4ff # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 6eb5fb1a05492f231d3ac07c8bea20f062297e73 +%global gitcommit_free dfe5286c876688a471bcd91ad21ca3cf2f6aa0a3 %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211116 -%global tarballtime 0835 +%global tarballdate 20211117 +%global tarballtime 0834 %global use_release 0 %global use_gitbare 1 From 8e9973a623f1528147b5bdd75ec507c3bca3ecfd Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 17 Nov 2021 16:27:54 +0900 Subject: [PATCH 021/260] rename --- .gitignore | 1 + create-ugene-git-bare-tarball.sh | 2 +- sources | 2 +- ugene.spec | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 588fdef..147f7dc 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,4 @@ /ugene-20211115T1940.tar.gz /ugene-20211116T0835.tar.gz /ugene-20211117T0834.tar.gz +/ugene-free-20211117T0834.tar.gz diff --git a/create-ugene-git-bare-tarball.sh b/create-ugene-git-bare-tarball.sh index 551b1fd..3ed73f6 100644 --- a/create-ugene-git-bare-tarball.sh +++ b/create-ugene-git-bare-tarball.sh @@ -9,7 +9,7 @@ GITURL=https://github.com/ugeneunipro/${REPONAME}.git DATE=$(date '+%Y%m%d') TIME=$(date '+%H%M') -TARNAME=${REPONAME}-${DATE}T${TIME}.tar.gz +TARNAME=${REPONAME}-clean-${DATE}T${TIME}.tar.gz PWDDIR=$(pwd) TMPDIR=$(mktemp -d /var/tmp/${REPONAME}-XXXXXX) diff --git a/sources b/sources index 7ba09b6..6447d03 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-20211117T0834.tar.gz) = c74a36fb8c23fb3cc3e1bd7a574334591d2e7bfac3d017557d44538250b5ef6de3dac7d519b57800f7693921c2267bd0eca4ad5dad41174d30c2ce025aeb63ff +SHA512 (ugene-free-20211117T0834.tar.gz) = c74a36fb8c23fb3cc3e1bd7a574334591d2e7bfac3d017557d44538250b5ef6de3dac7d519b57800f7693921c2267bd0eca4ad5dad41174d30c2ce025aeb63ff diff --git a/ugene.spec b/ugene.spec index 672702f..31a9562 100644 --- a/ugene.spec +++ b/ugene.spec @@ -48,7 +48,7 @@ URL: http://ugene.net Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz %endif %if 0%{?use_gitbare} >= 1 -Source0: %{name}-%{tarballdate}T%{tarballtime}.tar.gz +Source0: %{name}-clean-%{tarballdate}T%{tarballtime}.tar.gz %endif Source1: create-%{name}-git-bare-tarball.sh # This is not installed From 46298909150f72fb9c96019b1ce45fa7c8a0965e Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 17 Nov 2021 16:56:19 +0900 Subject: [PATCH 022/260] Surely remove nonfree code from tarball --- .gitignore | 1 + sources | 2 +- ugene.spec | 11 +++++++++-- 3 files changed, 11 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index f3dfdb7..42fe677 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ /ugene-33.0.tar.gz /ugene-34.0.tar.gz /ugene-40.1.tar.gz +/ugene-free-40.1.tar.gz diff --git a/sources b/sources index be82943..80069ac 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-40.1.tar.gz) = b2e056532a2ecf2a396d9bdd7a44f3af1e3e49d1ab2d95169be5583a4e59b43773d02224987b096fdd48f91568c65dc9fa575702a881b40fdabfdc776cd16af1 +SHA512 (ugene-free-40.1.tar.gz) = 1158142a82971d60f72f5c232d9795f549f52c2ed6fe5470d7a91ebc2cb74945a45a454ee21314be193d00ba36b1ef11f330f8c3a85cdc85eb5215ff5fd1386b diff --git a/ugene.spec b/ugene.spec index 8a30fb5..1693525 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,14 +2,18 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 40.1 -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 License: GPLv2+ and GPLv2 URL: http://ugene.net -Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz +#Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz +# Removing non-free part +Source0: %{name}-free-%{version}.tar.gz +# Source0 is created by # env VERSION=%%{version} source ./%{SOURCE1} +Source1: create-ugene-free-tarball.sh # Should be sent to be upstream Patch1: ugene-40.1-glibc-2_35.patch # Currently distro-specific @@ -112,6 +116,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Wed Nov 17 2021 Mamoru TASAKA - 41.1-2 +- Surely remove nonfree code from tarball + * Tue Nov 9 2021 Mamoru TASAKA - 41.1-1 - 41.1 From 6dc87c745865285a43a83ae1101161028dfb2cc5 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 17 Nov 2021 16:57:37 +0900 Subject: [PATCH 023/260] add script --- create-ugene-free-tarball.sh | 46 ++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 create-ugene-free-tarball.sh diff --git a/create-ugene-free-tarball.sh b/create-ugene-free-tarball.sh new file mode 100644 index 0000000..b07b9af --- /dev/null +++ b/create-ugene-free-tarball.sh @@ -0,0 +1,46 @@ +#!/bin/bash + +set -e +set -x + +umask 0022 + +VERSION=${VERSION:-40.1} +FEDORA_TAR_VERSION=${VERSION} + +REPONAME=ugene +TARNAME=${REPONAME} + +SOURCE_TOP_URL=https://github.com/ugeneunipro/${REPONAME}/archive/ + +CURRENT_DIR=$(pwd) +TMPDIR=$(mktemp -d /var/tmp/${REPONAME}-XXXXXX) + + +pushd $TMPDIR + +TARBALL_NAME=${TARNAME}-${FEDORA_TAR_VERSION}.tar.gz +SOURCE_URL=${SOURCE_TOP_URL}/${VERSION}/${TARBALL_NAME} + +wget -N ${SOURCE_URL} +rm -rf ${TARNAME}-${VERSION} +tar xzf ${TARBALL_NAME} + +pushd ${TARNAME}-${VERSION} + +echo "Removing nonfree code" +for NONFREE in \ + src/plugins_3rdparty/psipred +do + rm -rf $NONFREE +done + +echo "done" +popd + +tar czf ${TARNAME}-free-${FEDORA_TAR_VERSION}.tar.gz ${TARNAME}-${VERSION}/ +mv ${TARNAME}-free-${FEDORA_TAR_VERSION}.tar.gz ${CURRENT_DIR}/ + +popd +rm -rf $TMPDIR + From 7cd42de20f9d1d108678f82b2ac7db269a183fb5 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 18 Nov 2021 08:00:43 +0900 Subject: [PATCH 024/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 8 ++++---- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index 055e9d5..24abf94 100644 --- a/.gitignore +++ b/.gitignore @@ -12,3 +12,4 @@ /ugene-20211116T0835.tar.gz /ugene-20211117T0834.tar.gz /ugene-free-20211117T0834.tar.gz +/ugene-free-20211118T0755.tar.gz diff --git a/sources b/sources index 6447d03..418f538 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211117T0834.tar.gz) = c74a36fb8c23fb3cc3e1bd7a574334591d2e7bfac3d017557d44538250b5ef6de3dac7d519b57800f7693921c2267bd0eca4ad5dad41174d30c2ce025aeb63ff +SHA512 (ugene-free-20211118T0755.tar.gz) = eee6898bea7029e79aa4257aa6d42710e8cc3d44f40c3eaa6006274b3dab8b965fc9a492a5e3895c4633638d5af906607f521da27816b71d39b1d718a952920b diff --git a/ugene.spec b/ugene.spec index 02a4eb9..d95a01d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,12 +1,12 @@ %global gitdate 20211117 -%global gitcommit 3056f18b678421555a7d27b8f1a0ef7c0abab4ff +%global gitcommit e737afc40da349754ea01235486e3dbe1103b29e # New git commit with non-free part using "git filter-branch" -%global gitcommit_free dfe5286c876688a471bcd91ad21ca3cf2f6aa0a3 +%global gitcommit_free 15dd186c64848fa12f6aacd14ef68e113f7fba09 %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211117 -%global tarballtime 0834 +%global tarballdate 20211118 +%global tarballtime 0755 %global use_release 0 %global use_gitbare 1 From 33ed1b5f8e8129bd2ef22fe3e2decaf051c9c217 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 18 Nov 2021 10:37:47 +0900 Subject: [PATCH 025/260] add source --- create-ugene-free-tarball.sh | 46 ++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 create-ugene-free-tarball.sh diff --git a/create-ugene-free-tarball.sh b/create-ugene-free-tarball.sh new file mode 100644 index 0000000..b07b9af --- /dev/null +++ b/create-ugene-free-tarball.sh @@ -0,0 +1,46 @@ +#!/bin/bash + +set -e +set -x + +umask 0022 + +VERSION=${VERSION:-40.1} +FEDORA_TAR_VERSION=${VERSION} + +REPONAME=ugene +TARNAME=${REPONAME} + +SOURCE_TOP_URL=https://github.com/ugeneunipro/${REPONAME}/archive/ + +CURRENT_DIR=$(pwd) +TMPDIR=$(mktemp -d /var/tmp/${REPONAME}-XXXXXX) + + +pushd $TMPDIR + +TARBALL_NAME=${TARNAME}-${FEDORA_TAR_VERSION}.tar.gz +SOURCE_URL=${SOURCE_TOP_URL}/${VERSION}/${TARBALL_NAME} + +wget -N ${SOURCE_URL} +rm -rf ${TARNAME}-${VERSION} +tar xzf ${TARBALL_NAME} + +pushd ${TARNAME}-${VERSION} + +echo "Removing nonfree code" +for NONFREE in \ + src/plugins_3rdparty/psipred +do + rm -rf $NONFREE +done + +echo "done" +popd + +tar czf ${TARNAME}-free-${FEDORA_TAR_VERSION}.tar.gz ${TARNAME}-${VERSION}/ +mv ${TARNAME}-free-${FEDORA_TAR_VERSION}.tar.gz ${CURRENT_DIR}/ + +popd +rm -rf $TMPDIR + From d7ecad62c75f080d1ae19756c77691fbd1424ec1 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 19 Nov 2021 07:44:43 +0900 Subject: [PATCH 026/260] update to the latest git --- .gitignore | 1 + create-ugene-git-bare-tarball.sh | 6 +++--- sources | 2 +- ugene.spec | 12 ++++++------ 4 files changed, 11 insertions(+), 10 deletions(-) diff --git a/.gitignore b/.gitignore index 24abf94..2a4290a 100644 --- a/.gitignore +++ b/.gitignore @@ -13,3 +13,4 @@ /ugene-20211117T0834.tar.gz /ugene-free-20211117T0834.tar.gz /ugene-free-20211118T0755.tar.gz +/ugene-free-20211119T0709.tar.gz diff --git a/create-ugene-git-bare-tarball.sh b/create-ugene-git-bare-tarball.sh index 3dac851..05f5602 100644 --- a/create-ugene-git-bare-tarball.sh +++ b/create-ugene-git-bare-tarball.sh @@ -15,7 +15,7 @@ PWDDIR=$(pwd) TMPDIR=$(mktemp -d /var/tmp/${REPONAME}-XXXXXX) pushd $TMPDIR -git clone --depth 30 --mirror $GITURL +git clone --depth 30 --no-single-branch --mirror $GITURL pushd ${REPONAME}.git @@ -27,7 +27,7 @@ for NONFREE in \ src/plugins_3rdparty/psipred do env FILTER_BRANCH_SQUELCH_WARNING=1 \ - git filter-branch --index-filter "git rm -r --cached --ignore-unmatch $NONFREE" HEAD + git filter-branch --index-filter "git rm -r --cached --ignore-unmatch $NONFREE" -- --all done # And again show git head info @@ -35,7 +35,7 @@ git log 2>&1 | head -n 5 #grep version README.md echo -# Here again show original git head info +# Here again show original git head infob cat git-log-orig.txt echo rm -f git-log-orig.txt diff --git a/sources b/sources index 418f538..843230d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211118T0755.tar.gz) = eee6898bea7029e79aa4257aa6d42710e8cc3d44f40c3eaa6006274b3dab8b965fc9a492a5e3895c4633638d5af906607f521da27816b71d39b1d718a952920b +SHA512 (ugene-free-20211119T0709.tar.gz) = 20c7d7bbd3e640a00a526d8bb19c8f6df8cc319504dd34bf745d64af25ae34020fe9c2a44f164001dd6afecd9aab2a695e95580625f9a939009b92cab5e3c5c1 diff --git a/ugene.spec b/ugene.spec index d95a01d..a40435c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,12 +1,12 @@ %global gitdate 20211117 -%global gitcommit e737afc40da349754ea01235486e3dbe1103b29e +%global gitcommit 2d776cc668bc5019452e25ecc330c88093e75c48 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 15dd186c64848fa12f6aacd14ef68e113f7fba09 +%global gitcommit_free 02c04596cd6543ab44cc212ac1b383f825998b0e %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211118 -%global tarballtime 0755 +%global tarballdate 20211119 +%global tarballtime 0709 %global use_release 0 %global use_gitbare 1 @@ -22,7 +22,7 @@ %global GIT git %endif -%global mainrel 2.1 +%global mainrel 0.1 %undefine prever %if 0%{?use_release} >= 1 @@ -36,7 +36,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 40.1 +Version: 41.0 Release: %{fedorarel}%{?dist} #The entire source code is GPLv2+ except: From 882cae396be02320a93a38ffabbda0bc125a66e5 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 26 Nov 2021 09:39:50 +0900 Subject: [PATCH 027/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 17 +++++++++++++++-- 3 files changed, 17 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 2a4290a..8c18541 100644 --- a/.gitignore +++ b/.gitignore @@ -14,3 +14,4 @@ /ugene-free-20211117T0834.tar.gz /ugene-free-20211118T0755.tar.gz /ugene-free-20211119T0709.tar.gz +/ugene-free-20211126T0914.tar.gz diff --git a/sources b/sources index 843230d..b032795 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211119T0709.tar.gz) = 20c7d7bbd3e640a00a526d8bb19c8f6df8cc319504dd34bf745d64af25ae34020fe9c2a44f164001dd6afecd9aab2a695e95580625f9a939009b92cab5e3c5c1 +SHA512 (ugene-free-20211126T0914.tar.gz) = 605c581c5862da91f2705c3d036d56b98ddfbc71877b9b8939f76c1c3b22cafd74c6d5052bcb4650299e0c4d8a352a3505281aa0ebdedc5d99993641d10ba121 diff --git a/ugene.spec b/ugene.spec index a40435c..ce34b5b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -1,12 +1,25 @@ +%global use_release_branch 0 + +%if 0%{?use_release_branch} < 1 +# master +%global gitdate 20211125 +%global gitcommit 18d20612d4d2b6deb0085200ee91fd1c981aa983 +# New git commit with non-free part using "git filter-branch" +%global gitcommit_free c6cad806c4ce6b7531f4455c06e6bbf91ef509e0 +%else +# currently 41.0 branch %global gitdate 20211117 %global gitcommit 2d776cc668bc5019452e25ecc330c88093e75c48 # New git commit with non-free part using "git filter-branch" %global gitcommit_free 02c04596cd6543ab44cc212ac1b383f825998b0e +%endif + + %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211119 -%global tarballtime 0709 +%global tarballdate 20211126 +%global tarballtime 0914 %global use_release 0 %global use_gitbare 1 From 31cf127e040d4e92338a592080fe7de375f19538 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 27 Nov 2021 22:31:32 +0900 Subject: [PATCH 028/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 8c18541..ffd3e34 100644 --- a/.gitignore +++ b/.gitignore @@ -15,3 +15,4 @@ /ugene-free-20211118T0755.tar.gz /ugene-free-20211119T0709.tar.gz /ugene-free-20211126T0914.tar.gz +/ugene-free-20211127T2200.tar.gz diff --git a/sources b/sources index b032795..af29744 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211126T0914.tar.gz) = 605c581c5862da91f2705c3d036d56b98ddfbc71877b9b8939f76c1c3b22cafd74c6d5052bcb4650299e0c4d8a352a3505281aa0ebdedc5d99993641d10ba121 +SHA512 (ugene-free-20211127T2200.tar.gz) = 918d3cad897ad73cb4096fb339d193f0d396af94f88082a4f39339a66a4ebbf3fd7cfd6ba945b2393e29249eab94ef90665b5e7966e8155b33e94642c4e658cf diff --git a/ugene.spec b/ugene.spec index ce34b5b..2363c0a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211125 -%global gitcommit 18d20612d4d2b6deb0085200ee91fd1c981aa983 +%global gitdate 20211127 +%global gitcommit d8055237e9067f678108956b8de8c9e4b059b3a0 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free c6cad806c4ce6b7531f4455c06e6bbf91ef509e0 +%global gitcommit_free cd7ad408e02831e7bf9d82cd9fd0e405eacb1dc3 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211126 -%global tarballtime 0914 +%global tarballdate 20211127 +%global tarballtime 2200 %global use_release 0 %global use_gitbare 1 From c7318a1654b7e48f1e5175fdea822313b7d8c179 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 30 Nov 2021 22:57:37 +0900 Subject: [PATCH 029/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index ffd3e34..d32cde5 100644 --- a/.gitignore +++ b/.gitignore @@ -16,3 +16,4 @@ /ugene-free-20211119T0709.tar.gz /ugene-free-20211126T0914.tar.gz /ugene-free-20211127T2200.tar.gz +/ugene-free-20211130T2222.tar.gz diff --git a/sources b/sources index af29744..5c27e42 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211127T2200.tar.gz) = 918d3cad897ad73cb4096fb339d193f0d396af94f88082a4f39339a66a4ebbf3fd7cfd6ba945b2393e29249eab94ef90665b5e7966e8155b33e94642c4e658cf +SHA512 (ugene-free-20211130T2222.tar.gz) = 33e565115d6cbb263c729f679aa2267bae371730302297975f8db72ef222a40981a41e37d458cef1432b01737b5f3eb787a6bef1ab152d79ac437f352373a503 diff --git a/ugene.spec b/ugene.spec index 2363c0a..c1b8b58 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211127 -%global gitcommit d8055237e9067f678108956b8de8c9e4b059b3a0 +%global gitdate 20211130 +%global gitcommit 02132181117800f2b97679c2defa13b0dad88e1a # New git commit with non-free part using "git filter-branch" -%global gitcommit_free cd7ad408e02831e7bf9d82cd9fd0e405eacb1dc3 +%global gitcommit_free f707d30cbb4bbe735bd900c649d9ba27c99e29ba %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211127 -%global tarballtime 2200 +%global tarballdate 20211130 +%global tarballtime 2222 %global use_release 0 %global use_gitbare 1 From 331b991efe56f4a9f771059db10e2fd4b621e9dc Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 1 Dec 2021 09:29:45 +0900 Subject: [PATCH 030/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 8 ++++---- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index d32cde5..d7e3a74 100644 --- a/.gitignore +++ b/.gitignore @@ -17,3 +17,4 @@ /ugene-free-20211126T0914.tar.gz /ugene-free-20211127T2200.tar.gz /ugene-free-20211130T2222.tar.gz +/ugene-free-20211201T0800.tar.gz diff --git a/sources b/sources index 5c27e42..0f39c80 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211130T2222.tar.gz) = 33e565115d6cbb263c729f679aa2267bae371730302297975f8db72ef222a40981a41e37d458cef1432b01737b5f3eb787a6bef1ab152d79ac437f352373a503 +SHA512 (ugene-free-20211201T0800.tar.gz) = ffde227b19c60a41535e82a2dee2edf7047bc48bc76824a75a760b892b187975002a3f5ca60d4891acefb7dd99415dfbaacfedb53412edbaf784c54914dc2c9c diff --git a/ugene.spec b/ugene.spec index c1b8b58..cad7891 100644 --- a/ugene.spec +++ b/ugene.spec @@ -3,9 +3,9 @@ %if 0%{?use_release_branch} < 1 # master %global gitdate 20211130 -%global gitcommit 02132181117800f2b97679c2defa13b0dad88e1a +%global gitcommit 99c2ba244a25690ac23c305eac69efd8e2fded5b # New git commit with non-free part using "git filter-branch" -%global gitcommit_free f707d30cbb4bbe735bd900c649d9ba27c99e29ba +%global gitcommit_free 9a30c5ebadc436e4c3462b93039cdf63974e3b7e %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211130 -%global tarballtime 2222 +%global tarballdate 20211201 +%global tarballtime 0800 %global use_release 0 %global use_gitbare 1 From 9a8b4cf711fdd8e8bfed3bfb45d462c2d050f871 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 2 Dec 2021 15:02:43 +0900 Subject: [PATCH 031/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 8 ++++---- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index d7e3a74..81d6d8c 100644 --- a/.gitignore +++ b/.gitignore @@ -18,3 +18,4 @@ /ugene-free-20211127T2200.tar.gz /ugene-free-20211130T2222.tar.gz /ugene-free-20211201T0800.tar.gz +/ugene-free-20211202T1430.tar.gz diff --git a/sources b/sources index 0f39c80..4217242 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211201T0800.tar.gz) = ffde227b19c60a41535e82a2dee2edf7047bc48bc76824a75a760b892b187975002a3f5ca60d4891acefb7dd99415dfbaacfedb53412edbaf784c54914dc2c9c +SHA512 (ugene-free-20211202T1430.tar.gz) = 120efcdc3c19a946e9713868b3e61fc8353a6c4d0cac79ecc969ac41091324ec8ad885feb0101773185fe0e477da65c29df075861264083a2a0f41c06f3543e5 diff --git a/ugene.spec b/ugene.spec index cad7891..bd2efb7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -3,9 +3,9 @@ %if 0%{?use_release_branch} < 1 # master %global gitdate 20211130 -%global gitcommit 99c2ba244a25690ac23c305eac69efd8e2fded5b +%global gitcommit c2bf04ad677306b0a8355c93518756c8b5d74e50 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 9a30c5ebadc436e4c3462b93039cdf63974e3b7e +%global gitcommit_free 4ef9e1a826950053a2ef93d4495b738c8557903d %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211201 -%global tarballtime 0800 +%global tarballdate 20211202 +%global tarballtime 1430 %global use_release 0 %global use_gitbare 1 From bb8bfb7c1a87b6bee3ceeb0cbe6ff08b8f615e3a Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 4 Dec 2021 20:21:12 +0900 Subject: [PATCH 032/260] 41.0 --- .gitignore | 1 + sources | 2 +- ugene.spec | 15 +++++++++------ 3 files changed, 11 insertions(+), 7 deletions(-) diff --git a/.gitignore b/.gitignore index 81d6d8c..b5c0be9 100644 --- a/.gitignore +++ b/.gitignore @@ -19,3 +19,4 @@ /ugene-free-20211130T2222.tar.gz /ugene-free-20211201T0800.tar.gz /ugene-free-20211202T1430.tar.gz +/ugene-free-41.0.tar.gz diff --git a/sources b/sources index 4217242..dff99d0 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211202T1430.tar.gz) = 120efcdc3c19a946e9713868b3e61fc8353a6c4d0cac79ecc969ac41091324ec8ad885feb0101773185fe0e477da65c29df075861264083a2a0f41c06f3543e5 +SHA512 (ugene-free-41.0.tar.gz) = bc3d1e1dd627d7e3dba215abe3f08282668541d3c9f05870f88e1fca786f2f136a35163c13e2871edeea3aa6627162913ea79f288c842736df1bf6245e20597c diff --git a/ugene.spec b/ugene.spec index bd2efb7..65c5c29 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20211202 %global tarballtime 1430 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 0.1 +%global mainrel 1 %undefine prever %if 0%{?use_release} >= 1 @@ -254,11 +254,14 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog -* Wed Nov 17 2021 Mamoru TASAKA - 41.1-2 +* Sat Dec 4 2021 Mamoru TASAKA - 41.0-1 +- 41.0 + +* Wed Nov 17 2021 Mamoru TASAKA - 40.1-2 - Surely remove nonfree code from tarball -* Tue Nov 9 2021 Mamoru TASAKA - 41.1-1 -- 41.1 +* Tue Nov 9 2021 Mamoru TASAKA - 40.1-1 +- 40.1 * Fri Jul 23 2021 Fedora Release Engineering - 34.0-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild From de2f2ec85a7ee3fc6b4e9fb5d525e07e3a0918f5 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 7 Dec 2021 15:17:52 +0900 Subject: [PATCH 033/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index b5c0be9..bb349b4 100644 --- a/.gitignore +++ b/.gitignore @@ -20,3 +20,4 @@ /ugene-free-20211201T0800.tar.gz /ugene-free-20211202T1430.tar.gz /ugene-free-41.0.tar.gz +/ugene-free-20211207T1447.tar.gz diff --git a/sources b/sources index dff99d0..964187d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-41.0.tar.gz) = bc3d1e1dd627d7e3dba215abe3f08282668541d3c9f05870f88e1fca786f2f136a35163c13e2871edeea3aa6627162913ea79f288c842736df1bf6245e20597c +SHA512 (ugene-free-20211207T1447.tar.gz) = a50791efda13add0c450499baadfda14f37375de9e7f92e2e21b4ea6a411824c82dd3d60dd3f4d0697895534b8e736627e618baecb389b58064e2f6601d684d0 diff --git a/ugene.spec b/ugene.spec index 65c5c29..c165b6b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211130 -%global gitcommit c2bf04ad677306b0a8355c93518756c8b5d74e50 +%global gitdate 20211206 +%global gitcommit 6543066ae1536d4d6df47068bcdb9b7ccde10fa9 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 4ef9e1a826950053a2ef93d4495b738c8557903d +%global gitcommit_free 20d1b0dc14b35b05f29b2410d8834c08ccf87629 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211202 -%global tarballtime 1430 +%global tarballdate 20211207 +%global tarballtime 1447 %global use_release 1 %global use_gitbare 0 From 7303409399a9990dfe12b1a162a12d9c88858cde Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 7 Dec 2021 15:22:53 +0900 Subject: [PATCH 034/260] switch to git branch again --- ugene.spec | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ugene.spec b/ugene.spec index c165b6b..fe86269 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20211207 %global tarballtime 1447 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1 +%global mainrel 1.1 %undefine prever %if 0%{?use_release} >= 1 From a314a0ea0162a1ced5f9e658b52dba8b5e0a84e2 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 9 Dec 2021 16:24:55 +0900 Subject: [PATCH 035/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index bb349b4..c5e53ad 100644 --- a/.gitignore +++ b/.gitignore @@ -21,3 +21,4 @@ /ugene-free-20211202T1430.tar.gz /ugene-free-41.0.tar.gz /ugene-free-20211207T1447.tar.gz +/ugene-free-20211209T1419.tar.gz diff --git a/sources b/sources index 964187d..c5b006b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211207T1447.tar.gz) = a50791efda13add0c450499baadfda14f37375de9e7f92e2e21b4ea6a411824c82dd3d60dd3f4d0697895534b8e736627e618baecb389b58064e2f6601d684d0 +SHA512 (ugene-free-20211209T1419.tar.gz) = 5471fd216cd77f426014e8d76a2a2ef92f1fc4c91747cb804f26fb00b7082ae422898968f6578e229d31edd0bdb2f10d971685305525bc4f66bef19bfaed281b diff --git a/ugene.spec b/ugene.spec index fe86269..cf94954 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211206 -%global gitcommit 6543066ae1536d4d6df47068bcdb9b7ccde10fa9 +%global gitdate 20211209 +%global gitcommit 2ae381526e965cb659e062fa5091be46b76bea39 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 20d1b0dc14b35b05f29b2410d8834c08ccf87629 +%global gitcommit_free 37b14dc6c8f0c1eaf3718eb16a62b676c40a4fe9 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211207 -%global tarballtime 1447 +%global tarballdate 20211209 +%global tarballtime 1419 %global use_release 0 %global use_gitbare 1 From 9f8db69c43e50cef3e61745611950d67a9b69801 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 12 Dec 2021 09:42:55 +0900 Subject: [PATCH 036/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index c5e53ad..83b7826 100644 --- a/.gitignore +++ b/.gitignore @@ -22,3 +22,4 @@ /ugene-free-41.0.tar.gz /ugene-free-20211207T1447.tar.gz /ugene-free-20211209T1419.tar.gz +/ugene-free-20211212T0916.tar.gz diff --git a/sources b/sources index c5b006b..d6244d8 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211209T1419.tar.gz) = 5471fd216cd77f426014e8d76a2a2ef92f1fc4c91747cb804f26fb00b7082ae422898968f6578e229d31edd0bdb2f10d971685305525bc4f66bef19bfaed281b +SHA512 (ugene-free-20211212T0916.tar.gz) = 6f05cf30067b361d89cca4a1248c2ab7223111638ddb2b3301052d26a44c5e22c50edfd025d1ecc3d1046d1905a93ae6ef20fd6e91241990e9b9d25bdbd198aa diff --git a/ugene.spec b/ugene.spec index cf94954..4ce1b74 100644 --- a/ugene.spec +++ b/ugene.spec @@ -3,9 +3,9 @@ %if 0%{?use_release_branch} < 1 # master %global gitdate 20211209 -%global gitcommit 2ae381526e965cb659e062fa5091be46b76bea39 +%global gitcommit f9ea08e16b0be5f080313cd2395a68c8a3f799f7 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 37b14dc6c8f0c1eaf3718eb16a62b676c40a4fe9 +%global gitcommit_free 1c2658eff641e31e01a1575d0e8bb719b49b8556 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211209 -%global tarballtime 1419 +%global tarballdate 20211212 +%global tarballtime 0916 %global use_release 0 %global use_gitbare 1 @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1.1 +%global mainrel 1.2 %undefine prever %if 0%{?use_release} >= 1 From 3474d9dfc45e55bdda8db3bb9f83ea2bbf064d43 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 14 Dec 2021 11:24:12 +0900 Subject: [PATCH 037/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 83b7826..b8b966f 100644 --- a/.gitignore +++ b/.gitignore @@ -23,3 +23,4 @@ /ugene-free-20211207T1447.tar.gz /ugene-free-20211209T1419.tar.gz /ugene-free-20211212T0916.tar.gz +/ugene-free-20211214T1105.tar.gz diff --git a/sources b/sources index d6244d8..7702a5f 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211212T0916.tar.gz) = 6f05cf30067b361d89cca4a1248c2ab7223111638ddb2b3301052d26a44c5e22c50edfd025d1ecc3d1046d1905a93ae6ef20fd6e91241990e9b9d25bdbd198aa +SHA512 (ugene-free-20211214T1105.tar.gz) = 4811b69b489302ac6c340df4452094122a720c24b39168c2e772f54706eb79860bfa0b622750bc7d11cea6f962b0dd5151cbd217b257d5fbd1b88819fd2a59de diff --git a/ugene.spec b/ugene.spec index 4ce1b74..0817d06 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211209 -%global gitcommit f9ea08e16b0be5f080313cd2395a68c8a3f799f7 +%global gitdate 20211214 +%global gitcommit 113d9908d0110f85ce3e675ffa7fbbaa14aca162 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 1c2658eff641e31e01a1575d0e8bb719b49b8556 +%global gitcommit_free 3ecaef1fc3f2410d4d4822b4daa0fbb4da40cbbb %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211212 -%global tarballtime 0916 +%global tarballdate 20211214 +%global tarballtime 1105 %global use_release 0 %global use_gitbare 1 From e83bcb9550d03659c79ee5926b6208406c95bcdf Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 19 Dec 2021 09:05:22 +0900 Subject: [PATCH 038/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index b8b966f..230fb54 100644 --- a/.gitignore +++ b/.gitignore @@ -24,3 +24,4 @@ /ugene-free-20211209T1419.tar.gz /ugene-free-20211212T0916.tar.gz /ugene-free-20211214T1105.tar.gz +/ugene-free-20211219T0846.tar.gz diff --git a/sources b/sources index 7702a5f..578c116 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211214T1105.tar.gz) = 4811b69b489302ac6c340df4452094122a720c24b39168c2e772f54706eb79860bfa0b622750bc7d11cea6f962b0dd5151cbd217b257d5fbd1b88819fd2a59de +SHA512 (ugene-free-20211219T0846.tar.gz) = cc5c23174ea91130a4c0efadb31ac51e05768c50f739499f588a4de8295de47aef065a301be792846eb4628171b8975aa6d0ff53e3f7e0204889f650e261ae98 diff --git a/ugene.spec b/ugene.spec index 0817d06..494d843 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211214 -%global gitcommit 113d9908d0110f85ce3e675ffa7fbbaa14aca162 +%global gitdate 20211218 +%global gitcommit 0b816e2cf31ef7ac5c1f8520bc6d7e623f1e7e8f # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 3ecaef1fc3f2410d4d4822b4daa0fbb4da40cbbb +%global gitcommit_free a5811cd1560442431bdba2217c9a9c2a956dfcc6 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211214 -%global tarballtime 1105 +%global tarballdate 20211219 +%global tarballtime 0846 %global use_release 0 %global use_gitbare 1 From e9d1cd990d0fed67d21826e92bde12105bf294a4 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 21 Dec 2021 19:54:36 +0900 Subject: [PATCH 039/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 230fb54..c33a677 100644 --- a/.gitignore +++ b/.gitignore @@ -25,3 +25,4 @@ /ugene-free-20211212T0916.tar.gz /ugene-free-20211214T1105.tar.gz /ugene-free-20211219T0846.tar.gz +/ugene-free-20211221T1727.tar.gz diff --git a/sources b/sources index 578c116..ed6b274 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211219T0846.tar.gz) = cc5c23174ea91130a4c0efadb31ac51e05768c50f739499f588a4de8295de47aef065a301be792846eb4628171b8975aa6d0ff53e3f7e0204889f650e261ae98 +SHA512 (ugene-free-20211221T1727.tar.gz) = 96c62d6b3f72c08418607a4e493f65fd8001892b4ef818d4e33171b66ac42507336d3475b6a37405588444cab963ccef223e47afd46b33ee8634303981f679e2 diff --git a/ugene.spec b/ugene.spec index 494d843..c503802 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211218 -%global gitcommit 0b816e2cf31ef7ac5c1f8520bc6d7e623f1e7e8f +%global gitdate 20211221 +%global gitcommit e077dbe34eb44342b9d0a503b593f8d7155bf3e7 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free a5811cd1560442431bdba2217c9a9c2a956dfcc6 +%global gitcommit_free 77d8fa24c0701e2f5308025f3c33294fed6e71f2 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211219 -%global tarballtime 0846 +%global tarballdate 20211221 +%global tarballtime 1727 %global use_release 0 %global use_gitbare 1 From 7d13cf5215a8515e04cb8b01d2d2253e38e6cf75 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 23 Dec 2021 14:35:25 +0900 Subject: [PATCH 040/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index c33a677..132475b 100644 --- a/.gitignore +++ b/.gitignore @@ -26,3 +26,4 @@ /ugene-free-20211214T1105.tar.gz /ugene-free-20211219T0846.tar.gz /ugene-free-20211221T1727.tar.gz +/ugene-free-20211223T1411.tar.gz diff --git a/sources b/sources index ed6b274..f6ced44 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211221T1727.tar.gz) = 96c62d6b3f72c08418607a4e493f65fd8001892b4ef818d4e33171b66ac42507336d3475b6a37405588444cab963ccef223e47afd46b33ee8634303981f679e2 +SHA512 (ugene-free-20211223T1411.tar.gz) = 32178613e25718424578b1d4184c712cb59cfb743e640eb1ae7cf8047735033902cc82f551ad9d76d8f6954bf274df49747eabad0af7202abda7bed246c5ff98 diff --git a/ugene.spec b/ugene.spec index c503802..8472133 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211221 -%global gitcommit e077dbe34eb44342b9d0a503b593f8d7155bf3e7 +%global gitdate 20211223 +%global gitcommit a0b6c1c655b2e97248bdccb7c619c919c4483385 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 77d8fa24c0701e2f5308025f3c33294fed6e71f2 +%global gitcommit_free 5f941356d21b3432c2b462ce7eab285d3d6beb0f %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211221 -%global tarballtime 1727 +%global tarballdate 20211223 +%global tarballtime 1411 %global use_release 0 %global use_gitbare 1 From 1de6e0d6998c9f9e996d50638899e04344ff05d9 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 25 Dec 2021 22:52:59 +0900 Subject: [PATCH 041/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 8 ++++---- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index 132475b..03dbd29 100644 --- a/.gitignore +++ b/.gitignore @@ -27,3 +27,4 @@ /ugene-free-20211219T0846.tar.gz /ugene-free-20211221T1727.tar.gz /ugene-free-20211223T1411.tar.gz +/ugene-free-20211225T2229.tar.gz diff --git a/sources b/sources index f6ced44..c2c10c5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211223T1411.tar.gz) = 32178613e25718424578b1d4184c712cb59cfb743e640eb1ae7cf8047735033902cc82f551ad9d76d8f6954bf274df49747eabad0af7202abda7bed246c5ff98 +SHA512 (ugene-free-20211225T2229.tar.gz) = 38463fc1ae4e5618dcf8252b5e86c1559342054ed762170bb3cf2676be3b442c43278ebf023df20ecd7929084de07b8c1b70d5636e8dce57ff02be91b06a365b diff --git a/ugene.spec b/ugene.spec index 8472133..6368d92 100644 --- a/ugene.spec +++ b/ugene.spec @@ -3,9 +3,9 @@ %if 0%{?use_release_branch} < 1 # master %global gitdate 20211223 -%global gitcommit a0b6c1c655b2e97248bdccb7c619c919c4483385 +%global gitcommit d04cc6512dcdc6fa75b80a7a73c7d83d6ee73469 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 5f941356d21b3432c2b462ce7eab285d3d6beb0f +%global gitcommit_free bd306a45b862f649377422e3a2e9adfd2ff4ab9a %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211223 -%global tarballtime 1411 +%global tarballdate 20211225 +%global tarballtime 2229 %global use_release 0 %global use_gitbare 1 From 130811b12e7c81832ddfcbbe99b5dc3d76746c33 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 27 Dec 2021 14:12:16 +0900 Subject: [PATCH 042/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 03dbd29..5381ed6 100644 --- a/.gitignore +++ b/.gitignore @@ -28,3 +28,4 @@ /ugene-free-20211221T1727.tar.gz /ugene-free-20211223T1411.tar.gz /ugene-free-20211225T2229.tar.gz +/ugene-free-20211227T1355.tar.gz diff --git a/sources b/sources index c2c10c5..9cd13b0 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211225T2229.tar.gz) = 38463fc1ae4e5618dcf8252b5e86c1559342054ed762170bb3cf2676be3b442c43278ebf023df20ecd7929084de07b8c1b70d5636e8dce57ff02be91b06a365b +SHA512 (ugene-free-20211227T1355.tar.gz) = 9fd3ac51e927051d5878c0da8754ebe092c50e390fb486b43542a029f389306ef075e83ff5f15d139a0403c8c8b19f7160240f73c9ec42b0529b16d70ad6c729 diff --git a/ugene.spec b/ugene.spec index 6368d92..083719a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211223 -%global gitcommit d04cc6512dcdc6fa75b80a7a73c7d83d6ee73469 +%global gitdate 20211227 +%global gitcommit 05e9ae093e1b078539a5596f6bdec6fcbd7cf1c2 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free bd306a45b862f649377422e3a2e9adfd2ff4ab9a +%global gitcommit_free ac32684752a09139fbe0061017836868747e5bfd %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211225 -%global tarballtime 2229 +%global tarballdate 20211227 +%global tarballtime 1355 %global use_release 0 %global use_gitbare 1 From 920f74755c292698a7cf08d89266a022ce7562cb Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 29 Dec 2021 12:07:37 +0900 Subject: [PATCH 043/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 5381ed6..2361ada 100644 --- a/.gitignore +++ b/.gitignore @@ -29,3 +29,4 @@ /ugene-free-20211223T1411.tar.gz /ugene-free-20211225T2229.tar.gz /ugene-free-20211227T1355.tar.gz +/ugene-free-20211229T1154.tar.gz diff --git a/sources b/sources index 9cd13b0..a7f7236 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211227T1355.tar.gz) = 9fd3ac51e927051d5878c0da8754ebe092c50e390fb486b43542a029f389306ef075e83ff5f15d139a0403c8c8b19f7160240f73c9ec42b0529b16d70ad6c729 +SHA512 (ugene-free-20211229T1154.tar.gz) = db94bfec2c7b7fa34593f849331d00cf98b5843c66e36888e3f5f9bfc7e99a2dfeb425738d4dbb2bff7fbe48515e571ef8ce912a69d0ac18eedcd648888e60db diff --git a/ugene.spec b/ugene.spec index 083719a..fbcdacb 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211227 -%global gitcommit 05e9ae093e1b078539a5596f6bdec6fcbd7cf1c2 +%global gitdate 20211228 +%global gitcommit 9ab0006505c6338e7e7cd548c248a607725b1fa5 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free ac32684752a09139fbe0061017836868747e5bfd +%global gitcommit_free 849ec011a118b07290e92c1b5bf42a0d8a347d64 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211227 -%global tarballtime 1355 +%global tarballdate 20211229 +%global tarballtime 1154 %global use_release 0 %global use_gitbare 1 From 74212c37e4c782f27a627560e02597db46018785 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 2 Jan 2022 16:51:41 +0900 Subject: [PATCH 044/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 2361ada..9e6a548 100644 --- a/.gitignore +++ b/.gitignore @@ -30,3 +30,4 @@ /ugene-free-20211225T2229.tar.gz /ugene-free-20211227T1355.tar.gz /ugene-free-20211229T1154.tar.gz +/ugene-free-20220102T1518.tar.gz diff --git a/sources b/sources index a7f7236..06a2699 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20211229T1154.tar.gz) = db94bfec2c7b7fa34593f849331d00cf98b5843c66e36888e3f5f9bfc7e99a2dfeb425738d4dbb2bff7fbe48515e571ef8ce912a69d0ac18eedcd648888e60db +SHA512 (ugene-free-20220102T1518.tar.gz) = 9b708c1cee88ae70ee3059907227dbdd34b47ca31c8429c6311f7c2c1c827556b32ed77977e813482c62b6478faa3acb2f04db434f9eb2b0c624a8055dbf4494 diff --git a/ugene.spec b/ugene.spec index fbcdacb..c5b3fdd 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20211228 -%global gitcommit 9ab0006505c6338e7e7cd548c248a607725b1fa5 +%global gitdate 20220102 +%global gitcommit 7275bd7ef51a2b37421b23d846ae6fbadce1d60c # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 849ec011a118b07290e92c1b5bf42a0d8a347d64 +%global gitcommit_free c6642c01984837186d0008766ee61c410cc85580 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20211229 -%global tarballtime 1154 +%global tarballdate 20220102 +%global tarballtime 1518 %global use_release 0 %global use_gitbare 1 From 6070d064a36c381009ed2f728d209b6f96014b5f Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 6 Jan 2022 15:20:24 +0900 Subject: [PATCH 045/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 26 +++++++++++++------------- 3 files changed, 15 insertions(+), 14 deletions(-) diff --git a/.gitignore b/.gitignore index 9e6a548..559a753 100644 --- a/.gitignore +++ b/.gitignore @@ -31,3 +31,4 @@ /ugene-free-20211227T1355.tar.gz /ugene-free-20211229T1154.tar.gz /ugene-free-20220102T1518.tar.gz +/ugene-free-20220106T1444.tar.gz diff --git a/sources b/sources index 06a2699..cafd72f 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220102T1518.tar.gz) = 9b708c1cee88ae70ee3059907227dbdd34b47ca31c8429c6311f7c2c1c827556b32ed77977e813482c62b6478faa3acb2f04db434f9eb2b0c624a8055dbf4494 +SHA512 (ugene-free-20220106T1444.tar.gz) = 98021c4a5d3db0f7d188c0fdff817ce0323959cd58d469d85c7c33844b475a0af3fc8312ff33bdeaf1c97f6a4fed8e7e704a9aa9e8108d0b19b0b24d5f562e4b diff --git a/ugene.spec b/ugene.spec index c5b3fdd..ccad165 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220102 -%global gitcommit 7275bd7ef51a2b37421b23d846ae6fbadce1d60c +%global gitdate 20220105 +%global gitcommit b77bcf8e0b1a3204488fedc4e31aff7adc08e417 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free c6642c01984837186d0008766ee61c410cc85580 +%global gitcommit_free 7d6a6d4a1c85711e15a75e08325eb8cc45279676 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220102 -%global tarballtime 1518 +%global tarballdate 20220106 +%global tarballtime 1444 %global use_release 0 %global use_gitbare 1 @@ -134,21 +134,21 @@ git config user.name "%{name} Fedora maintainer" git config user.email "%{name}-maintainers@fedoraproject.org" %endif -%patch1 -p1 -b .glibc_2_35 +%patch1 -p1 -b .glibc_2_35 -Z %GIT commit -m "Build fix for glibc 2.35 change" -a -%patch101 -p1 -b .cpuid +%patch101 -p1 -b .cpuid -Z %GIT commit -m "ugenem: support architecture not supporting cpuid" -a -%patch102 -p1 -b .sys_mmap +%patch102 -p1 -b .sys_mmap -Z %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a -%patch103 -p1 -b .unwind +%patch103 -p1 -b .unwind -Z %GIT commit -m "libs_3rdparty/breakpad: workaround for arch not supporting unwind" -a -%patch104 -p1 -b .sse +%patch104 -p1 -b .sse -Z %GIT commit -m "plugins_3rdparty/hmm2: support architecture not supporting SSE2" -a -%patch105 -p1 -b .port +%patch105 -p1 -b .port -Z %GIT commit -m "libs_3rdparty/breakpad: workaround for arch not ported by the upstream" -a -%patch106 -p1 -b .sse_2 +%patch106 -p1 -b .sse_2 -Z %GIT commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a -%patch107 -p1 -b .char_bigen +%patch107 -p1 -b .char_bigen -Z %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' From e0e8c63c9a746e7d4435117b0032ee9e20df506b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 9 Jan 2022 22:14:42 +0900 Subject: [PATCH 046/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 559a753..a5e011f 100644 --- a/.gitignore +++ b/.gitignore @@ -32,3 +32,4 @@ /ugene-free-20211229T1154.tar.gz /ugene-free-20220102T1518.tar.gz /ugene-free-20220106T1444.tar.gz +/ugene-free-20220109T2202.tar.gz diff --git a/sources b/sources index cafd72f..0683c0b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220106T1444.tar.gz) = 98021c4a5d3db0f7d188c0fdff817ce0323959cd58d469d85c7c33844b475a0af3fc8312ff33bdeaf1c97f6a4fed8e7e704a9aa9e8108d0b19b0b24d5f562e4b +SHA512 (ugene-free-20220109T2202.tar.gz) = 5e46fb782b797cec945bee1f17a6247c0324d7635d6d20bce02fea8cc716b12562e70c8a372b4f6c97832472812f365270f01155c00c57173d5b5ed6368c9800 diff --git a/ugene.spec b/ugene.spec index ccad165..e9b23e3 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220105 -%global gitcommit b77bcf8e0b1a3204488fedc4e31aff7adc08e417 +%global gitdate 20220109 +%global gitcommit c33a2a051df6549b47eb3d9de7ceba779e34e3bf # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 7d6a6d4a1c85711e15a75e08325eb8cc45279676 +%global gitcommit_free ffd5dbeafc7a4bd7b7e9a60e2f053577a4ae9e49 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220106 -%global tarballtime 1444 +%global tarballdate 20220109 +%global tarballtime 2202 %global use_release 0 %global use_gitbare 1 From 3099ec05f899e1ff37dad4978f32063da8fadb78 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 13 Jan 2022 14:51:25 +0900 Subject: [PATCH 047/260] update to the latest git --- .gitignore | 1 + sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index a5e011f..ebd0822 100644 --- a/.gitignore +++ b/.gitignore @@ -33,3 +33,4 @@ /ugene-free-20220102T1518.tar.gz /ugene-free-20220106T1444.tar.gz /ugene-free-20220109T2202.tar.gz +/ugene-free-20220113T1434.tar.gz diff --git a/sources b/sources index 0683c0b..1212caf 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220109T2202.tar.gz) = 5e46fb782b797cec945bee1f17a6247c0324d7635d6d20bce02fea8cc716b12562e70c8a372b4f6c97832472812f365270f01155c00c57173d5b5ed6368c9800 +SHA512 (ugene-free-20220113T1434.tar.gz) = 74cbfcebb1d59e61390d909fd7c2478ca684fabafd160c4945ca576840946321f529fbe2cb6e5de2fe19d03b778d45058f42c4ba9f0ec99a56bedd605b76d093 diff --git a/ugene.spec b/ugene.spec index e9b23e3..9ed953c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220109 -%global gitcommit c33a2a051df6549b47eb3d9de7ceba779e34e3bf +%global gitdate 20220111 +%global gitcommit 857470c4820f2b27c0f714adb05c5e09216f19ca # New git commit with non-free part using "git filter-branch" -%global gitcommit_free ffd5dbeafc7a4bd7b7e9a60e2f053577a4ae9e49 +%global gitcommit_free 5cb971a247fbda2cced0657bcf2c1673c566345f %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220109 -%global tarballtime 2202 +%global tarballdate 20220113 +%global tarballtime 1434 %global use_release 0 %global use_gitbare 1 From 8dae9201669d5de8d117c107c7991ff9ec9661c9 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 22 Jan 2022 03:26:52 +0000 Subject: [PATCH 048/260] - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 65c5c29..c481a7d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 41.0 -Release: %{fedorarel}%{?dist} +Release: %{fedorarel}%{?dist}.1 #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -254,6 +254,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sat Jan 22 2022 Fedora Release Engineering - 41.0-1.1 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild + * Sat Dec 4 2021 Mamoru TASAKA - 41.0-1 - 41.0 From e495f2b2d1781339e8f8506b368304502cfd986c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 9 Mar 2022 19:07:08 +0900 Subject: [PATCH 049/260] update to 42.0 --- .gitignore | 37 +------------------ sources | 2 +- ...t-plgins-smith_waterman-nonsse2-arch.patch | 6 +-- ...2.0-plugins_3rdparty-hmm2-nosse-arch.patch | 28 +++++++------- ...ene-42.0-ugenem-cpuid-supported-arch.patch | 6 +-- ugene.spec | 16 ++++---- 6 files changed, 29 insertions(+), 66 deletions(-) rename ugene-40.1-git-plgins-smith_waterman-nonsse2-arch.patch => ugene-42.0-git-plgins-smith_waterman-nonsse2-arch.patch (97%) rename ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch => ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch (71%) rename ugene-40.1-ugenem-cpuid-supported-arch.patch => ugene-42.0-ugenem-cpuid-supported-arch.patch (73%) diff --git a/.gitignore b/.gitignore index ebd0822..d0a90d7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,36 +1 @@ -/ugene-1.*.tar.gz -/ugene-33.0.tar.gz -/ugene-34.0.tar.gz -/ugene-40.1.tar.gz -/ugene-free-40.1.tar.gz -/ugene-20211111T1455.tar.gz -/ugene-20211111T2046.tar.gz -/ugene-20211113T2002.tar.gz -/ugene-20211114T2118.tar.gz -/ugene-20211115T0821.tar.gz -/ugene-20211115T1940.tar.gz -/ugene-20211116T0835.tar.gz -/ugene-20211117T0834.tar.gz -/ugene-free-20211117T0834.tar.gz -/ugene-free-20211118T0755.tar.gz -/ugene-free-20211119T0709.tar.gz -/ugene-free-20211126T0914.tar.gz -/ugene-free-20211127T2200.tar.gz -/ugene-free-20211130T2222.tar.gz -/ugene-free-20211201T0800.tar.gz -/ugene-free-20211202T1430.tar.gz -/ugene-free-41.0.tar.gz -/ugene-free-20211207T1447.tar.gz -/ugene-free-20211209T1419.tar.gz -/ugene-free-20211212T0916.tar.gz -/ugene-free-20211214T1105.tar.gz -/ugene-free-20211219T0846.tar.gz -/ugene-free-20211221T1727.tar.gz -/ugene-free-20211223T1411.tar.gz -/ugene-free-20211225T2229.tar.gz -/ugene-free-20211227T1355.tar.gz -/ugene-free-20211229T1154.tar.gz -/ugene-free-20220102T1518.tar.gz -/ugene-free-20220106T1444.tar.gz -/ugene-free-20220109T2202.tar.gz -/ugene-free-20220113T1434.tar.gz +/ugene-free-*.tar.gz diff --git a/sources b/sources index 1212caf..7d018a7 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220113T1434.tar.gz) = 74cbfcebb1d59e61390d909fd7c2478ca684fabafd160c4945ca576840946321f529fbe2cb6e5de2fe19d03b778d45058f42c4ba9f0ec99a56bedd605b76d093 +SHA512 (ugene-free-42.0.tar.gz) = 57b13c74574978280be1c2a1030552d884e7ce2b09ef43f24d58b732b3334a0fee5851c9296ac90e382115476ae6240552e8122cb6e4266b69a00858cce4aa20 diff --git a/ugene-40.1-git-plgins-smith_waterman-nonsse2-arch.patch b/ugene-42.0-git-plgins-smith_waterman-nonsse2-arch.patch similarity index 97% rename from ugene-40.1-git-plgins-smith_waterman-nonsse2-arch.patch rename to ugene-42.0-git-plgins-smith_waterman-nonsse2-arch.patch index c7d8e27..4859dbf 100644 --- a/ugene-40.1-git-plgins-smith_waterman-nonsse2-arch.patch +++ b/ugene-42.0-git-plgins-smith_waterman-nonsse2-arch.patch @@ -32,7 +32,7 @@ assert(0); @@ -267,7 +269,12 @@ - SmithWatermanAlgorithm *sw = nullptr; + SmithWatermanAlgorithm* sw = nullptr; if (algType == SW_sse2) { +#if defined(__SSE2__) sw = new SmithWatermanAlgorithmSSE2; @@ -45,7 +45,7 @@ sw = new SmithWatermanAlgorithmCUDA; @@ -581,7 +588,11 @@ - SmithWatermanAlgorithm *sw = nullptr; + SmithWatermanAlgorithm* sw = nullptr; if (algType == SW_sse2) { +#if defined(__SSE2__) sw = new SmithWatermanAlgorithmSSE2; @@ -56,7 +56,7 @@ #ifdef SW2_BUILD_WITH_CUDA sw = new SmithWatermanAlgorithmCUDA; @@ -745,6 +756,7 @@ - sqnc->left(c.chunkSize * c.nThreads), + sqnc->left(c.chunkSize * c.nThreads), SmithWatermanSettings::MULTIPLE_ALIGNMENT); break; +#ifdef __SSE2__ diff --git a/ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch b/ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch similarity index 71% rename from ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch rename to ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch index b163a98..63457d9 100644 --- a/ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch +++ b/ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch @@ -1,8 +1,8 @@ --- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/HMMSearchDialogController.cpp.sse 2021-10-11 15:41:23.000000000 +0900 +++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/HMMSearchDialogController.cpp 2021-11-09 01:34:30.052988784 +0900 @@ -81,7 +81,9 @@ - QWidget *w = createController->getWidget(); - QVBoxLayout *l = qobject_cast(layout()); + QWidget* w = createController->getWidget(); + QVBoxLayout* l = qobject_cast(layout()); l->insertWidget(1, w); +#if defined (__SSE2__) algoCombo->addItem(tr("SSE optimized"), HMMSearchAlgo_SSEOptimized); @@ -13,9 +13,9 @@ --- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp.sse 2021-10-11 15:41:23.000000000 +0900 +++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp 2021-11-09 01:34:30.052988784 +0900 @@ -56,9 +56,15 @@ - tophit_s *dhit = AllocTophits(200); // domain hits: 200=lumpsize + tophit_s* dhit = AllocTophits(200); // domain hits: 200=lumpsize - int nseq = 0; // number of sequences searched + int nseq = 0; // number of sequences searched +#if defined(__SSE2__) if (s.alg == HMMSearchAlgo_SSEOptimized) { main_loop_opt(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si, sseScoring); @@ -29,19 +29,17 @@ main_loop_serial(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si); } else { assert(false && "bad hmmsearch algorithm selected"); ---- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp.sse 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp 2021-11-09 01:41:17.023845328 +0900 -@@ -6,6 +6,7 @@ - #include - +--- ugene-42.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp.sse 2022-03-09 15:37:14.586340751 +0900 ++++ ugene-42.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp 2022-03-09 15:47:23.559077800 +0900 +@@ -1,4 +1,5 @@ #include +#if defined (__SSE2__) #include + #include - using namespace U2; -@@ -490,3 +491,4 @@ - - return results; +@@ -488,3 +489,4 @@ QList sseScoring(unsigned char* d + + return results; } +#endif --- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.h.sse 2021-10-11 15:41:23.000000000 +0900 @@ -51,7 +49,7 @@ #define __HMMSEARCH_SSE_H__ +#if defined(__SSE2__) - QList sseScoring( unsigned char * dsq, int seqlen, plan7_s* hmm, HMMSeqGranulation * gr, U2::TaskStateInfo& ti ); + QList sseScoring(unsigned char* dsq, int seqlen, plan7_s* hmm, HMMSeqGranulation* gr, U2::TaskStateInfo& ti); +#endif - #endif // __HMMSEARCH_SSE_H__ + #endif // __HMMSEARCH_SSE_H__ diff --git a/ugene-40.1-ugenem-cpuid-supported-arch.patch b/ugene-42.0-ugenem-cpuid-supported-arch.patch similarity index 73% rename from ugene-40.1-ugenem-cpuid-supported-arch.patch rename to ugene-42.0-ugenem-cpuid-supported-arch.patch index 878a7ff..10a04bd 100644 --- a/ugene-40.1-ugenem-cpuid-supported-arch.patch +++ b/ugene-42.0-ugenem-cpuid-supported-arch.patch @@ -1,5 +1,5 @@ ---- ugene-40.1/src/ugenem/src/SendReportDialog.cpp.cpuid 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/ugenem/src/SendReportDialog.cpp 2021-11-08 19:56:32.468424643 +0900 +--- ugene-42.0/src/ugenem/src/SendReportDialog.cpp.cpuid 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-42.0/src/ugenem/src/SendReportDialog.cpp 2021-11-08 19:56:32.468424643 +0900 @@ -425,7 +425,7 @@ return (int)(getMemorySize() / (1024 * 1024)); } @@ -8,7 +8,7 @@ +#if defined(__x86_64__) || defined (__i386__) void cpuID(unsigned i, unsigned regs[4]) { # ifdef _WIN32 - __cpuid((int *)regs, (int)i); + __cpuid((int*)regs, (int)i); @@ -441,7 +441,7 @@ QString ReportSender::getCPUInfo() { diff --git a/ugene.spec b/ugene.spec index 9ed953c..b1c690a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20220113 %global tarballtime 1434 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1.2 +%global mainrel 1 %undefine prever %if 0%{?use_release} >= 1 @@ -49,8 +49,8 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 41.0 -Release: %{fedorarel}%{?dist} +Version: 42.0 +Release: %{fedorarel}%{?dist}.1 #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -73,12 +73,12 @@ Source10: ugene.wrapper # Should be sent to be upstream Patch1: ugene-40.1-glibc-2_35.patch # Currently distro-specific -Patch101: ugene-40.1-ugenem-cpuid-supported-arch.patch +Patch101: ugene-42.0-ugenem-cpuid-supported-arch.patch Patch102: ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch -Patch104: ugene-40.1-plugins_3rdparty-hmm2-nosse-arch.patch +Patch104: ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch -Patch106: ugene-40.1-git-plgins-smith_waterman-nonsse2-arch.patch +Patch106: ugene-42.0-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch BuildRequires: make From 1bdbf69ff0c55a3c69e5df153ae961e6965e755b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 9 Mar 2022 19:08:04 +0900 Subject: [PATCH 050/260] once reback version to ease merge --- ugene.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index b1c690a..6d8c460 100644 --- a/ugene.spec +++ b/ugene.spec @@ -49,7 +49,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 42.0 +Version: 41.0 Release: %{fedorarel}%{?dist}.1 #The entire source code is GPLv2+ except: From 6f0c9383d388926abe148ba91670cbe9993bd97d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 9 Mar 2022 19:08:59 +0900 Subject: [PATCH 051/260] again set EVR to 42 after merge --- ugene.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/ugene.spec b/ugene.spec index bc4d936..6f87e35 100644 --- a/ugene.spec +++ b/ugene.spec @@ -49,8 +49,8 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 41.0 -Release: %{fedorarel}%{?dist}.1 +Version: 42.0 +Release: %{fedorarel}%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -254,6 +254,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Wed Mar 9 2022 Mamoru TASAKA - 42.0-1 +- 42.0 + * Sat Jan 22 2022 Fedora Release Engineering - 41.0-1.1 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild From 2fb59919d5393f761ba44b8bb02ff4a277528089 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 13 Mar 2022 15:25:07 +0900 Subject: [PATCH 052/260] update to the latest git --- sources | 2 +- ugene.spec | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/sources b/sources index 7d018a7..b5e6a7b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-42.0.tar.gz) = 57b13c74574978280be1c2a1030552d884e7ce2b09ef43f24d58b732b3334a0fee5851c9296ac90e382115476ae6240552e8122cb6e4266b69a00858cce4aa20 +SHA512 (ugene-free-20220313T1457.tar.gz) = 616bb3f0e1421dbaadc3cec1f3d7c6a6a50676d95343d675ea224f4d7e31c44e2670ca98cf540db7d1bf74157bedea030e0ea3264ce7a2e8a364ca1b2e8861e7 diff --git a/ugene.spec b/ugene.spec index 6f87e35..22a2320 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220111 -%global gitcommit 857470c4820f2b27c0f714adb05c5e09216f19ca +%global gitdate 20220307 +%global gitcommit 2ec47dd8f9b7ebf016205cdfc9453f6e3c866b6c # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 5cb971a247fbda2cced0657bcf2c1673c566345f +%global gitcommit_free 414b4286857aba3794a3daf2afe880ed932b3691 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220113 -%global tarballtime 1434 +%global tarballdate 20220313 +%global tarballtime 1457 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1 +%global mainrel 1.1 %undefine prever %if 0%{?use_release} >= 1 From 31774aaf03a0fa8c9daf890e5a89765cbea3d056 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 22 Mar 2022 20:53:44 +0900 Subject: [PATCH 053/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index b5e6a7b..d6044ed 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220313T1457.tar.gz) = 616bb3f0e1421dbaadc3cec1f3d7c6a6a50676d95343d675ea224f4d7e31c44e2670ca98cf540db7d1bf74157bedea030e0ea3264ce7a2e8a364ca1b2e8861e7 +SHA512 (ugene-free-20220322T2033.tar.gz) = 2aaa1e3097bae7fae9f6b9482352e049befadbf5a4ee2886931a69f96d09a8a7693e0710a364ee022ecfd5e2396d9581b932b4580f4311d1e67922ee644523b1 diff --git a/ugene.spec b/ugene.spec index 22a2320..9ec2774 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220307 -%global gitcommit 2ec47dd8f9b7ebf016205cdfc9453f6e3c866b6c +%global gitdate 20220322 +%global gitcommit d50a8aceb49db44aee27e7fc6a32439b4547ac05 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 414b4286857aba3794a3daf2afe880ed932b3691 +%global gitcommit_free 34922b146a99653bb71594da1eb99d52d96aee19 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220313 -%global tarballtime 1457 +%global tarballdate 20220322 +%global tarballtime 2033 %global use_release 0 %global use_gitbare 1 From 723831474001f8c695220be561188b2b280bd206 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 27 Mar 2022 16:22:31 +0900 Subject: [PATCH 054/260] update to the latest git --- sources | 2 +- ugene-40.1-glibc-2_35.patch | 11 ----------- ...rty-breakpad-sys_mmap_use_system_mmap.patch | 14 +++++++------- ugene.spec | 18 +++++++----------- 4 files changed, 15 insertions(+), 30 deletions(-) delete mode 100644 ugene-40.1-glibc-2_35.patch rename ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch => ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch (90%) diff --git a/sources b/sources index d6044ed..aa82e6d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220322T2033.tar.gz) = 2aaa1e3097bae7fae9f6b9482352e049befadbf5a4ee2886931a69f96d09a8a7693e0710a364ee022ecfd5e2396d9581b932b4580f4311d1e67922ee644523b1 +SHA512 (ugene-free-20220327T1527.tar.gz) = 82ad2dcc6cd1966408a39875c6fa21eb0a89df6db43e6e77e751f1cbd0af24370f66103eae1c925238730764932df110f4b788bb007419346208c63345991894 diff --git a/ugene-40.1-glibc-2_35.patch b/ugene-40.1-glibc-2_35.patch deleted file mode 100644 index e97b97c..0000000 --- a/ugene-40.1-glibc-2_35.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc.glibc 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc 2021-11-08 15:45:23.563723022 +0900 -@@ -141,7 +141,7 @@ void InstallAlternateStackLocked() { - // SIGSTKSZ may be too small to prevent the signal handlers from overrunning - // the alternative stack. Ensure that the size of the alternative stack is - // large enough. -- static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); -+ static const unsigned kSigStackSize = std::max(16384L, (long)SIGSTKSZ); - - // Only set an alternative stack if there isn't already one, or if the current - // one is too small. diff --git a/ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch b/ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch similarity index 90% rename from ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch rename to ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch index 5ca0423..726b799 100644 --- a/ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch +++ b/ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch @@ -17,15 +17,15 @@ #include "third_party/lss/linux_syscall_support.h" #endif ---- ugene-40.1/src/libs_3rdparty/breakpad/src/third_party/lss/linux_syscall_support.h.sys_mmap 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/libs_3rdparty/breakpad/src/third_party/lss/linux_syscall_support.h 2021-11-09 00:46:06.363362301 +0900 +--- ugene-42.x/src/libs_3rdparty/breakpad/src/third_party/lss/linux_syscall_support.h.sys_mmap 2021-10-11 15:41:23.000000000 +0900 ++++ ugene-42.x/src/libs_3rdparty/breakpad/src/third_party/lss/linux_syscall_support.h 2021-11-09 00:46:06.363362301 +0900 @@ -85,10 +85,7 @@ - /* We currently only support x86-32, x86-64, ARM, MIPS, and PPC on Linux. + * on Linux. * Porting to other related platforms should not be difficult. */ -#if (defined(__i386__) || defined(__x86_64__) || defined(__ARM_ARCH_3__) || \ - defined(__mips__) || defined(__PPC__) || defined(__ARM_EABI__) || \ -- defined(__aarch64__)) \ +- defined(__aarch64__) || defined(__s390__) || defined(__e2k__)) \ - && (defined(__linux) || defined(__ANDROID__)) +#if defined(__linux) || defined(__ANDROID__) @@ -53,10 +53,10 @@ + #ifdef __mips__ /* Include definitions of the ABI currently in use. */ - #include + #ifdef __ANDROID__ @@ -4021,6 +4024,48 @@ struct kernel_statfs { - # pragma pop_macro("lstat64") - #endif + #pragma pop_macro("pwrite64") + #pragma pop_macro("getdents64") +#endif +#endif diff --git a/ugene.spec b/ugene.spec index 9ec2774..f33d231 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220322 -%global gitcommit d50a8aceb49db44aee27e7fc6a32439b4547ac05 -# New git commit with non-free part using "git filter-branch" -%global gitcommit_free 34922b146a99653bb71594da1eb99d52d96aee19 +%global gitdate 20220324 +%global gitcommit 98ee8ad618dfb74a1dcacff44a8c267379be0a5b +# New git commit with non-free part removed using "git filter-branch" +%global gitcommit_free 50b0d1046996621639ffea9d90796359fce063ba %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220322 -%global tarballtime 2033 +%global tarballdate 20220327 +%global tarballtime 1527 %global use_release 0 %global use_gitbare 1 @@ -70,11 +70,9 @@ Source1: create-ugene-free-tarball.sh Source2: create-%{name}-git-bare-tarball.sh # This is not installed Source10: ugene.wrapper -# Should be sent to be upstream -Patch1: ugene-40.1-glibc-2_35.patch # Currently distro-specific Patch101: ugene-42.0-ugenem-cpuid-supported-arch.patch -Patch102: ugene-40.1-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch +Patch102: ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch Patch104: ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch @@ -134,8 +132,6 @@ git config user.name "%{name} Fedora maintainer" git config user.email "%{name}-maintainers@fedoraproject.org" %endif -%patch1 -p1 -b .glibc_2_35 -Z - %GIT commit -m "Build fix for glibc 2.35 change" -a %patch101 -p1 -b .cpuid -Z %GIT commit -m "ugenem: support architecture not supporting cpuid" -a %patch102 -p1 -b .sys_mmap -Z From 2596a88a57d436003ebe9fea8eba132e739b8229 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 31 Mar 2022 15:10:56 +0900 Subject: [PATCH 055/260] update to the latest git --- sources | 2 +- ugene.spec | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/sources b/sources index aa82e6d..139fee1 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220327T1527.tar.gz) = 82ad2dcc6cd1966408a39875c6fa21eb0a89df6db43e6e77e751f1cbd0af24370f66103eae1c925238730764932df110f4b788bb007419346208c63345991894 +SHA512 (ugene-free-20220331T1436.tar.gz) = 2cb83fb29ee355b1f649f772f1fe14411a3497bd83b4f80ac1ce0c7e041398c2281b98e879fe33310fd58ca4896e6f2e011f34ad98cbfe40892160f090c4c784 diff --git a/ugene.spec b/ugene.spec index f33d231..cf0c40f 100644 --- a/ugene.spec +++ b/ugene.spec @@ -3,9 +3,9 @@ %if 0%{?use_release_branch} < 1 # master %global gitdate 20220324 -%global gitcommit 98ee8ad618dfb74a1dcacff44a8c267379be0a5b +%global gitcommit 33c6c018fc393b0930b6e78a8178685340a05937 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 50b0d1046996621639ffea9d90796359fce063ba +%global gitcommit_free e1c008fd73bd0dcd6f6b2634f94ebc31a5ab513a %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220327 -%global tarballtime 1527 +%global tarballdate 20220331 +%global tarballtime 1436 %global use_release 0 %global use_gitbare 1 From 584919d386d8a07a96ce08f6e85fe5c762da025e Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 1 Apr 2022 11:11:23 +0900 Subject: [PATCH 056/260] fix date --- ugene.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index cf0c40f..a02362c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,7 +2,7 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220324 +%global gitdate 20220331 %global gitcommit 33c6c018fc393b0930b6e78a8178685340a05937 # New git commit with non-free part removed using "git filter-branch" %global gitcommit_free e1c008fd73bd0dcd6f6b2634f94ebc31a5ab513a From 44b06ebc1d1019a62883b5f57d45870a28e677ff Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 3 Apr 2022 15:17:40 +0900 Subject: [PATCH 057/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 139fee1..7e24dd9 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220331T1436.tar.gz) = 2cb83fb29ee355b1f649f772f1fe14411a3497bd83b4f80ac1ce0c7e041398c2281b98e879fe33310fd58ca4896e6f2e011f34ad98cbfe40892160f090c4c784 +SHA512 (ugene-free-20220403T1502.tar.gz) = 1476ab1db84cf0e8b33a59d5fb8c7c3d08e8ae334cd7e4c8e57cb3f3a159a0418ce76a130c762b48453e41fc7f7a7d156ce448958300d63b9eda137cba18996e diff --git a/ugene.spec b/ugene.spec index a02362c..088f0e3 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220331 -%global gitcommit 33c6c018fc393b0930b6e78a8178685340a05937 +%global gitdate 20220403 +%global gitcommit c3317a10287d315dd1a5a4bfab87eea5da95c4f0 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free e1c008fd73bd0dcd6f6b2634f94ebc31a5ab513a +%global gitcommit_free b42403d0846218b82fb47dc452f6c5af42587bb8 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220331 -%global tarballtime 1436 +%global tarballdate 20220403 +%global tarballtime 1502 %global use_release 0 %global use_gitbare 1 From 9399ee959d254abef37059827ddaa2041329ceb5 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 5 Apr 2022 17:20:12 +0900 Subject: [PATCH 058/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 7e24dd9..f823a33 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220403T1502.tar.gz) = 1476ab1db84cf0e8b33a59d5fb8c7c3d08e8ae334cd7e4c8e57cb3f3a159a0418ce76a130c762b48453e41fc7f7a7d156ce448958300d63b9eda137cba18996e +SHA512 (ugene-free-20220405T1622.tar.gz) = 10eb339e95cc4c8f6a6c711bf6f2e329f7e1fac8ed5109d3519fd938d25802abe1e1a4bb8189039095f076dacdcd82a31480c88e903bdf5ab570761a4dbac1b0 diff --git a/ugene.spec b/ugene.spec index 088f0e3..6ce5839 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220403 -%global gitcommit c3317a10287d315dd1a5a4bfab87eea5da95c4f0 +%global gitdate 20220405 +%global gitcommit 44dd1a5d4b712eed5800d7314f261cee47759335 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b42403d0846218b82fb47dc452f6c5af42587bb8 +%global gitcommit_free 84035d7ff12c76f10d14fda75820cf4e3f12a7e4 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220403 -%global tarballtime 1502 +%global tarballdate 20220405 +%global tarballtime 1622 %global use_release 0 %global use_gitbare 1 From 21eb6472e27db825f8e8e0f3d9db3e80f18ba59d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 10 Apr 2022 14:41:01 +0900 Subject: [PATCH 059/260] update to the latest git --- sources | 2 +- ugene.spec | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/sources b/sources index f823a33..d13b0b1 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220405T1622.tar.gz) = 10eb339e95cc4c8f6a6c711bf6f2e329f7e1fac8ed5109d3519fd938d25802abe1e1a4bb8189039095f076dacdcd82a31480c88e903bdf5ab570761a4dbac1b0 +SHA512 (ugene-free-20220410T1250.tar.gz) = 1cb8af4c77f75b7c0fab89341b81d29ec57bfce484439410f2a5642dc964a76aa3e3f9f58fee52a0d683aa9b3059cdc7456b405a9f8ea734e7c94e95731f54a2 diff --git a/ugene.spec b/ugene.spec index 6ce5839..ab44dbc 100644 --- a/ugene.spec +++ b/ugene.spec @@ -3,9 +3,9 @@ %if 0%{?use_release_branch} < 1 # master %global gitdate 20220405 -%global gitcommit 44dd1a5d4b712eed5800d7314f261cee47759335 +%global gitcommit ef0ded6db81eec71d61ef0f42f735d99943bb818 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 84035d7ff12c76f10d14fda75820cf4e3f12a7e4 +%global gitcommit_free 756a550c733821e6b91e215eb906abb7d9d68bdb %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220405 -%global tarballtime 1622 +%global tarballdate 20220410 +%global tarballtime 1250 %global use_release 0 %global use_gitbare 1 From 91c8118dc465f9feb5ebaf8a65082d0bf37daa3b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 17 Apr 2022 14:58:57 +0900 Subject: [PATCH 060/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index d13b0b1..1ae7ea0 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220410T1250.tar.gz) = 1cb8af4c77f75b7c0fab89341b81d29ec57bfce484439410f2a5642dc964a76aa3e3f9f58fee52a0d683aa9b3059cdc7456b405a9f8ea734e7c94e95731f54a2 +SHA512 (ugene-free-20220417T1420.tar.gz) = d320193640f9d92c2ae16196bb04f85219f533c28ba90372fa436d8f3d38a160f0df0b634726d22169d8113b3181cc2e794885731eb94a4fcd14964bef46727d diff --git a/ugene.spec b/ugene.spec index ab44dbc..de49da4 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220405 -%global gitcommit ef0ded6db81eec71d61ef0f42f735d99943bb818 +%global gitdate 20220414 +%global gitcommit fa1114c53d305bdec36df5af060ccb7ebea261ba # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 756a550c733821e6b91e215eb906abb7d9d68bdb +%global gitcommit_free 195957cdeb9ce564fe07c8b799d9f527da11635b %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220410 -%global tarballtime 1250 +%global tarballdate 20220417 +%global tarballtime 1420 %global use_release 0 %global use_gitbare 1 From 91e0b89ecc9bbd3e2051fc07dc4d0d47ed5301f9 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 24 Apr 2022 19:08:46 +0900 Subject: [PATCH 061/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 1ae7ea0..a0aea15 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220417T1420.tar.gz) = d320193640f9d92c2ae16196bb04f85219f533c28ba90372fa436d8f3d38a160f0df0b634726d22169d8113b3181cc2e794885731eb94a4fcd14964bef46727d +SHA512 (ugene-free-20220424T1602.tar.gz) = 5299cfffd0f7fd907551c45949019f3f4e99a5f76f755ae7a67aabd2a4f0bb18fc3e1263a8757bafc6c49c93ad7661c0853531d3c3fa5c2e5d6ebfacd289513b diff --git a/ugene.spec b/ugene.spec index de49da4..56eb776 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220414 -%global gitcommit fa1114c53d305bdec36df5af060ccb7ebea261ba +%global gitdate 20220421 +%global gitcommit 6dab1efa2e6792b39bfe569b5b880e027c95b0d6 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 195957cdeb9ce564fe07c8b799d9f527da11635b +%global gitcommit_free 5204bc45dbf7d8478378284df1ff23ce81222efe %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220417 -%global tarballtime 1420 +%global tarballdate 20220424 +%global tarballtime 1602 %global use_release 0 %global use_gitbare 1 From 1e409ff8a7ab2f91702f8143f64b84f53dee6880 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 2 May 2022 18:09:58 +0900 Subject: [PATCH 062/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index a0aea15..5559329 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220424T1602.tar.gz) = 5299cfffd0f7fd907551c45949019f3f4e99a5f76f755ae7a67aabd2a4f0bb18fc3e1263a8757bafc6c49c93ad7661c0853531d3c3fa5c2e5d6ebfacd289513b +SHA512 (ugene-free-20220502T1737.tar.gz) = 66d67c55bba437b094c5c546d7110ce889a690ab29ffb7be5457bcd9c612624a7430a1b73fbb317a1dbe3a3dcd2d85185a33c843ef32093b5da150b72cb67301 diff --git a/ugene.spec b/ugene.spec index 56eb776..dd8562a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220421 -%global gitcommit 6dab1efa2e6792b39bfe569b5b880e027c95b0d6 +%global gitdate 20220501 +%global gitcommit 53ab0fd01c88d46bf6b55a7f12416adc94dfd10e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 5204bc45dbf7d8478378284df1ff23ce81222efe +%global gitcommit_free af85e4c261ca1b0268e505ca0f056ae124287dc7 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220424 -%global tarballtime 1602 +%global tarballdate 20220502 +%global tarballtime 1737 %global use_release 0 %global use_gitbare 1 From 67377a371a020fdbcb5df71d19b6ee4efb12b6da Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 12 May 2022 16:12:03 +0900 Subject: [PATCH 063/260] try the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 5559329..627fd3c 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220502T1737.tar.gz) = 66d67c55bba437b094c5c546d7110ce889a690ab29ffb7be5457bcd9c612624a7430a1b73fbb317a1dbe3a3dcd2d85185a33c843ef32093b5da150b72cb67301 +SHA512 (ugene-free-20220512T1556.tar.gz) = c56a632ee855c5e6babbb3f4016a635d4714598723f43f6d19d6bb917ce07bb37d35863848954f390d63658a4ad36e6e2ef50ce098e2719fa52ee15e8889ba38 diff --git a/ugene.spec b/ugene.spec index dd8562a..c438163 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220501 -%global gitcommit 53ab0fd01c88d46bf6b55a7f12416adc94dfd10e +%global gitdate 20220510 +%global gitcommit 12f603f07d7af765f17346362e451a3c87b27302 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free af85e4c261ca1b0268e505ca0f056ae124287dc7 +%global gitcommit_free 8c17c49d7b8ed4b10f9c31ca07a9d5ebb2977497 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220502 -%global tarballtime 1737 +%global tarballdate 20220512 +%global tarballtime 1556 %global use_release 0 %global use_gitbare 1 From 1403aebf152be65df269577dde1038ec74ba0cce Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 26 May 2022 22:19:51 +0900 Subject: [PATCH 064/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 627fd3c..ef8c55b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220512T1556.tar.gz) = c56a632ee855c5e6babbb3f4016a635d4714598723f43f6d19d6bb917ce07bb37d35863848954f390d63658a4ad36e6e2ef50ce098e2719fa52ee15e8889ba38 +SHA512 (ugene-free-20220526T1619.tar.gz) = 095ac891cfa3dd4c046272b1f8a36b73b8ff3cae11fbe94e2c80d960b355764178037d85729692e9dd204c8982d48eb168d517123087a2512ed89e927289be33 diff --git a/ugene.spec b/ugene.spec index c438163..21ea26f 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220510 -%global gitcommit 12f603f07d7af765f17346362e451a3c87b27302 +%global gitdate 20220525 +%global gitcommit af1161051f9430596bde16052b2cbb153a648852 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 8c17c49d7b8ed4b10f9c31ca07a9d5ebb2977497 +%global gitcommit_free d72bda16afad368c64fcf9af1d1344b8f0f54fea %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220512 -%global tarballtime 1556 +%global tarballdate 20220526 +%global tarballtime 1619 %global use_release 0 %global use_gitbare 1 From 1b1a8543ee3e4b46133ba2ec25e258b9fa4314f3 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 31 May 2022 19:37:18 +0900 Subject: [PATCH 065/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index ef8c55b..23baf3b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220526T1619.tar.gz) = 095ac891cfa3dd4c046272b1f8a36b73b8ff3cae11fbe94e2c80d960b355764178037d85729692e9dd204c8982d48eb168d517123087a2512ed89e927289be33 +SHA512 (ugene-free-20220531T1416.tar.gz) = 1c64f1871180d156afc257823ad1b3ff2461908b382998526958f97763ccff2e18ca5959e4024ad26a63856e2650ca89389d7c067503c879d710b9585a08b6c0 diff --git a/ugene.spec b/ugene.spec index 21ea26f..76c6b9e 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220525 -%global gitcommit af1161051f9430596bde16052b2cbb153a648852 +%global gitdate 20220528 +%global gitcommit 4b23579dea07e4e55aa9da64eefdd045b455a90f # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free d72bda16afad368c64fcf9af1d1344b8f0f54fea +%global gitcommit_free 52647cc73d46e82f0fb7829a53d60acd0e4582c6 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220526 -%global tarballtime 1619 +%global tarballdate 20220531 +%global tarballtime 1416 %global use_release 0 %global use_gitbare 1 From 5ae68473fd464f891decfec744b2f31bfa2a16d0 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 6 Jun 2022 12:10:28 +0900 Subject: [PATCH 066/260] 43.0 --- sources | 2 +- ugene.spec | 11 +++++++---- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/sources b/sources index 23baf3b..b24837d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220531T1416.tar.gz) = 1c64f1871180d156afc257823ad1b3ff2461908b382998526958f97763ccff2e18ca5959e4024ad26a63856e2650ca89389d7c067503c879d710b9585a08b6c0 +SHA512 (ugene-free-43.0.tar.gz) = ec9e636536f577beecdea179cda490fc3775a5c1f9abbbca2ae3c9e3fc6744046528ba5ebb674be4875c0262bafad0354f7f7f8ca6065d6a6a9156b895811cfe diff --git a/ugene.spec b/ugene.spec index 76c6b9e..080c845 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20220531 %global tarballtime 1416 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1.1 +%global mainrel 1 %undefine prever %if 0%{?use_release} >= 1 @@ -49,7 +49,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 42.0 +Version: 43.0 Release: %{fedorarel}%{?dist} #The entire source code is GPLv2+ except: @@ -250,6 +250,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Mon Jun 6 2022 Mamoru TASAKA - 43.0-1 +- 43.0 + * Wed Mar 9 2022 Mamoru TASAKA - 42.0-1 - 42.0 From f4c10cfb052a6ed803410ba87b4c7c689257af43 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 16 Jun 2022 22:32:50 +0900 Subject: [PATCH 067/260] bump release --- ugene.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 080c845..fad03ac 100644 --- a/ugene.spec +++ b/ugene.spec @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1 +%global mainrel 2 %undefine prever %if 0%{?use_release} >= 1 From 7820c9e9ace00ead703d0e41c13eca537c0f5d7f Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 16 Jun 2022 22:45:15 +0900 Subject: [PATCH 068/260] try the latest git --- sources | 2 +- ...-git-plgins-smith_waterman-nonsse2-arch.patch | 2 +- ugene.spec | 16 ++++++++-------- 3 files changed, 10 insertions(+), 10 deletions(-) rename ugene-42.0-git-plgins-smith_waterman-nonsse2-arch.patch => ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch (99%) diff --git a/sources b/sources index b24837d..ff8d8fc 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-43.0.tar.gz) = ec9e636536f577beecdea179cda490fc3775a5c1f9abbbca2ae3c9e3fc6744046528ba5ebb674be4875c0262bafad0354f7f7f8ca6065d6a6a9156b895811cfe +SHA512 (ugene-free-20220616T2209.tar.gz) = 47eba40d29088da4fcc523932985d00d332851c84177e9ae07518f073ca612ef078347f05319d9bbb502256c314b18370913a80425e51f72ba626861ac77a3ba diff --git a/ugene-42.0-git-plgins-smith_waterman-nonsse2-arch.patch b/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch similarity index 99% rename from ugene-42.0-git-plgins-smith_waterman-nonsse2-arch.patch rename to ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch index 4859dbf..44aea3c 100644 --- a/ugene-42.0-git-plgins-smith_waterman-nonsse2-arch.patch +++ b/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch @@ -78,9 +78,9 @@ */ +#if defined(__SSE2__) - #include "SmithWatermanAlgorithmSSE2.h" #include #include + @@ -1210,3 +1211,4 @@ } diff --git a/ugene.spec b/ugene.spec index fad03ac..18cedbe 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220528 -%global gitcommit 4b23579dea07e4e55aa9da64eefdd045b455a90f +%global gitdate 20220615 +%global gitcommit 5ca741e94450802f55128f31fdf8155f5f05212b # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 52647cc73d46e82f0fb7829a53d60acd0e4582c6 +%global gitcommit_free 5f4960a339c39b9b416d382057ad31f76c37f80e %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220531 -%global tarballtime 1416 +%global tarballdate 20220616 +%global tarballtime 2209 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force @@ -76,7 +76,7 @@ Patch102: ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch Patch104: ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch -Patch106: ugene-42.0-git-plgins-smith_waterman-nonsse2-arch.patch +Patch106: ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch BuildRequires: make From b2d257da0e512468a8dd33c7dd0dc2dc2fca3379 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 21 Jun 2022 15:57:29 +0900 Subject: [PATCH 069/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index ff8d8fc..1b72458 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220616T2209.tar.gz) = 47eba40d29088da4fcc523932985d00d332851c84177e9ae07518f073ca612ef078347f05319d9bbb502256c314b18370913a80425e51f72ba626861ac77a3ba +SHA512 (ugene-free-20220621T1519.tar.gz) = 1f7613ce0bc919f185a897acab783f3ae4c151e2dec4d9490412d2a3516ed766a36d286339d51c060c7800dd01082beba09af5d2a3f207149e142d75364d4ae1 diff --git a/ugene.spec b/ugene.spec index 18cedbe..ce8def6 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220615 -%global gitcommit 5ca741e94450802f55128f31fdf8155f5f05212b +%global gitdate 20220621 +%global gitcommit 8d043902f8d62e815abcb2005c54929c3f48e5d8 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 5f4960a339c39b9b416d382057ad31f76c37f80e +%global gitcommit_free 90b355e5691e487f6572e70d6afb1af71f64c418 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220616 -%global tarballtime 2209 +%global tarballdate 20220621 +%global tarballtime 1519 %global use_release 0 %global use_gitbare 1 From 746f86566035f4a75eb3cc473f2b5b0e1104b06e Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 1 Jul 2022 15:15:58 +0900 Subject: [PATCH 070/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 1b72458..684c8be 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220621T1519.tar.gz) = 1f7613ce0bc919f185a897acab783f3ae4c151e2dec4d9490412d2a3516ed766a36d286339d51c060c7800dd01082beba09af5d2a3f207149e142d75364d4ae1 +SHA512 (ugene-free-20220701T1044.tar.gz) = 10a5e724bbccee248a96a8c0d1f5d1256dca9f35214b7fef4040381d045d6e6e002f752e1d03f6fd7aed2c1f9a66b7bf42646fb3865827a2154fbfdc6dec3ffc diff --git a/ugene.spec b/ugene.spec index ce8def6..5cde29e 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220621 -%global gitcommit 8d043902f8d62e815abcb2005c54929c3f48e5d8 +%global gitdate 20220629 +%global gitcommit 1f4223332c473bb617afdb5f9655cc4b8e2d9cc3 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 90b355e5691e487f6572e70d6afb1af71f64c418 +%global gitcommit_free 99200341dbc51571f0baa879a1f828159596d8c9 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220621 -%global tarballtime 1519 +%global tarballdate 20220701 +%global tarballtime 1044 %global use_release 0 %global use_gitbare 1 From 2ab9990445c996333f57fef276a0c0140905a5c8 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 13 Jul 2022 22:30:22 +0900 Subject: [PATCH 071/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 684c8be..f5300a1 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220701T1044.tar.gz) = 10a5e724bbccee248a96a8c0d1f5d1256dca9f35214b7fef4040381d045d6e6e002f752e1d03f6fd7aed2c1f9a66b7bf42646fb3865827a2154fbfdc6dec3ffc +SHA512 (ugene-free-20220713T1437.tar.gz) = 58b0ced28bc6d90d13a6d3b52cee26dd61ebbe60bc1539c408e19aab4fb36930b6f74e56666391b7d13e97f6338478ddf2da358e0833f487582c871492d65435 diff --git a/ugene.spec b/ugene.spec index 5cde29e..74718c0 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220629 -%global gitcommit 1f4223332c473bb617afdb5f9655cc4b8e2d9cc3 +%global gitdate 20220712 +%global gitcommit 14b99181d291375d62c6dd8a9990297e4e385e6b # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 99200341dbc51571f0baa879a1f828159596d8c9 +%global gitcommit_free b9cfc8c53e148b029072c7549d67a7977c566855 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220701 -%global tarballtime 1044 +%global tarballdate 20220713 +%global tarballtime 1437 %global use_release 0 %global use_gitbare 1 From a56a2937aa01211e7da3a114975f6a434a6cb066 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 23 Jul 2022 11:18:40 +0000 Subject: [PATCH 072/260] Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index fad03ac..6887871 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 43.0 -Release: %{fedorarel}%{?dist} +Release: %{fedorarel}%{?dist}.1 #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -250,6 +250,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sat Jul 23 2022 Fedora Release Engineering - 43.0-2.1 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild + * Mon Jun 6 2022 Mamoru TASAKA - 43.0-1 - 43.0 From 8d3bb2d3e345c5f82bbeb3b3bfeb9736b9f2ff15 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 30 Jul 2022 23:37:23 +0900 Subject: [PATCH 073/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index f5300a1..5206554 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220713T1437.tar.gz) = 58b0ced28bc6d90d13a6d3b52cee26dd61ebbe60bc1539c408e19aab4fb36930b6f74e56666391b7d13e97f6338478ddf2da358e0833f487582c871492d65435 +SHA512 (ugene-free-20220730T2238.tar.gz) = 194158a03571c8b20701532a4843eb6d1f1724a6e1d1cf2516aac482dd162cf85a13de39f33c53243aedbcc2c2a3be6f113ed6332125e096dfed357a9b6dd398 diff --git a/ugene.spec b/ugene.spec index 74718c0..7065eaa 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220712 -%global gitcommit 14b99181d291375d62c6dd8a9990297e4e385e6b +%global gitdate 20220730 +%global gitcommit 7e8380e0ecd5a4cd1a2fc8d73cd5b7c195eb3583 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b9cfc8c53e148b029072c7549d67a7977c566855 +%global gitcommit_free 37283aa8b8e718b646ab6570eec75d49ca7e9701 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220713 -%global tarballtime 1437 +%global tarballdate 20220730 +%global tarballtime 2238 %global use_release 0 %global use_gitbare 1 From 4e7fdd44a209505cba1f90e208d122aba40e2a17 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 17 Aug 2022 16:00:55 +0900 Subject: [PATCH 074/260] update to the latest git --- sources | 2 +- ugene-42.0-ugenem-cpuid-supported-arch.patch | 20 -------------------- ugene.spec | 13 +++++-------- 3 files changed, 6 insertions(+), 29 deletions(-) delete mode 100644 ugene-42.0-ugenem-cpuid-supported-arch.patch diff --git a/sources b/sources index 5206554..dd712ef 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220730T2238.tar.gz) = 194158a03571c8b20701532a4843eb6d1f1724a6e1d1cf2516aac482dd162cf85a13de39f33c53243aedbcc2c2a3be6f113ed6332125e096dfed357a9b6dd398 +SHA512 (ugene-free-20220817T1514.tar.gz) = 95bbb9adae45eb61e53c699f321731a67bc28c57113203fa86838015b32b6428dc61421557b928f6417474ce49596b39e27c8510a1244b5c49fa445f046fbd6b diff --git a/ugene-42.0-ugenem-cpuid-supported-arch.patch b/ugene-42.0-ugenem-cpuid-supported-arch.patch deleted file mode 100644 index 10a04bd..0000000 --- a/ugene-42.0-ugenem-cpuid-supported-arch.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- ugene-42.0/src/ugenem/src/SendReportDialog.cpp.cpuid 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-42.0/src/ugenem/src/SendReportDialog.cpp 2021-11-08 19:56:32.468424643 +0900 -@@ -425,7 +425,7 @@ - return (int)(getMemorySize() / (1024 * 1024)); - } - --#ifndef Q_OS_DARWIN -+#if defined(__x86_64__) || defined (__i386__) - void cpuID(unsigned i, unsigned regs[4]) { - # ifdef _WIN32 - __cpuid((int*)regs, (int)i); -@@ -441,7 +441,7 @@ - - QString ReportSender::getCPUInfo() { - QString result; --#ifndef Q_OS_DARWIN -+#if defined(__x86_64__) || defined (__i386__) - unsigned regs[4]; - - // Get vendor diff --git a/ugene.spec b/ugene.spec index 7065eaa..bbbb2a6 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220730 -%global gitcommit 7e8380e0ecd5a4cd1a2fc8d73cd5b7c195eb3583 +%global gitdate 20220815 +%global gitcommit 8b6c9d5487227e26e414d93442a5083c3e705091 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 37283aa8b8e718b646ab6570eec75d49ca7e9701 +%global gitcommit_free 94307b664095fb0e88062f570c8c765d8cbf5cc5 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220730 -%global tarballtime 2238 +%global tarballdate 20220817 +%global tarballtime 1514 %global use_release 0 %global use_gitbare 1 @@ -71,7 +71,6 @@ Source2: create-%{name}-git-bare-tarball.sh # This is not installed Source10: ugene.wrapper # Currently distro-specific -Patch101: ugene-42.0-ugenem-cpuid-supported-arch.patch Patch102: ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch Patch104: ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch @@ -132,8 +131,6 @@ git config user.name "%{name} Fedora maintainer" git config user.email "%{name}-maintainers@fedoraproject.org" %endif -%patch101 -p1 -b .cpuid -Z - %GIT commit -m "ugenem: support architecture not supporting cpuid" -a %patch102 -p1 -b .sys_mmap -Z %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a %patch103 -p1 -b .unwind -Z From 15e44588ab4a27331ebba2156e98e37a79402fcd Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 17 Aug 2022 21:01:29 +0900 Subject: [PATCH 075/260] add patch to fix wrong elif --- ugene-43.x-wrong-elif-SendReportDialog.patch | 17 +++++++++++++++++ ugene.spec | 3 +++ 2 files changed, 20 insertions(+) create mode 100644 ugene-43.x-wrong-elif-SendReportDialog.patch diff --git a/ugene-43.x-wrong-elif-SendReportDialog.patch b/ugene-43.x-wrong-elif-SendReportDialog.patch new file mode 100644 index 0000000..ac49ca0 --- /dev/null +++ b/ugene-43.x-wrong-elif-SendReportDialog.patch @@ -0,0 +1,17 @@ +--- ugene-43.0/src/ugenem/src/SendReportDialog.cpp.elif 2022-08-17 15:55:45.936686547 +0900 ++++ ugene-43.0/src/ugenem/src/SendReportDialog.cpp 2022-08-17 20:56:02.123046050 +0900 +@@ -497,11 +497,11 @@ + QString ReportSender::getArchSuffix() const { + #ifdef Q_PROCESSOR_X86_64 + return " x64"; +-#elif Q_PROCESSOR_X86_32 ++#elif defined(Q_PROCESSOR_X86_32) + return " x86"; +-#elif Q_PROCESSOR_ARM_64 ++#elif defined(Q_PROCESSOR_ARM_64) + return " arm-64"; +-#elif Q_PROCESSOR_ARM_32 ++#elif defined(Q_PROCESSOR_ARM_32) + return " arm-32"; + #else + return " unknown-arch"; diff --git a/ugene.spec b/ugene.spec index bbbb2a6..a61c1c9 100644 --- a/ugene.spec +++ b/ugene.spec @@ -77,6 +77,7 @@ Patch104: ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch Patch106: ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch +Patch108: ugene-43.x-wrong-elif-SendReportDialog.patch BuildRequires: make BuildRequires: gcc-c++ @@ -143,6 +144,8 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %GIT commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a %patch107 -p1 -b .char_bigen -Z %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a +%patch108 -p1 -b .elif -Z + %GIT commit -m "ugenem/src/SendReportDialog.cpp: fix wrong elif usage" -a sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d' From b4e83fb2be0fd3b8d31c4a9e0ecc1f310483a6b5 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 21 Aug 2022 22:35:34 +0900 Subject: [PATCH 076/260] reset release for merge --- ugene.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 6887871..c9acaff 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 43.0 -Release: %{fedorarel}%{?dist}.1 +Release: %{fedorarel}%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 From 6201b11ff2506d6eb43bc2cf4e56e1f677c0d726 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 21 Aug 2022 22:36:54 +0900 Subject: [PATCH 077/260] update to 44.0 --- sources | 2 +- ugene.spec | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/sources b/sources index dd712ef..0a319e8 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220817T1514.tar.gz) = 95bbb9adae45eb61e53c699f321731a67bc28c57113203fa86838015b32b6428dc61421557b928f6417474ce49596b39e27c8510a1244b5c49fa445f046fbd6b +SHA512 (ugene-free-44.0.tar.gz) = 2bc39e98335a5a89267759d438bb7b3fc61c44077a95385d0f2b39affbc07ac17956da35e64f7ae8df16c4ea469d1a937092592c34af2775c3eaa0a6ecd9f6dd diff --git a/ugene.spec b/ugene.spec index a61c1c9..5519e41 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20220817 %global tarballtime 1514 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 2 +%global mainrel 1 %undefine prever %if 0%{?use_release} >= 1 @@ -49,7 +49,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 43.0 +Version: 44.0 Release: %{fedorarel}%{?dist} #The entire source code is GPLv2+ except: From a686200eb7f30efc3c42697204393249c582d94d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 21 Aug 2022 22:37:31 +0900 Subject: [PATCH 078/260] add changelog --- ugene.spec | 3 +++ 1 file changed, 3 insertions(+) diff --git a/ugene.spec b/ugene.spec index ecc4505..9dfb7d8 100644 --- a/ugene.spec +++ b/ugene.spec @@ -250,6 +250,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sun Aug 21 2022 Mamoru TASAKA - 44.0-1 +- 44.0 + * Sat Jul 23 2022 Fedora Release Engineering - 43.0-2.1 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild From 188690e6e543541a0ad84660bd746a0e9bdd4a50 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 2 Sep 2022 14:25:44 +0900 Subject: [PATCH 079/260] update to the latest git --- sources | 2 +- ugene.spec | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/sources b/sources index 0a319e8..64edd5a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-44.0.tar.gz) = 2bc39e98335a5a89267759d438bb7b3fc61c44077a95385d0f2b39affbc07ac17956da35e64f7ae8df16c4ea469d1a937092592c34af2775c3eaa0a6ecd9f6dd +SHA512 (ugene-free-20220902T1349.tar.gz) = a6d03020ab97a448c43d1fb176be6b715ead34fc896be72130d0b888313fffb238384ba64c2b905eb84fcc5a7b54a18891297fbffe3e4233deccfd1646a81ad4 diff --git a/ugene.spec b/ugene.spec index 9dfb7d8..4ce39e0 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220815 -%global gitcommit 8b6c9d5487227e26e414d93442a5083c3e705091 +%global gitdate 20220902 +%global gitcommit 3bee9ad48edc30f82bf5a7b905b9e8f3b205ae69 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 94307b664095fb0e88062f570c8c765d8cbf5cc5 +%global gitcommit_free 723e25eb78cbe4460f43239c61713adfe6b43a5e %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220817 -%global tarballtime 1514 +%global tarballdate 20220902 +%global tarballtime 1349 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1 +%global mainrel 1.1 %undefine prever %if 0%{?use_release} >= 1 From 515647b3f587d1d145efdf9c677240e847f638cd Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 23 Sep 2022 15:58:32 +0900 Subject: [PATCH 080/260] update to the latest git --- sources | 2 +- ugene-40.1-qbswap-bigendian-workaround.patch | 2 +- ...t-plgins-smith_waterman-nonsse2-arch.patch | 38 ++++++++++--------- ...ty-breakpad-sys_mmap_use_system_mmap.patch | 6 +-- ugene.spec | 12 +++--- 5 files changed, 32 insertions(+), 28 deletions(-) rename ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch => ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch (96%) diff --git a/sources b/sources index 64edd5a..14c7526 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220902T1349.tar.gz) = a6d03020ab97a448c43d1fb176be6b715ead34fc896be72130d0b888313fffb238384ba64c2b905eb84fcc5a7b54a18891297fbffe3e4233deccfd1646a81ad4 +SHA512 (ugene-free-20220923T1431.tar.gz) = 6be5a896861465a90be56987a7df9b1d7c9c06cc58a57d145a5ce5096f3af634a888b261763fd965ab641c2a103ee39f61298c422c9841d347b1d8179d3fb26b diff --git a/ugene-40.1-qbswap-bigendian-workaround.patch b/ugene-40.1-qbswap-bigendian-workaround.patch index 7733aef..813d7a8 100644 --- a/ugene-40.1-qbswap-bigendian-workaround.patch +++ b/ugene-40.1-qbswap-bigendian-workaround.patch @@ -42,4 +42,4 @@ + namespace U2 { - static quint8 cigarOp2samtools(U2CigarOp op, U2OpStatus &os) { + static quint8 cigarOp2samtools(U2CigarOp op, U2OpStatus& os) { diff --git a/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch b/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch index 44aea3c..59756dd 100644 --- a/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch +++ b/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch @@ -1,20 +1,24 @@ --- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp.sse_2 2021-11-11 15:42:19.590500062 +0900 +++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp 2021-11-11 15:42:26.384496818 +0900 -@@ -99,9 +99,11 @@ +@@ -90,13 +90,15 @@ + swar->registerFactory(new SWTaskFactory(SW_classic), QString("Classic 2")); // ADV search register par->registerAlgorithm(new SWPairwiseAlignmentAlgorithm()); - regDependedIMPLFromOtherPlugins(); +#if defined (__SSE2__) coreLog.trace("Registering SSE2 SW implementation"); swar->registerFactory(new SWTaskFactory(SW_sse2), QString("SSE2")); - par->getAlgorithm("Smith-Waterman")->addAlgorithmRealization(new PairwiseAlignmentSmithWatermanTaskFactory(SW_sse2), new PairwiseAlignmentSmithWatermanGUIExtensionFactory(SW_sse2), "SSE2"); + par->getAlgorithm("Smith-Waterman") + ->addAlgorithmRealization( + new PairwiseAlignmentSmithWatermanTaskFactory(SW_sse2), + new PairwiseAlignmentSmithWatermanGUIExtensionFactory(SW_sse2), + "SSE2"); +#endif - - this->connect(AppContext::getPluginSupport(), SIGNAL(si_allStartUpPluginsLoaded()), SLOT(regDependedIMPLFromOtherPlugins())); } + + QList SWAlgorithmTests::createTestFactories() { --- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp.sse_2 2021-11-11 15:42:19.590500062 +0900 +++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp 2021-11-11 15:46:26.960369309 +0900 -@@ -181,6 +181,7 @@ +@@ -146,6 +146,7 @@ sWatermanConfig.sqnc.left(c.chunkSize * c.nThreads), sWatermanConfig.resultView); break; @@ -22,7 +26,7 @@ case SW_sse2: neededRam = SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(sWatermanConfig.ptrn, sWatermanConfig.sqnc.left(c.chunkSize * c.nThreads), -@@ -189,6 +190,7 @@ +@@ -154,6 +155,7 @@ minScore, maxScore, sWatermanConfig.resultView); @@ -30,7 +34,7 @@ break; default: assert(0); -@@ -267,7 +269,12 @@ +@@ -182,7 +184,12 @@ SmithWatermanAlgorithm* sw = nullptr; if (algType == SW_sse2) { @@ -40,10 +44,10 @@ + coreLog.error("SSE2 was not enabled in this build"); + return; +#endif - } else if (algType == SW_cuda) { - #ifdef SW2_BUILD_WITH_CUDA - sw = new SmithWatermanAlgorithmCUDA; -@@ -581,7 +588,11 @@ + } else { + assert(algType == SW_classic); + sw = new SmithWatermanAlgorithm; +@@ -458,7 +465,11 @@ SmithWatermanAlgorithm* sw = nullptr; if (algType == SW_sse2) { @@ -52,10 +56,10 @@ +#else + coreLog.error("SSE2 was not enabled in this build"); +#endif - } else if (algType == SW_cuda) { - #ifdef SW2_BUILD_WITH_CUDA - sw = new SmithWatermanAlgorithmCUDA; -@@ -745,6 +756,7 @@ + } else { + assert(algType == SW_classic); + sw = new SmithWatermanAlgorithm; +@@ -582,6 +593,7 @@ sqnc->left(c.chunkSize * c.nThreads), SmithWatermanSettings::MULTIPLE_ALIGNMENT); break; @@ -63,7 +67,7 @@ case SW_sse2: neededRam = SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(*ptrn, sqnc->left(c.chunkSize * c.nThreads), -@@ -753,6 +765,7 @@ +@@ -590,6 +602,7 @@ minScore, maxScore, SmithWatermanSettings::MULTIPLE_ALIGNMENT); diff --git a/ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch b/ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch similarity index 96% rename from ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch rename to ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch index 726b799..5497653 100644 --- a/ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch +++ b/ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch @@ -19,7 +19,7 @@ --- ugene-42.x/src/libs_3rdparty/breakpad/src/third_party/lss/linux_syscall_support.h.sys_mmap 2021-10-11 15:41:23.000000000 +0900 +++ ugene-42.x/src/libs_3rdparty/breakpad/src/third_party/lss/linux_syscall_support.h 2021-11-09 00:46:06.363362301 +0900 -@@ -85,10 +85,7 @@ +@@ -86,10 +86,7 @@ * on Linux. * Porting to other related platforms should not be difficult. */ @@ -31,7 +31,7 @@ #ifndef SYS_CPLUSPLUS #ifdef __cplusplus -@@ -107,15 +104,21 @@ extern "C" { +@@ -108,15 +105,21 @@ extern "C" { #include #include #include @@ -54,7 +54,7 @@ #ifdef __mips__ /* Include definitions of the ABI currently in use. */ #ifdef __ANDROID__ -@@ -4021,6 +4024,48 @@ struct kernel_statfs { +@@ -4859,6 +4862,48 @@ struct kernel_statfs { #pragma pop_macro("pwrite64") #pragma pop_macro("getdents64") diff --git a/ugene.spec b/ugene.spec index 4ce39e0..5bf5098 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220902 -%global gitcommit 3bee9ad48edc30f82bf5a7b905b9e8f3b205ae69 +%global gitdate 20220922 +%global gitcommit 41c84f94ef7ae4afced3569e7e18f9a5f99faa23 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 723e25eb78cbe4460f43239c61713adfe6b43a5e +%global gitcommit_free ab6a7f54c6d141300aad9c1d64e4c66d7490a7c7 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220902 -%global tarballtime 1349 +%global tarballdate 20220923 +%global tarballtime 1431 %global use_release 0 %global use_gitbare 1 @@ -71,7 +71,7 @@ Source2: create-%{name}-git-bare-tarball.sh # This is not installed Source10: ugene.wrapper # Currently distro-specific -Patch102: ugene-42.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch +Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch Patch104: ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch From 21e19b095210a0c7fdaf23b39f8f94849961dde3 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 25 Sep 2022 21:48:48 +0900 Subject: [PATCH 081/260] Update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 14c7526..8d8a278 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220923T1431.tar.gz) = 6be5a896861465a90be56987a7df9b1d7c9c06cc58a57d145a5ce5096f3af634a888b261763fd965ab641c2a103ee39f61298c422c9841d347b1d8179d3fb26b +SHA512 (ugene-free-20220925T2105.tar.gz) = 2dfd4020816d383fad3179d712c36f58e9428838dbf82bc050d12edb51e4e1b6b6e2e26e2892e2fa6de1435cbefc9e379f6609d9539ee07bdc630de597fa682b diff --git a/ugene.spec b/ugene.spec index 5bf5098..b78c43c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220922 -%global gitcommit 41c84f94ef7ae4afced3569e7e18f9a5f99faa23 +%global gitdate 20220924 +%global gitcommit 25934d10b2e52679f9ec395e4a5acae6777caa4e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free ab6a7f54c6d141300aad9c1d64e4c66d7490a7c7 +%global gitcommit_free d857d173eb400a020189563cb260d7fb18d04606 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220923 -%global tarballtime 1431 +%global tarballdate 20220925 +%global tarballtime 2105 %global use_release 0 %global use_gitbare 1 From 72a613bd3eded96d9279f6acf1311a71a2c00e4d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 6 Oct 2022 14:17:50 +0900 Subject: [PATCH 082/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 8d8a278..b3c4cf8 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20220925T2105.tar.gz) = 2dfd4020816d383fad3179d712c36f58e9428838dbf82bc050d12edb51e4e1b6b6e2e26e2892e2fa6de1435cbefc9e379f6609d9539ee07bdc630de597fa682b +SHA512 (ugene-free-20221006T1206.tar.gz) = 194dfd1aa9419cbf22d2ca6a80bac2c3ba64d44189d8c9111869781bd39e9883c1f9c9266343b70fb331e812d1971e51a9e5a4268114e27059c69f5689e0732f diff --git a/ugene.spec b/ugene.spec index b78c43c..7239a7d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20220924 -%global gitcommit 25934d10b2e52679f9ec395e4a5acae6777caa4e +%global gitdate 20221005 +%global gitcommit 40f1bd56ee87062e92d654e9df9264fd75efa705 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free d857d173eb400a020189563cb260d7fb18d04606 +%global gitcommit_free 1eb0ec474d09476b0d1b7a08aecacf98f66022e4 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20220925 -%global tarballtime 2105 +%global tarballdate 20221006 +%global tarballtime 1206 %global use_release 0 %global use_gitbare 1 From cc327cac272b194157b1d103a182e36614c81445 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 9 Oct 2022 17:09:25 +0900 Subject: [PATCH 083/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index b3c4cf8..04996fd 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221006T1206.tar.gz) = 194dfd1aa9419cbf22d2ca6a80bac2c3ba64d44189d8c9111869781bd39e9883c1f9c9266343b70fb331e812d1971e51a9e5a4268114e27059c69f5689e0732f +SHA512 (ugene-free-20221009T1650.tar.gz) = 9623746ad86e02608be0f73dd061a7c8426be1f6692b4ac5eca7a8d96a5544b5bd3ba14bbd7da5ecae9096a7f5bc8522beac1fec2577afc5cab8b38b65bd33fd diff --git a/ugene.spec b/ugene.spec index 7239a7d..cf19ee8 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221005 -%global gitcommit 40f1bd56ee87062e92d654e9df9264fd75efa705 +%global gitdate 20221006 +%global gitcommit 86e15e13fc5d7caf1c2806e27e8cad5a8759b44c # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 1eb0ec474d09476b0d1b7a08aecacf98f66022e4 +%global gitcommit_free 7a6b4e76d7fe2f86b3efdeb4e9d1ebfc2e7ea8ca %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221006 -%global tarballtime 1206 +%global tarballdate 20221009 +%global tarballtime 1650 %global use_release 0 %global use_gitbare 1 From 742bb97c0af29adf6ddc5dc40255d9a00133e5e3 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 18 Oct 2022 00:06:42 +0900 Subject: [PATCH 084/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 04996fd..393c7ab 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221009T1650.tar.gz) = 9623746ad86e02608be0f73dd061a7c8426be1f6692b4ac5eca7a8d96a5544b5bd3ba14bbd7da5ecae9096a7f5bc8522beac1fec2577afc5cab8b38b65bd33fd +SHA512 (ugene-free-20221017T2338.tar.gz) = 670690b6cbca62b799cdd2dbdd4a84147b0d12aed9914a0dba6c5df29a0f0540f88869e56b6d86fae3521a3b5e18369f9376e4f7c9b53ad661ed416dfae8b558 diff --git a/ugene.spec b/ugene.spec index cf19ee8..e03d741 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221006 -%global gitcommit 86e15e13fc5d7caf1c2806e27e8cad5a8759b44c +%global gitdate 20221017 +%global gitcommit 04c402d7fdc06104c0b5213e300725d5c019c62e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 7a6b4e76d7fe2f86b3efdeb4e9d1ebfc2e7ea8ca +%global gitcommit_free b06f05d79ebc63df9c328243e8382c7ba35b85ed %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221009 -%global tarballtime 1650 +%global tarballdate 20221017 +%global tarballtime 2338 %global use_release 0 %global use_gitbare 1 From 7c274321792193dbf437359bdd26d44dbe796d2a Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 21 Oct 2022 12:08:59 +0900 Subject: [PATCH 085/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 393c7ab..0f5d783 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221017T2338.tar.gz) = 670690b6cbca62b799cdd2dbdd4a84147b0d12aed9914a0dba6c5df29a0f0540f88869e56b6d86fae3521a3b5e18369f9376e4f7c9b53ad661ed416dfae8b558 +SHA512 (ugene-free-20221021T1121.tar.gz) = 0898815fa74717cba85fb971882958cf58131ad02beeecbdb2bc4320d0c3bc27caa272298d02dd7c5f6f2b74ab09e1e3af2a9e4d0dab49e0a00394b561e15c10 diff --git a/ugene.spec b/ugene.spec index e03d741..c63e339 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221017 -%global gitcommit 04c402d7fdc06104c0b5213e300725d5c019c62e +%global gitdate 20221019 +%global gitcommit 4e0b5c049dd817fc7b0eb448a0e31aa5948dc774 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b06f05d79ebc63df9c328243e8382c7ba35b85ed +%global gitcommit_free 906efec9b2607a11aea8d6c33a3d968a352fed4b %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221017 -%global tarballtime 2338 +%global tarballdate 20221021 +%global tarballtime 1121 %global use_release 0 %global use_gitbare 1 From 021519d849fb4fbf10dd0e78c95336efdadafdd6 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 23 Oct 2022 22:03:41 +0900 Subject: [PATCH 086/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0f5d783..106790b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221021T1121.tar.gz) = 0898815fa74717cba85fb971882958cf58131ad02beeecbdb2bc4320d0c3bc27caa272298d02dd7c5f6f2b74ab09e1e3af2a9e4d0dab49e0a00394b561e15c10 +SHA512 (ugene-free-20221023T2121.tar.gz) = 4b67bd56b85b662e0f303bc8f361094b852339e22ef2cb0e73906fc9ea3723b3b7d03f757011614d6e577c66b13d107c74ab7fa6bea949e114d70fa0a31d035e diff --git a/ugene.spec b/ugene.spec index c63e339..d2513ce 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221019 -%global gitcommit 4e0b5c049dd817fc7b0eb448a0e31aa5948dc774 +%global gitdate 20221021 +%global gitcommit c9b42eda47dc6e911a93f0174bf45b1ce879ea8b # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 906efec9b2607a11aea8d6c33a3d968a352fed4b +%global gitcommit_free 01f7f096f3f9b229f394b0be74ca36e12a118d4c %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221021 -%global tarballtime 1121 +%global tarballdate 20221023 +%global tarballtime 2121 %global use_release 0 %global use_gitbare 1 From 6933d4e16893998d91a1caed83fc9be8d18ee1ed Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 27 Oct 2022 10:09:57 +0900 Subject: [PATCH 087/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 106790b..9dddf4e 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221023T2121.tar.gz) = 4b67bd56b85b662e0f303bc8f361094b852339e22ef2cb0e73906fc9ea3723b3b7d03f757011614d6e577c66b13d107c74ab7fa6bea949e114d70fa0a31d035e +SHA512 (ugene-free-20221027T0926.tar.gz) = 9736c42e7db972767a18de6d5eca8ddb8740cc13e1ceed47fba1ce21b197bacb699a459fc16400d2e0ec35737304654838252d7ac032d060878f056c2f5fffa4 diff --git a/ugene.spec b/ugene.spec index d2513ce..ab37364 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221021 -%global gitcommit c9b42eda47dc6e911a93f0174bf45b1ce879ea8b +%global gitdate 20221026 +%global gitcommit 5e384f5ed9165298e2602ec4e097390432ee0e3e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 01f7f096f3f9b229f394b0be74ca36e12a118d4c +%global gitcommit_free 4ec81a4d9d4dfd903bb92b078566dd383c4540c1 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221023 -%global tarballtime 2121 +%global tarballdate 20221027 +%global tarballtime 0926 %global use_release 0 %global use_gitbare 1 From eee45c9f2e205d19b0e2dacb70f30761c1e98236 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 1 Nov 2022 23:36:07 +0900 Subject: [PATCH 088/260] Update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 9dddf4e..5eea821 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221027T0926.tar.gz) = 9736c42e7db972767a18de6d5eca8ddb8740cc13e1ceed47fba1ce21b197bacb699a459fc16400d2e0ec35737304654838252d7ac032d060878f056c2f5fffa4 +SHA512 (ugene-free-20221101T2024.tar.gz) = fe105b8e04fe4ed1b5bdf71000ac67373170b31c211b69d4fc56192b74bbab729d402fa66bb8c4301596eab741450e2ab16aead002b09706c34f75c6c214075b diff --git a/ugene.spec b/ugene.spec index ab37364..e92bcba 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221026 -%global gitcommit 5e384f5ed9165298e2602ec4e097390432ee0e3e +%global gitdate 20221030 +%global gitcommit 511ebffa4fcd1ac2aecf43e98f21166c26218bd8 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 4ec81a4d9d4dfd903bb92b078566dd383c4540c1 +%global gitcommit_free d805c2e417c1627f4cf70bea5cb6722ba0075525 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221027 -%global tarballtime 0926 +%global tarballdate 20221101 +%global tarballtime 2024 %global use_release 0 %global use_gitbare 1 From 53d18c37159aaf271ba14f949fe6961f129df44e Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 6 Nov 2022 16:26:40 +0900 Subject: [PATCH 089/260] update to the latest one --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 5eea821..ec49830 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221101T2024.tar.gz) = fe105b8e04fe4ed1b5bdf71000ac67373170b31c211b69d4fc56192b74bbab729d402fa66bb8c4301596eab741450e2ab16aead002b09706c34f75c6c214075b +SHA512 (ugene-free-20221106T1540.tar.gz) = badc6ebdf60c768fb22effec24447f4e1c753135dcc0b338dd6991d20ce751e68c2322dfa40b3cf2e451866493d5b9565d87e6d6d2c82e7544e092706ba9348c diff --git a/ugene.spec b/ugene.spec index e92bcba..733a8c0 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221030 -%global gitcommit 511ebffa4fcd1ac2aecf43e98f21166c26218bd8 +%global gitdate 20221106 +%global gitcommit 116253ae0aeba5ee97f7e9a62c37efdfbfb73b2e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free d805c2e417c1627f4cf70bea5cb6722ba0075525 +%global gitcommit_free f4cfeaae3ba653c5000e8b25e803371375f81f35 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221101 -%global tarballtime 2024 +%global tarballdate 20221106 +%global tarballtime 1540 %global use_release 0 %global use_gitbare 1 From f7f801f967f771c3309ad51b1470476805993fdd Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 14 Nov 2022 23:24:54 +0900 Subject: [PATCH 090/260] 43.0 --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index ec49830..d807d5c 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221106T1540.tar.gz) = badc6ebdf60c768fb22effec24447f4e1c753135dcc0b338dd6991d20ce751e68c2322dfa40b3cf2e451866493d5b9565d87e6d6d2c82e7544e092706ba9348c +SHA512 (ugene-free-20221114T2249.tar.gz) = ce927eb6d4c5793b31cca20e2e05e82b434f7f20438434457f9703d18d65ff201137dac905962684e28ff446ecc289718db9c18f08f62b1ad4eb582da83077fe diff --git a/ugene.spec b/ugene.spec index 733a8c0..4ff8bbb 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,8 +2,8 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221106 -%global gitcommit 116253ae0aeba5ee97f7e9a62c37efdfbfb73b2e +%global gitdate 20221114 +%global gitcommit cd5510d9a89ba264bf258532046ec3154088f928 # New git commit with non-free part removed using "git filter-branch" %global gitcommit_free f4cfeaae3ba653c5000e8b25e803371375f81f35 %else @@ -11,15 +11,15 @@ %global gitdate 20211117 %global gitcommit 2d776cc668bc5019452e25ecc330c88093e75c48 # New git commit with non-free part using "git filter-branch" -%global gitcommit_free 02c04596cd6543ab44cc212ac1b383f825998b0e +%global gitcommit_free f995e33068c5959c1bab249cd04ed3776e9b2d96 %endif %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221106 -%global tarballtime 1540 +%global tarballdate 20221114 +%global tarballtime 2249 %global use_release 0 %global use_gitbare 1 From a013fc91910261b8270c954c8c45717ebfec29fd Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 20 Nov 2022 09:32:38 +0900 Subject: [PATCH 091/260] 45.0 --- sources | 2 +- ugene.spec | 11 +++++++---- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/sources b/sources index d807d5c..9806cb5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221114T2249.tar.gz) = ce927eb6d4c5793b31cca20e2e05e82b434f7f20438434457f9703d18d65ff201137dac905962684e28ff446ecc289718db9c18f08f62b1ad4eb582da83077fe +SHA512 (ugene-free-45.0.tar.gz) = a0a1eb84b23df11b031d0f0df77809d35296bce2a9a04c1ea558409a5b1188a870ee45e0125ab7d5cd112abe13fd7be26e13d8811346be965bca7d3d28f478ab diff --git a/ugene.spec b/ugene.spec index 4ff8bbb..be4f656 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20221114 %global tarballtime 2249 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1.1 +%global mainrel 1 %undefine prever %if 0%{?use_release} >= 1 @@ -49,7 +49,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 44.0 +Version: 45.0 Release: %{fedorarel}%{?dist} #The entire source code is GPLv2+ except: @@ -250,6 +250,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sun Nov 20 2022 Mamoru TASAKA - 45.0-1 +- 45.0 + * Sun Aug 21 2022 Mamoru TASAKA - 44.0-1 - 44.0 From 281a22fe0a0bf5e760973ac52741b995be612664 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 28 Nov 2022 16:02:16 +0900 Subject: [PATCH 092/260] update to the latest git --- sources | 2 +- ugene.spec | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/sources b/sources index 9806cb5..860014d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-45.0.tar.gz) = a0a1eb84b23df11b031d0f0df77809d35296bce2a9a04c1ea558409a5b1188a870ee45e0125ab7d5cd112abe13fd7be26e13d8811346be965bca7d3d28f478ab +SHA512 (ugene-free-20221128T1422.tar.gz) = a3d9be154ee117c817ab7a1223b096367e0540e563c1a47ade772c7dfbffb1c8ca866132426accc0cd14d60f03b2f8ae7905ea557ec50673b41c41e43fa33194 diff --git a/ugene.spec b/ugene.spec index be4f656..e0632fa 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221114 -%global gitcommit cd5510d9a89ba264bf258532046ec3154088f928 +%global gitdate 20221125 +%global gitcommit 3eb3a6e303736a423a22b46ec562bdeb78eeeb8c # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free f4cfeaae3ba653c5000e8b25e803371375f81f35 +%global gitcommit_free c6b98f0fb4c878cdfafa246f7ee113f53affe7e5 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221114 -%global tarballtime 2249 +%global tarballdate 20221128 +%global tarballtime 1422 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1 +%global mainrel 1.1 %undefine prever %if 0%{?use_release} >= 1 From a1dfba7945013da85fb36b143089327b6298ddef Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 1 Dec 2022 14:09:42 +0900 Subject: [PATCH 093/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 860014d..e9d9d52 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221128T1422.tar.gz) = a3d9be154ee117c817ab7a1223b096367e0540e563c1a47ade772c7dfbffb1c8ca866132426accc0cd14d60f03b2f8ae7905ea557ec50673b41c41e43fa33194 +SHA512 (ugene-free-20221201T1115.tar.gz) = 885bdf407f247f92758248a09d23030edbc67c894c043ef8829219b3ec2b57dbbc568608996dff1dd5966f3202a305c34ae6b78a9de17151176c4020a075a0bc diff --git a/ugene.spec b/ugene.spec index e0632fa..b57089c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221125 -%global gitcommit 3eb3a6e303736a423a22b46ec562bdeb78eeeb8c +%global gitdate 20221130 +%global gitcommit 2abff2dbdd337591a8aeee8961d92622f18e1598 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free c6b98f0fb4c878cdfafa246f7ee113f53affe7e5 +%global gitcommit_free 8a984298f931d8e57649378221eda5ffcc33992a %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221128 -%global tarballtime 1422 +%global tarballdate 20221201 +%global tarballtime 1115 %global use_release 0 %global use_gitbare 1 From c560bd49c3d86af8cd24ece3baf320dc08a74306 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 10 Dec 2022 22:29:41 +0900 Subject: [PATCH 094/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index e9d9d52..bb1bc2a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221201T1115.tar.gz) = 885bdf407f247f92758248a09d23030edbc67c894c043ef8829219b3ec2b57dbbc568608996dff1dd5966f3202a305c34ae6b78a9de17151176c4020a075a0bc +SHA512 (ugene-free-20221210T2152.tar.gz) = 38f06b385524b627bb4a2cd18d74a08eee5df1ac8600e826d8dab1b700872233043242612b1e1da5ecfa1506a2f3b180c6ebe30ce85ad599bd878a9dd99aebd7 diff --git a/ugene.spec b/ugene.spec index b57089c..4a664d2 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221130 -%global gitcommit 2abff2dbdd337591a8aeee8961d92622f18e1598 +%global gitdate 20221208 +%global gitcommit d089bfa79643d9ac6a602cffccbdc78259960a7e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 8a984298f931d8e57649378221eda5ffcc33992a +%global gitcommit_free 2588a255e0f001a0fc3832346246bb400028b199 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221201 -%global tarballtime 1115 +%global tarballdate 20221210 +%global tarballtime 2152 %global use_release 0 %global use_gitbare 1 From 1db1ad13227c404b1a8c7d6afbeec3007499edc8 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 15 Dec 2022 00:11:37 +0900 Subject: [PATCH 095/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index bb1bc2a..e30a07b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221210T2152.tar.gz) = 38f06b385524b627bb4a2cd18d74a08eee5df1ac8600e826d8dab1b700872233043242612b1e1da5ecfa1506a2f3b180c6ebe30ce85ad599bd878a9dd99aebd7 +SHA512 (ugene-free-20221214T2306.tar.gz) = 5bcd28a683fd5f9457ecf64891a361de8cb3df29db25a5fbb93e8085920fca36530a50e5cfdd320f55f4c7384ed9a86b2a94b14ada6a7a862e0278bf1a6d87ba diff --git a/ugene.spec b/ugene.spec index 4a664d2..762eef9 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221208 -%global gitcommit d089bfa79643d9ac6a602cffccbdc78259960a7e +%global gitdate 20221214 +%global gitcommit a8c7ed9daaa098410b84b2f81827700cc061c985 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 2588a255e0f001a0fc3832346246bb400028b199 +%global gitcommit_free 91e71e8c4ce45163fc864f110fe9c7d70748f264 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221210 -%global tarballtime 2152 +%global tarballdate 20221214 +%global tarballtime 2306 %global use_release 0 %global use_gitbare 1 From 06a445cd086f0b7775e2d193e47748218ba1ee4d Mon Sep 17 00:00:00 2001 From: Florian Weimer Date: Tue, 20 Dec 2022 11:12:56 +0100 Subject: [PATCH 096/260] Apply upstream patch to fix C99 compatibility issue Related to: --- ugene-c99.patch | 19 +++++++++++++++++++ ugene.spec | 8 +++++++- 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 ugene-c99.patch diff --git a/ugene-c99.patch b/ugene-c99.patch new file mode 100644 index 0000000..538f5f6 --- /dev/null +++ b/ugene-c99.patch @@ -0,0 +1,19 @@ +commit a8c7ed9daaa098410b84b2f81827700cc061c985 +Author: Yuliya Algaer +Date: Wed Dec 14 16:14:44 2022 +0700 + + Replace 'ugene_custom_open' with a standard 'open' (#1034) + +diff --git a/src/libs_3rdparty/samtools/src/samtools/bgzf.c b/src/libs_3rdparty/samtools/src/samtools/bgzf.c +index 4a6852e7d9..0df061e2a3 100644 +--- a/src/libs_3rdparty/samtools/src/samtools/bgzf.c ++++ b/src/libs_3rdparty/samtools/src/samtools/bgzf.c +@@ -210,7 +210,7 @@ bgzf_open(const char* __restrict path, const char* __restrict mode) + #ifdef _WIN32 + oflag |= O_BINARY; + #endif +- fd = ugene_custom_open(path, oflag); ++ fd = open(path, oflag); + if (fd == -1) return 0; + fp = open_read(fd); + #endif diff --git a/ugene.spec b/ugene.spec index be4f656..cefffb7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1 +%global mainrel 2 %undefine prever %if 0%{?use_release} >= 1 @@ -78,6 +78,7 @@ Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch Patch106: ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch Patch108: ugene-43.x-wrong-elif-SendReportDialog.patch +Patch109: ugene-c99.patch BuildRequires: make BuildRequires: gcc-c++ @@ -146,6 +147,8 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a %patch108 -p1 -b .elif -Z %GIT commit -m "ugenem/src/SendReportDialog.cpp: fix wrong elif usage" -a +%patch109 -p1 -b .c99 -Z + %GIT commit -m "ugenem/src/SendReportDialog.cpp: fix wrong elif usage" -a sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d' @@ -250,6 +253,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Tue Dec 20 2022 Florian Weimer - 45.0-2 +- Apply upstream patch to fix C99 compatibility issue + * Sun Nov 20 2022 Mamoru TASAKA - 45.0-1 - 45.0 From c62eba5da2826d3a66ec3043f14e61ff42af8b5d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 25 Dec 2022 11:05:21 +0900 Subject: [PATCH 097/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index e30a07b..238776a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221214T2306.tar.gz) = 5bcd28a683fd5f9457ecf64891a361de8cb3df29db25a5fbb93e8085920fca36530a50e5cfdd320f55f4c7384ed9a86b2a94b14ada6a7a862e0278bf1a6d87ba +SHA512 (ugene-free-20221225T1004.tar.gz) = b8a17394d8f9d01f4d9b1497302021533063a45042cd811061a3d7226344e2833889106708722e0611bfbca3432dff7e6f8a88558f35187dd5706f9ec99e483c diff --git a/ugene.spec b/ugene.spec index 762eef9..c60618c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221214 -%global gitcommit a8c7ed9daaa098410b84b2f81827700cc061c985 +%global gitdate 20221224 +%global gitcommit 823b7e59fc56788f5afba3457816ebaca21399e0 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 91e71e8c4ce45163fc864f110fe9c7d70748f264 +%global gitcommit_free 6e559c7d73305f1fd511c043f0135d0c3cce44fd %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221214 -%global tarballtime 2306 +%global tarballdate 20221225 +%global tarballtime 1004 %global use_release 0 %global use_gitbare 1 From 5753a01f305952881cebae6ff2d26c19f8a5d07a Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 30 Dec 2022 12:15:56 +0900 Subject: [PATCH 098/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 238776a..0747ab5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221225T1004.tar.gz) = b8a17394d8f9d01f4d9b1497302021533063a45042cd811061a3d7226344e2833889106708722e0611bfbca3432dff7e6f8a88558f35187dd5706f9ec99e483c +SHA512 (ugene-free-20221229T2127.tar.gz) = 7c0316594a70e08e24861ee0d84452016d2c10806cc132eae3075415b906e63d37b353bc29e5694e286e679e3cc86899c303e321cabdc54797b318daced80031 diff --git a/ugene.spec b/ugene.spec index c60618c..0e38e3e 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221224 -%global gitcommit 823b7e59fc56788f5afba3457816ebaca21399e0 +%global gitdate 20221227 +%global gitcommit 14af2cf9a692e0c5caa119403e8dc1e858ade384 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 6e559c7d73305f1fd511c043f0135d0c3cce44fd +%global gitcommit_free d5af47e1b012eed1bd3bf1e2a819b6e561566403 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221225 -%global tarballtime 1004 +%global tarballdate 20221229 +%global tarballtime 2127 %global use_release 0 %global use_gitbare 1 From ac7447018dc2f214e63661b8180c2e363d29f5d3 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 31 Dec 2022 15:25:22 +0900 Subject: [PATCH 099/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0747ab5..5c4b92a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221229T2127.tar.gz) = 7c0316594a70e08e24861ee0d84452016d2c10806cc132eae3075415b906e63d37b353bc29e5694e286e679e3cc86899c303e321cabdc54797b318daced80031 +SHA512 (ugene-free-20221231T1427.tar.gz) = 2a09fa3eec9a1d9908b5caca5d1fddec4be85487a17e87661231a7a80d6e16b5faf61743d887d989efae268d7e254b6ce42669d9e1537c2293b419fcf889c4a5 diff --git a/ugene.spec b/ugene.spec index 0e38e3e..515e775 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221227 -%global gitcommit 14af2cf9a692e0c5caa119403e8dc1e858ade384 +%global gitdate 20221231 +%global gitcommit 43b637f4443fd5dcadb96165d5c95f8aa8303d27 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free d5af47e1b012eed1bd3bf1e2a819b6e561566403 +%global gitcommit_free f190f98f666220017087930c79d39f081fba6783 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221229 -%global tarballtime 2127 +%global tarballdate 20221231 +%global tarballtime 1427 %global use_release 0 %global use_gitbare 1 From 94d2471a81ca97995c6c04e4586c721f37f287d8 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 1 Jan 2023 10:11:42 +0900 Subject: [PATCH 100/260] A Happy New Year 45.1 release --- sources | 2 +- ugene.spec | 11 +++++++---- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/sources b/sources index 5c4b92a..a748f67 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20221231T1427.tar.gz) = 2a09fa3eec9a1d9908b5caca5d1fddec4be85487a17e87661231a7a80d6e16b5faf61743d887d989efae268d7e254b6ce42669d9e1537c2293b419fcf889c4a5 +SHA512 (ugene-free-45.1.tar.gz) = 10a20ea04dc167a82135ff99ad284bb8acdf35c0c9fa0344db631870de59afa091c20fbbab65f38f8259f86c185a8775ab608613aaaf2711d0554ee832b5959b diff --git a/ugene.spec b/ugene.spec index 515e775..2870c3b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20221231 %global tarballtime 1427 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1.1 +%global mainrel 1 %undefine prever %if 0%{?use_release} >= 1 @@ -49,7 +49,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 45.0 +Version: 45.1 Release: %{fedorarel}%{?dist} #The entire source code is GPLv2+ except: @@ -250,6 +250,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sun Jan 1 2023 Mamoru TASAKA - 45.1-1 +- A Happy New Year 45.1 release + * Sun Nov 20 2022 Mamoru TASAKA - 45.0-1 - 45.0 From d733d0274f2f2c726f5bb256ec51e1ab57cf0c5b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 1 Jan 2023 10:15:09 +0900 Subject: [PATCH 101/260] back mainrel --- ugene.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 083e9d0..c95d4f5 100644 --- a/ugene.spec +++ b/ugene.spec @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 2 +%global mainrel 1 %undefine prever %if 0%{?use_release} >= 1 From 8ca8a45f4e211f9835083ef551de981e1b43d289 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 4 Jan 2023 18:07:09 +0900 Subject: [PATCH 102/260] update to the latest git --- ugene.spec | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/ugene.spec b/ugene.spec index c95d4f5..0d742fe 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20221231 -%global gitcommit 43b637f4443fd5dcadb96165d5c95f8aa8303d27 +%global gitdate 20230103 +%global gitcommit c0ceba5fb05f1455e0534f33c7bfb47cdbe1db6e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free f190f98f666220017087930c79d39f081fba6783 +%global gitcommit_free e58b5783879f86900bef56255e989e18a4227b62 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20221231 -%global tarballtime 1427 +%global tarballdate 20230104 +%global tarballtime 1724 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1 +%global mainrel 1.1 %undefine prever %if 0%{?use_release} >= 1 From 9de443ff3624ad042bf88284a7152ac0544a04e1 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 4 Jan 2023 18:14:12 +0900 Subject: [PATCH 103/260] update to the latest git --- sources | 2 +- ugene-c99.patch | 19 ------------------- 2 files changed, 1 insertion(+), 20 deletions(-) delete mode 100644 ugene-c99.patch diff --git a/sources b/sources index a748f67..05b5034 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-45.1.tar.gz) = 10a20ea04dc167a82135ff99ad284bb8acdf35c0c9fa0344db631870de59afa091c20fbbab65f38f8259f86c185a8775ab608613aaaf2711d0554ee832b5959b +SHA512 (ugene-free-20230104T1724.tar.gz) = a5321d67b3f627a0fdc242b8193f550a8970139ebd9e4b8b896f9663af9398e057040a6416f24475c0845037ee2006fe7e3afb82ef8383b503ac2b4f2c6faf2d diff --git a/ugene-c99.patch b/ugene-c99.patch deleted file mode 100644 index 538f5f6..0000000 --- a/ugene-c99.patch +++ /dev/null @@ -1,19 +0,0 @@ -commit a8c7ed9daaa098410b84b2f81827700cc061c985 -Author: Yuliya Algaer -Date: Wed Dec 14 16:14:44 2022 +0700 - - Replace 'ugene_custom_open' with a standard 'open' (#1034) - -diff --git a/src/libs_3rdparty/samtools/src/samtools/bgzf.c b/src/libs_3rdparty/samtools/src/samtools/bgzf.c -index 4a6852e7d9..0df061e2a3 100644 ---- a/src/libs_3rdparty/samtools/src/samtools/bgzf.c -+++ b/src/libs_3rdparty/samtools/src/samtools/bgzf.c -@@ -210,7 +210,7 @@ bgzf_open(const char* __restrict path, const char* __restrict mode) - #ifdef _WIN32 - oflag |= O_BINARY; - #endif -- fd = ugene_custom_open(path, oflag); -+ fd = open(path, oflag); - if (fd == -1) return 0; - fp = open_read(fd); - #endif From 9aceedd398dff6f357f5cda8a94da80d88b8a403 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 17 Jan 2023 14:33:03 +0900 Subject: [PATCH 104/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 05b5034..e760a85 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230104T1724.tar.gz) = a5321d67b3f627a0fdc242b8193f550a8970139ebd9e4b8b896f9663af9398e057040a6416f24475c0845037ee2006fe7e3afb82ef8383b503ac2b4f2c6faf2d +SHA512 (ugene-free-20230117T1409.tar.gz) = 22496fe660e45df5e81ce9ddcfce54800abeeac7f7131610422b5abea0ff1bb9913339de4f5971ec0ed7f2a54c06ad7729e472775a4e819bfd991a7c8d82633f diff --git a/ugene.spec b/ugene.spec index 0d742fe..d9d9272 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230103 -%global gitcommit c0ceba5fb05f1455e0534f33c7bfb47cdbe1db6e +%global gitdate 20230116 +%global gitcommit 959b7d5775242c84cbec866897676f366fe372b1 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free e58b5783879f86900bef56255e989e18a4227b62 +%global gitcommit_free ce0246a7c9d15dd96fb81c67b514485cf9e2b844 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230104 -%global tarballtime 1724 +%global tarballdate 20230117 +%global tarballtime 1409 %global use_release 0 %global use_gitbare 1 From 4f79185d749f262d4551ca4d8aeab076339d2035 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 18 Jan 2023 23:26:25 +0900 Subject: [PATCH 105/260] Header file inclusion fix for gcc13 --- ugene-45.1-gcc13-header-inclusion.patch | 10 ++++++++++ ugene.spec | 9 ++++++++- 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 ugene-45.1-gcc13-header-inclusion.patch diff --git a/ugene-45.1-gcc13-header-inclusion.patch b/ugene-45.1-gcc13-header-inclusion.patch new file mode 100644 index 0000000..893da10 --- /dev/null +++ b/ugene-45.1-gcc13-header-inclusion.patch @@ -0,0 +1,10 @@ +--- ugene-45.1/src/libs_3rdparty/breakpad/src/client/linux/handler/minidump_descriptor.h.gcc13 2022-12-31 14:29:47.000000000 +0900 ++++ ugene-45.1/src/libs_3rdparty/breakpad/src/client/linux/handler/minidump_descriptor.h 2023-01-18 20:37:30.580774335 +0900 +@@ -34,6 +34,7 @@ + #include + + #include ++#include + + #include "client/linux/handler/microdump_extra_info.h" + #include "common/using_std_string.h" diff --git a/ugene.spec b/ugene.spec index c95d4f5..2bd078a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 1 +%global mainrel 2 %undefine prever %if 0%{?use_release} >= 1 @@ -70,6 +70,7 @@ Source1: create-ugene-free-tarball.sh Source2: create-%{name}-git-bare-tarball.sh # This is not installed Source10: ugene.wrapper +Patch1: ugene-45.1-gcc13-header-inclusion.patch # Currently distro-specific Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch @@ -132,6 +133,9 @@ git config user.name "%{name} Fedora maintainer" git config user.email "%{name}-maintainers@fedoraproject.org" %endif +%patch1 -p1 -b .gcc13 -Z + %GIT commit -m "add missing header file" -a + %patch102 -p1 -b .sys_mmap -Z %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a %patch103 -p1 -b .unwind -Z @@ -250,6 +254,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Wed Jan 18 2023 Mamoru TASAKA - 45.1-2 +- Header file inclusion fix for gcc13 + * Sun Jan 1 2023 Mamoru TASAKA - 45.1-1 - A Happy New Year 45.1 release From 527fb4ae49e16ddee4b1cff6d0400416302a06ae Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 21 Jan 2023 05:43:41 +0000 Subject: [PATCH 106/260] Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 2bd078a..8b570f6 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 45.1 -Release: %{fedorarel}%{?dist} +Release: %{fedorarel}%{?dist}.1 #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -254,6 +254,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sat Jan 21 2023 Fedora Release Engineering - 45.1-2.1 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild + * Wed Jan 18 2023 Mamoru TASAKA - 45.1-2 - Header file inclusion fix for gcc13 From 3ae284daeda4ed9bb8c4982de715a81832ae272b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 22 Jan 2023 22:45:50 +0900 Subject: [PATCH 107/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index e760a85..9cf4bf7 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230117T1409.tar.gz) = 22496fe660e45df5e81ce9ddcfce54800abeeac7f7131610422b5abea0ff1bb9913339de4f5971ec0ed7f2a54c06ad7729e472775a4e819bfd991a7c8d82633f +SHA512 (ugene-free-20230122T2115.tar.gz) = 9c5d77ecce9e0afc0e78fc0149184f26bf341a5cfaebfe29ab87e8e2f7d2e88b07618fd277db76a93dbe9e0e7ac2cb6376803d382e3af3565af936eb6fa9cb32 diff --git a/ugene.spec b/ugene.spec index 3d744c7..6b92cde 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230116 -%global gitcommit 959b7d5775242c84cbec866897676f366fe372b1 +%global gitdate 20230122 +%global gitcommit fc120922b59b2603a18af669e09bd2e1d67a2d3f # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free ce0246a7c9d15dd96fb81c67b514485cf9e2b844 +%global gitcommit_free 28920f1b0ec6436bc4a86a3c732ad6105183c62c %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230117 -%global tarballtime 1409 +%global tarballdate 20230122 +%global tarballtime 2115 %global use_release 0 %global use_gitbare 1 From eeb078a06a16a445469d30c9f0f469c654bb7f5d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 30 Jan 2023 22:52:52 +0900 Subject: [PATCH 108/260] update to the latest git --- sources | 2 +- ...-git-plgins-smith_waterman-nonsse2-arch.patch | 16 ++++++++-------- ugene.spec | 10 +++++----- 3 files changed, 14 insertions(+), 14 deletions(-) diff --git a/sources b/sources index 9cf4bf7..7c25fc5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230122T2115.tar.gz) = 9c5d77ecce9e0afc0e78fc0149184f26bf341a5cfaebfe29ab87e8e2f7d2e88b07618fd277db76a93dbe9e0e7ac2cb6376803d382e3af3565af936eb6fa9cb32 +SHA512 (ugene-free-20230130T1643.tar.gz) = ea13f53bd212b3192dd34fdefc3724509981e5063ed0967bdd39254b148dd3b1b912f81cd90c8291d4a3f2b922e70172ee4e34c3b955c94883c34cc77fce42f2 diff --git a/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch b/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch index 59756dd..f482645 100644 --- a/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch +++ b/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch @@ -77,7 +77,7 @@ assert(0); --- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.sse_2 2021-11-11 15:42:19.591500062 +0900 +++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp 2021-11-11 15:42:26.385496818 +0900 -@@ -19,6 +19,7 @@ +@@ -23,6 +23,7 @@ * MA 02110-1301, USA. */ @@ -85,23 +85,23 @@ #include #include -@@ -1210,3 +1211,4 @@ +@@ -1214,3 +1215,4 @@ } } // namespace U2 +#endif --- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2 2021-11-11 15:42:19.592500061 +0900 +++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h 2021-11-11 15:42:26.385496818 +0900 -@@ -22,6 +22,7 @@ - #ifndef _SMITHWATERMANALGORITHM_SSE2_H - #define _SMITHWATERMANALGORITHM_SSE2_H +@@ -21,6 +21,7 @@ + + #pragma once +#if defined(__SSE2__) #include #include "SmithWatermanAlgorithm.h" -@@ -55,3 +56,4 @@ - } // namespace U2 +@@ -52,3 +53,4 @@ + }; - #endif + } // namespace U2 +#endif diff --git a/ugene.spec b/ugene.spec index 6b92cde..cd5fca4 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230122 -%global gitcommit fc120922b59b2603a18af669e09bd2e1d67a2d3f +%global gitdate 20230130 +%global gitcommit 3a08e57b25c5fea78918c08536abe9f02f0dfd85 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 28920f1b0ec6436bc4a86a3c732ad6105183c62c +%global gitcommit_free 85c85d103561d0202594cb7cf72a2d7b6dfff2f9 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230122 -%global tarballtime 2115 +%global tarballdate 20230130 +%global tarballtime 1643 %global use_release 0 %global use_gitbare 1 From 75d2ef1f5115060074b61ca24ccc4c3a6063a91c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 10 Feb 2023 14:56:42 +0900 Subject: [PATCH 109/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 7c25fc5..6cc1cb6 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230130T1643.tar.gz) = ea13f53bd212b3192dd34fdefc3724509981e5063ed0967bdd39254b148dd3b1b912f81cd90c8291d4a3f2b922e70172ee4e34c3b955c94883c34cc77fce42f2 +SHA512 (ugene-free-20230210T1413.tar.gz) = d9b840c8b008eea24a6a23b9db4ba97aa1f57d9d8e0de7276dec9526949002044a80a614bb0d0469be833894a4fd7cf542af04995bbfd5d2f9d64daf5f2ff5ad diff --git a/ugene.spec b/ugene.spec index cd5fca4..a37c2f1 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230130 -%global gitcommit 3a08e57b25c5fea78918c08536abe9f02f0dfd85 +%global gitdate 20230210 +%global gitcommit 664fd1738f582219b263e5517fd78c6464e3537b # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 85c85d103561d0202594cb7cf72a2d7b6dfff2f9 +%global gitcommit_free 5f8891bf785f1a5730d18f484ea9c95bf63143b5 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230130 -%global tarballtime 1643 +%global tarballdate 20230210 +%global tarballtime 1413 %global use_release 0 %global use_gitbare 1 From 1f0ddc882bf153cf68428c6a59f2f4b8ed840199 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 14 Feb 2023 17:27:55 +0900 Subject: [PATCH 110/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 6cc1cb6..cd4727f 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230210T1413.tar.gz) = d9b840c8b008eea24a6a23b9db4ba97aa1f57d9d8e0de7276dec9526949002044a80a614bb0d0469be833894a4fd7cf542af04995bbfd5d2f9d64daf5f2ff5ad +SHA512 (ugene-free-20230214T1421.tar.gz) = 3c118ed82ca07942b8f06d34ad73d9ceed45572fa1afbf18abd9a3fec778b9d401a0994b095e4f63710861498e3536ef42b5b7368f0bef8d0fa0a7149cdd7e6f diff --git a/ugene.spec b/ugene.spec index a37c2f1..00c115b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230210 -%global gitcommit 664fd1738f582219b263e5517fd78c6464e3537b +%global gitdate 20230214 +%global gitcommit 15acb35b017bfa4c4c90dc14079bd52d7252c398 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 5f8891bf785f1a5730d18f484ea9c95bf63143b5 +%global gitcommit_free 16ffa2676c45f566400d78162c62fa56c5f1a15d %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230210 -%global tarballtime 1413 +%global tarballdate 20230214 +%global tarballtime 1421 %global use_release 0 %global use_gitbare 1 From d631aea34ab7d1ca94b88f4499bdfec047e0baba Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 24 Feb 2023 14:42:16 +0900 Subject: [PATCH 111/260] 46.0 --- sources | 2 +- ugene.spec | 13 ++++++++----- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/sources b/sources index cd4727f..ba31f26 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230214T1421.tar.gz) = 3c118ed82ca07942b8f06d34ad73d9ceed45572fa1afbf18abd9a3fec778b9d401a0994b095e4f63710861498e3536ef42b5b7368f0bef8d0fa0a7149cdd7e6f +SHA512 (ugene-free-46.0.tar.gz) = 755fb767b981187f5c60bd800995397c9fba4e07e72f19cd2034eafa79c77b147fb444bc8e047e64c70b377a766e88271365066285f235560c3b8510b361a53d diff --git a/ugene.spec b/ugene.spec index ee7edc4..8c74fc5 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20230214 %global tarballtime 1421 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainrel 2.1 +%global mainrel 1 %undefine prever %if 0%{?use_release} >= 1 @@ -49,8 +49,8 @@ Name: ugene Summary: Integrated bioinformatics toolkit -Version: 45.1 -Release: %{fedorarel}%{?dist}.1 +Version: 46.0 +Release: %{fedorarel}%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -254,6 +254,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Fri Feb 24 2023 Mamoru TASAKA - 46.0-1 +- 46.0 + * Sat Jan 21 2023 Fedora Release Engineering - 45.1-2.1 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild From 7e856173852d7beecf2dc6db896ba6b1b18fa839 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 6 Mar 2023 15:47:37 +0900 Subject: [PATCH 112/260] update to the latest git --- sources | 2 +- ...6.x-plugins_3rdparty-hmm2-nosse-arch.patch | 2 +- ugene.spec | 36 +++++++++---------- 3 files changed, 20 insertions(+), 20 deletions(-) rename ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch => ugene-46.x-plugins_3rdparty-hmm2-nosse-arch.patch (97%) diff --git a/sources b/sources index ba31f26..d48d4ef 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-46.0.tar.gz) = 755fb767b981187f5c60bd800995397c9fba4e07e72f19cd2034eafa79c77b147fb444bc8e047e64c70b377a766e88271365066285f235560c3b8510b361a53d +SHA512 (ugene-free-20230306T1511.tar.gz) = f773ed20b9e395e8875b7edae06b9fa31dbf7e6bb518292f35686a9c85ec075bb5858bddc6d5d993c1f401d3d9095d7935a161801171644baad619c5f6d14a6b diff --git a/ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch b/ugene-46.x-plugins_3rdparty-hmm2-nosse-arch.patch similarity index 97% rename from ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch rename to ugene-46.x-plugins_3rdparty-hmm2-nosse-arch.patch index 63457d9..32a238a 100644 --- a/ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch +++ b/ugene-46.x-plugins_3rdparty-hmm2-nosse-arch.patch @@ -2,7 +2,7 @@ +++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/HMMSearchDialogController.cpp 2021-11-09 01:34:30.052988784 +0900 @@ -81,7 +81,9 @@ QWidget* w = createController->getWidget(); - QVBoxLayout* l = qobject_cast(layout()); + auto l = qobject_cast(layout()); l->insertWidget(1, w); +#if defined (__SSE2__) algoCombo->addItem(tr("SSE optimized"), HMMSearchAlgo_SSEOptimized); diff --git a/ugene.spec b/ugene.spec index 8c74fc5..a307f00 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230214 -%global gitcommit 15acb35b017bfa4c4c90dc14079bd52d7252c398 +%global gitdate 20230305 +%global gitcommit 84fee15a01bb73ffb44ecb7f7b4aeaa09ff68cf5 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 16ffa2676c45f566400d78162c62fa56c5f1a15d +%global gitcommit_free 522bf6942e42b07beb44e13c119ad5b39bdd097d %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230214 -%global tarballtime 1421 +%global tarballdate 20230306 +%global tarballtime 1511 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force @@ -35,22 +35,22 @@ %global GIT git %endif -%global mainrel 1 +%global mainver 46.0 %undefine prever %if 0%{?use_release} >= 1 -%global fedorarel %{?prever:0.}%{mainrel}%{?prever:.%{prerpmver}} +%global fedoraver %{mainver}%{?prever:~%{prerpmver}} %endif %if 0%{?use_gitbare} >= 1 -%global fedorarel %{mainrel}.%{git_version} +%global fedoraver %{mainver}%{?git_version:^%{git_version}} %endif Name: ugene Summary: Integrated bioinformatics toolkit -Version: 46.0 -Release: %{fedorarel}%{?dist} +Version: %{fedoraver} +Release: 0.100%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -58,10 +58,10 @@ Release: %{fedorarel}%{?dist} License: GPLv2+ and GPLv2 URL: http://ugene.net %if 0%{?use_release} >= 1 -#Source0: https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz +#Source0: https://github.com/ugeneunipro/ugene/archive/%{mainver}.tar.gz/#/%{name}-%{mainver}.tar.gz # Removing non-free part -Source0: %{name}-free-%{version}.tar.gz -# Source0 is created by # env VERSION=%%{version} source ./%{SOURCE1} +Source0: %{name}-free-%{mainver}.tar.gz +# Source0 is created by # env VERSION=%%{mainver} source ./%{SOURCE1} %endif %if 0%{?use_gitbare} >= 1 Source0: %{name}-free-%{tarballdate}T%{tarballtime}.tar.gz @@ -74,7 +74,7 @@ Patch1: ugene-45.1-gcc13-header-inclusion.patch # Currently distro-specific Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch -Patch104: ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch +Patch104: ugene-46.x-plugins_3rdparty-hmm2-nosse-arch.patch Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch Patch106: ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch @@ -123,12 +123,12 @@ sed -i.desktop ugene.pri -e '\@desktop@s|etc/share/|etc/shared/|' %endif %if 0%{?use_gitbare} >= 1 -%setup -q -c -T -a 0 +%setup -q -c -n %{name}-%{mainver}%{?git_version:-%{git_version}} -T -a 0 git clone ./%{name}.git/ cd %{name} cp -a [A-Z]* .. -git checkout -b %{version}-fedora %{gitcommit_free} +git checkout -b %{mainver}-fedora %{gitcommit_free} git config user.name "%{name} Fedora maintainer" git config user.email "%{name}-maintainers@fedoraproject.org" %endif From 79ee058e2f239b93c3df69e90a09ef3491cec302 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 6 Mar 2023 17:17:43 +0900 Subject: [PATCH 113/260] fix release --- ugene.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index a307f00..aace6ba 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 0.100%{?dist} +Release: 1%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 From 283d71d94391c1d7458fbd495e9370c35df30c16 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 7 Mar 2023 20:11:59 +0900 Subject: [PATCH 114/260] update to the latest git --- create-ugene-git-bare-tarball.sh | 2 +- sources | 2 +- ugene.spec | 10 +++++----- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/create-ugene-git-bare-tarball.sh b/create-ugene-git-bare-tarball.sh index 05f5602..e1c57aa 100644 --- a/create-ugene-git-bare-tarball.sh +++ b/create-ugene-git-bare-tarball.sh @@ -12,7 +12,7 @@ TIME=$(date '+%H%M') TARNAME=${REPONAME}-free-${DATE}T${TIME}.tar.gz PWDDIR=$(pwd) -TMPDIR=$(mktemp -d /var/tmp/${REPONAME}-XXXXXX) +TMPDIR=$(mktemp -d $(pwd)/tmp-${REPONAME}-XXXXXX) pushd $TMPDIR git clone --depth 30 --no-single-branch --mirror $GITURL diff --git a/sources b/sources index d48d4ef..8e7bd77 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230306T1511.tar.gz) = f773ed20b9e395e8875b7edae06b9fa31dbf7e6bb518292f35686a9c85ec075bb5858bddc6d5d993c1f401d3d9095d7935a161801171644baad619c5f6d14a6b +SHA512 (ugene-free-20230307T1422.tar.gz) = e18df75a58484576e17d2691023ac36e7bdc90073d641c1dd75e4334ad1e9beed406c941ef4dfc3759f8a7ff2934c291929009805f3098fbf199bfcd559faf4f diff --git a/ugene.spec b/ugene.spec index aace6ba..fca7e33 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230305 -%global gitcommit 84fee15a01bb73ffb44ecb7f7b4aeaa09ff68cf5 +%global gitdate 20230307 +%global gitcommit 873e8f701bac422459d52cc292cbaf3ca5fd2a32 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 522bf6942e42b07beb44e13c119ad5b39bdd097d +%global gitcommit_free 9f5a3f98696e0f633201ca2da81629fcce691b6d %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230306 -%global tarballtime 1511 +%global tarballdate 20230307 +%global tarballtime 1422 %global use_release 0 %global use_gitbare 1 From d79e205c61dd1d6920b9adfcbb7d997da7fd2803 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 13 Mar 2023 10:44:12 +0900 Subject: [PATCH 115/260] rename release macro to make rpmdev-bumprelease work --- ugene.spec | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ugene.spec b/ugene.spec index 8c74fc5..7adaa80 100644 --- a/ugene.spec +++ b/ugene.spec @@ -39,10 +39,10 @@ %undefine prever %if 0%{?use_release} >= 1 -%global fedorarel %{?prever:0.}%{mainrel}%{?prever:.%{prerpmver}} +%global baserelease %{?prever:0.}%{mainrel}%{?prever:.%{prerpmver}} %endif %if 0%{?use_gitbare} >= 1 -%global fedorarel %{mainrel}.%{git_version} +%global baserelease %{mainrel}.%{git_version} %endif @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: 46.0 -Release: %{fedorarel}%{?dist} +Release: %{baserelease}%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 From 775bdae2a7ddf94f4f817705cf9ce72139ba2ed8 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 13 Mar 2023 12:04:29 +0900 Subject: [PATCH 116/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 8e7bd77..abf28d6 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230307T1422.tar.gz) = e18df75a58484576e17d2691023ac36e7bdc90073d641c1dd75e4334ad1e9beed406c941ef4dfc3759f8a7ff2934c291929009805f3098fbf199bfcd559faf4f +SHA512 (ugene-free-20230313T1136.tar.gz) = 83f374c8be51ba2881d869946fa08d2d9ec5bee2dc4d5be4d45e062b12dda34f545a6babec7efebfddb38aa8222bfd8a80754811b03eabd0b389b8661d6c2232 diff --git a/ugene.spec b/ugene.spec index fca7e33..fee8a6b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230307 -%global gitcommit 873e8f701bac422459d52cc292cbaf3ca5fd2a32 +%global gitdate 20230313 +%global gitcommit e75608b5fabcf657b2a72cef22045dba5095fb2e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 9f5a3f98696e0f633201ca2da81629fcce691b6d +%global gitcommit_free 32bc1ca30dac221facb7a522ecdadf3378c64a16 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230307 -%global tarballtime 1422 +%global tarballdate 20230313 +%global tarballtime 1136 %global use_release 0 %global use_gitbare 1 From 4761ec2695bd662629d8568decad573f6dae3bff Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 19 Mar 2023 23:49:07 +0900 Subject: [PATCH 117/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index abf28d6..27e15f5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230313T1136.tar.gz) = 83f374c8be51ba2881d869946fa08d2d9ec5bee2dc4d5be4d45e062b12dda34f545a6babec7efebfddb38aa8222bfd8a80754811b03eabd0b389b8661d6c2232 +SHA512 (ugene-free-20230319T2320.tar.gz) = 91d0e836bf1cf0f62fd143534cd4afe9e17424b7ede8da57648e2172f541d17f6963918d076bcc97910f02efbb0c2efab630de47a92b37c2786ac0f406147b70 diff --git a/ugene.spec b/ugene.spec index fee8a6b..948e1c6 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230313 -%global gitcommit e75608b5fabcf657b2a72cef22045dba5095fb2e +%global gitdate 20230318 +%global gitcommit 494c561bbd5f0ec3a7513a3b3946eb3f5e6d8d8f # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 32bc1ca30dac221facb7a522ecdadf3378c64a16 +%global gitcommit_free 64945659de0b09b908f0a85455f9cfc46a07c2a7 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230313 -%global tarballtime 1136 +%global tarballdate 20230319 +%global tarballtime 2320 %global use_release 0 %global use_gitbare 1 From 3ebb44fe7db38e034752e0e88f27abc0bf5ed567 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 24 Mar 2023 15:22:21 +0900 Subject: [PATCH 118/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 27e15f5..0cdb6f8 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230319T2320.tar.gz) = 91d0e836bf1cf0f62fd143534cd4afe9e17424b7ede8da57648e2172f541d17f6963918d076bcc97910f02efbb0c2efab630de47a92b37c2786ac0f406147b70 +SHA512 (ugene-free-20230324T1346.tar.gz) = 6bfa9238a7a8705721fb503bf69e728197a40bbe237b0701f85aa5fefa6ce4cd6896873f2897c9871ae7127ea8d445894a9355eeacda90a29b4b474558360af8 diff --git a/ugene.spec b/ugene.spec index 948e1c6..ef6a81a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230318 -%global gitcommit 494c561bbd5f0ec3a7513a3b3946eb3f5e6d8d8f +%global gitdate 20230323 +%global gitcommit ee6335c41dda1a168ee08bd724ab8dc49538b31c # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 64945659de0b09b908f0a85455f9cfc46a07c2a7 +%global gitcommit_free 7c3bb1b14010f8e924ae040631dd7c19642e51f4 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230319 -%global tarballtime 2320 +%global tarballdate 20230324 +%global tarballtime 1346 %global use_release 0 %global use_gitbare 1 From 7aa5e92f42a60300e007471d05dc70f30dd05872 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 26 Mar 2023 16:18:10 +0900 Subject: [PATCH 119/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0cdb6f8..317244f 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230324T1346.tar.gz) = 6bfa9238a7a8705721fb503bf69e728197a40bbe237b0701f85aa5fefa6ce4cd6896873f2897c9871ae7127ea8d445894a9355eeacda90a29b4b474558360af8 +SHA512 (ugene-free-20230326T1553.tar.gz) = 127b0195d8294b05f86005408f16664e77f968e738190a68bcfc5892a1dcab64ff596b2858b0060f52a5c3f894001200b35930fd93c309d7a694a596d15b6741 diff --git a/ugene.spec b/ugene.spec index ef6a81a..38bb496 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230323 -%global gitcommit ee6335c41dda1a168ee08bd724ab8dc49538b31c +%global gitdate 20230326 +%global gitcommit 23cbd92d791960b2d2f0ea1122a34dbb00709542 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 7c3bb1b14010f8e924ae040631dd7c19642e51f4 +%global gitcommit_free fbed0b81920e7315260de3c0236d39746828a1a0 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230324 -%global tarballtime 1346 +%global tarballdate 20230326 +%global tarballtime 1553 %global use_release 0 %global use_gitbare 1 From 5e79e46be48f8e694600f9514441ec993d4d5c15 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 1 Apr 2023 17:10:55 +0900 Subject: [PATCH 120/260] update to the latest git --- ugene.spec | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/ugene.spec b/ugene.spec index 38bb496..01239e7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230326 -%global gitcommit 23cbd92d791960b2d2f0ea1122a34dbb00709542 +%global gitdate 20230330 +%global gitcommit 79dcd3f513a16833c618fdc6920438e051561725 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free fbed0b81920e7315260de3c0236d39746828a1a0 +%global gitcommit_free ddae2b1d19ea0d154968a0b3a4d130a7eb14f828 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230326 -%global tarballtime 1553 +%global tarballdate 20230401 +%global tarballtime 1645 %global use_release 0 %global use_gitbare 1 @@ -133,22 +133,22 @@ git config user.name "%{name} Fedora maintainer" git config user.email "%{name}-maintainers@fedoraproject.org" %endif -%patch1 -p1 -b .gcc13 -Z +%patch -P1 -p1 -b .gcc13 -Z %GIT commit -m "add missing header file" -a -%patch102 -p1 -b .sys_mmap -Z +%patch -P102 -p1 -b .sys_mmap -Z %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a -%patch103 -p1 -b .unwind -Z +%patch -P103 -p1 -b .unwind -Z %GIT commit -m "libs_3rdparty/breakpad: workaround for arch not supporting unwind" -a -%patch104 -p1 -b .sse -Z +%patch -P104 -p1 -b .sse -Z %GIT commit -m "plugins_3rdparty/hmm2: support architecture not supporting SSE2" -a -%patch105 -p1 -b .port -Z +%patch -P105 -p1 -b .port -Z %GIT commit -m "libs_3rdparty/breakpad: workaround for arch not ported by the upstream" -a -%patch106 -p1 -b .sse_2 -Z +%patch -P106 -p1 -b .sse_2 -Z %GIT commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a -%patch107 -p1 -b .char_bigen -Z +%patch -P107 -p1 -b .char_bigen -Z %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a -%patch108 -p1 -b .elif -Z +%patch -P108 -p1 -b .elif -Z %GIT commit -m "ugenem/src/SendReportDialog.cpp: fix wrong elif usage" -a sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' From dfc0fce00e317621b5cbec246136f9424380b358 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 1 Apr 2023 17:20:14 +0900 Subject: [PATCH 121/260] update to the latest git --- sources | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sources b/sources index 317244f..00c0f59 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230326T1553.tar.gz) = 127b0195d8294b05f86005408f16664e77f968e738190a68bcfc5892a1dcab64ff596b2858b0060f52a5c3f894001200b35930fd93c309d7a694a596d15b6741 +SHA512 (ugene-free-20230401T1645.tar.gz) = 646779787d53cbcff2c215f0e6c659e0c0836991e2bfba6a257c53c548368d452a1c735e9fc9aef970d010e0af135c31b86590d6fd1c1c5d09e371f0a749196f From 05b6a1a6edf65928d067f7501de4942ca23fe285 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 9 Apr 2023 17:22:12 +0900 Subject: [PATCH 122/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 00c0f59..b67f439 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230401T1645.tar.gz) = 646779787d53cbcff2c215f0e6c659e0c0836991e2bfba6a257c53c548368d452a1c735e9fc9aef970d010e0af135c31b86590d6fd1c1c5d09e371f0a749196f +SHA512 (ugene-free-20230409T1551.tar.gz) = fb2853e9f10c0555fefe632d7876f750c294c12927ff9a1afba3c574c631e65937b687970055dfcc6a4ea6a2e9f3bcda0eaf6fc79b29228f655d5613c2877472 diff --git a/ugene.spec b/ugene.spec index 01239e7..f5cc3f3 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230330 -%global gitcommit 79dcd3f513a16833c618fdc6920438e051561725 +%global gitdate 20230407 +%global gitcommit 66abc6f898c3b0daa16743c45b96e288f54aaf72 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free ddae2b1d19ea0d154968a0b3a4d130a7eb14f828 +%global gitcommit_free 9e2ae5825ee5f7faf52264aaa6a87e9b32786396 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230401 -%global tarballtime 1645 +%global tarballdate 20230409 +%global tarballtime 1551 %global use_release 0 %global use_gitbare 1 From fb5c43a3453457f57ef622537a55ed49c4033304 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 17 Apr 2023 16:49:08 +0900 Subject: [PATCH 123/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index b67f439..09910ec 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230409T1551.tar.gz) = fb2853e9f10c0555fefe632d7876f750c294c12927ff9a1afba3c574c631e65937b687970055dfcc6a4ea6a2e9f3bcda0eaf6fc79b29228f655d5613c2877472 +SHA512 (ugene-free-20230417T1613.tar.gz) = bed8618314418c46f82ec23dd3797054e30ba6a17bc71915dac9fb106394e46a747557d8e4b1ac8da5b403b2456736c0ae572537c2ca5dab1aeddfd55aabebbf diff --git a/ugene.spec b/ugene.spec index f5cc3f3..0f2d6ef 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230407 -%global gitcommit 66abc6f898c3b0daa16743c45b96e288f54aaf72 +%global gitdate 20230415 +%global gitcommit 14cf5b8afb7d5de7157f7068e70b1a9e24417ef4 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 9e2ae5825ee5f7faf52264aaa6a87e9b32786396 +%global gitcommit_free ae1835d482a5e2a813c61469526d9358a33c2239 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230409 -%global tarballtime 1551 +%global tarballdate 20230417 +%global tarballtime 1613 %global use_release 0 %global use_gitbare 1 From 2d7982c6393a9e1f52b2765d8503eff612862b5f Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 19 Apr 2023 17:31:06 +0900 Subject: [PATCH 124/260] update to the latest git --- sources | 2 +- ugene-40.1-libs_3rdparty-breakpad-arch-port.patch | 8 ++++---- ugene-43.x-wrong-elif-SendReportDialog.patch | 2 +- ugene.spec | 10 +++++----- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/sources b/sources index 09910ec..8f20c5f 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230417T1613.tar.gz) = bed8618314418c46f82ec23dd3797054e30ba6a17bc71915dac9fb106394e46a747557d8e4b1ac8da5b403b2456736c0ae572537c2ca5dab1aeddfd55aabebbf +SHA512 (ugene-free-20230419T1659.tar.gz) = 9f78f8329e3c49d92d5cb8bef2acdf316c852211e69ad339b7783c12701100b2cb6b5f1947dade6f864e6015135be4004ec99afa15f51c98e6ef1689d48f3d66 diff --git a/ugene-40.1-libs_3rdparty-breakpad-arch-port.patch b/ugene-40.1-libs_3rdparty-breakpad-arch-port.patch index 323159e..cf06c23 100644 --- a/ugene-40.1-libs_3rdparty-breakpad-arch-port.patch +++ b/ugene-40.1-libs_3rdparty-breakpad-arch-port.patch @@ -61,7 +61,7 @@ } // namespace google_breakpad --- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc.port 2021-11-09 11:04:57.135469882 +0900 +++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc 2021-11-09 12:06:47.875738562 +0900 -@@ -441,6 +441,7 @@ int ExceptionHandler::ThreadEntry(void* +@@ -442,6 +442,7 @@ int ExceptionHandler::ThreadEntry(void* // This function runs in a compromised context: see the top of the file. // Runs on the crashing thread. bool ExceptionHandler::HandleSignal(int /*sig*/, siginfo_t* info, void* uc) { @@ -69,7 +69,7 @@ if (filter_ && !filter_(callback_context_)) return false; -@@ -482,6 +483,9 @@ bool ExceptionHandler::HandleSignal(int +@@ -483,6 +484,9 @@ bool ExceptionHandler::HandleSignal(int } } return GenerateDump(&g_crash_context_); @@ -79,7 +79,7 @@ } // This is a public interface to HandleSignal that allows the client to -@@ -660,6 +664,7 @@ bool ExceptionHandler::WriteMinidump(con +@@ -661,6 +665,7 @@ bool ExceptionHandler::WriteMinidump(con __attribute__((optimize("no-omit-frame-pointer"))) #endif bool ExceptionHandler::WriteMinidump() { @@ -87,7 +87,7 @@ if (!IsOutOfProcess() && !minidump_descriptor_.IsFD() && !minidump_descriptor_.IsMicrodumpOnConsole()) { // Update the path of the minidump so that this can be called multiple times -@@ -734,6 +739,9 @@ bool ExceptionHandler::WriteMinidump() { +@@ -735,6 +740,9 @@ bool ExceptionHandler::WriteMinidump() { #endif return GenerateDump(&context); diff --git a/ugene-43.x-wrong-elif-SendReportDialog.patch b/ugene-43.x-wrong-elif-SendReportDialog.patch index ac49ca0..85bc8df 100644 --- a/ugene-43.x-wrong-elif-SendReportDialog.patch +++ b/ugene-43.x-wrong-elif-SendReportDialog.patch @@ -1,6 +1,6 @@ --- ugene-43.0/src/ugenem/src/SendReportDialog.cpp.elif 2022-08-17 15:55:45.936686547 +0900 +++ ugene-43.0/src/ugenem/src/SendReportDialog.cpp 2022-08-17 20:56:02.123046050 +0900 -@@ -497,11 +497,11 @@ +@@ -402,11 +402,11 @@ QString ReportSender::getArchSuffix() const { #ifdef Q_PROCESSOR_X86_64 return " x64"; diff --git a/ugene.spec b/ugene.spec index 0f2d6ef..ea718e8 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230415 -%global gitcommit 14cf5b8afb7d5de7157f7068e70b1a9e24417ef4 +%global gitdate 20230419 +%global gitcommit 24f2e0c7fc194be059c8f181cb6474f305cd401d # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free ae1835d482a5e2a813c61469526d9358a33c2239 +%global gitcommit_free c6b8608b50bcfedd885bcb8ccfeb9a49506e607f %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230417 -%global tarballtime 1613 +%global tarballdate 20230419 +%global tarballtime 1659 %global use_release 0 %global use_gitbare 1 From 48ac2a3d146c039ea301d780ae8f925a9e4294b1 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 21 Apr 2023 12:14:56 +0900 Subject: [PATCH 125/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 8f20c5f..b242485 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230419T1659.tar.gz) = 9f78f8329e3c49d92d5cb8bef2acdf316c852211e69ad339b7783c12701100b2cb6b5f1947dade6f864e6015135be4004ec99afa15f51c98e6ef1689d48f3d66 +SHA512 (ugene-free-20230421T1115.tar.gz) = a45b6bbca42bf1466442ef4f9371b52d892fc9f7b07fcb1322f569fc1f478e5e2564155cef467ffe594f6b35df782540e7f91f877f0519ead60e4bce4adff9d1 diff --git a/ugene.spec b/ugene.spec index ea718e8..70de1d9 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230419 -%global gitcommit 24f2e0c7fc194be059c8f181cb6474f305cd401d +%global gitdate 20230420 +%global gitcommit c8b3ca62c600a6fbfd8372892aadf3c8a17e4f0d # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free c6b8608b50bcfedd885bcb8ccfeb9a49506e607f +%global gitcommit_free 5785dc4acb3cd2d7f9e6cde51d2f8cfda0f17e22 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230419 -%global tarballtime 1659 +%global tarballdate 20230421 +%global tarballtime 1115 %global use_release 0 %global use_gitbare 1 From e16ba5505d2e895ec031a254fa3a13912068e117 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 4 May 2023 23:38:03 +0900 Subject: [PATCH 126/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index b242485..2150cd3 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230421T1115.tar.gz) = a45b6bbca42bf1466442ef4f9371b52d892fc9f7b07fcb1322f569fc1f478e5e2564155cef467ffe594f6b35df782540e7f91f877f0519ead60e4bce4adff9d1 +SHA512 (ugene-free-20230504T2141.tar.gz) = cde3ac08d94bb562f9d1d981ec9a5960885b8b1e578aa0a722a8c4ed1b388661a8d6f6532df34e87a4c8ac5acd0bdd2c2378c62c7960902621568d854dcb869c diff --git a/ugene.spec b/ugene.spec index 70de1d9..a5f5cec 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230420 -%global gitcommit c8b3ca62c600a6fbfd8372892aadf3c8a17e4f0d +%global gitdate 20230504 +%global gitcommit 59702d4f5d0b7b1a9d451d41c79dacb589e69b22 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 5785dc4acb3cd2d7f9e6cde51d2f8cfda0f17e22 +%global gitcommit_free 99cfe5f5367e3f44f7d3b5938a479a7b4f8c8f93 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version D%{gitdate}git%{shortcommit} -%global tarballdate 20230421 -%global tarballtime 1115 +%global tarballdate 20230504 +%global tarballtime 2141 %global use_release 0 %global use_gitbare 1 From ad91bc3b1638c1249013125e77b10783811b3fe0 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 6 May 2023 13:22:44 +0900 Subject: [PATCH 127/260] update to the latest git --- sources | 2 +- ugene.spec | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/sources b/sources index 2150cd3..0cc9d53 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230504T2141.tar.gz) = cde3ac08d94bb562f9d1d981ec9a5960885b8b1e578aa0a722a8c4ed1b388661a8d6f6532df34e87a4c8ac5acd0bdd2c2378c62c7960902621568d854dcb869c +SHA512 (ugene-free-20230506T1209.tar.gz) = f58b428e234dd52f207ffaebc4bb32a9bced7e7b3fdd7459d3ff10f8bd60ad0120d183c07bf21aba12933adc54fdbd1da46c7b2af77b262b1e8edcc7db0c8e01 diff --git a/ugene.spec b/ugene.spec index a5f5cec..cb27b9f 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230504 -%global gitcommit 59702d4f5d0b7b1a9d451d41c79dacb589e69b22 +%global gitdate 20230505 +%global gitcommit 75e21a73e8b677e0aa4d2729246b644793383e4e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 99cfe5f5367e3f44f7d3b5938a479a7b4f8c8f93 +%global gitcommit_free 85b455ff2b7ac74f36e9bc82e34c2b1f051f67ab %else # currently 41.0 branch %global gitdate 20211117 @@ -16,10 +16,10 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) -%global git_version D%{gitdate}git%{shortcommit} +%global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230504 -%global tarballtime 2141 +%global tarballdate 20230506 +%global tarballtime 1209 %global use_release 0 %global use_gitbare 1 From 86ae16987ea546b2375308eafc4e74d878975296 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 15 May 2023 08:46:54 +0900 Subject: [PATCH 128/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0cc9d53..5b58c07 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230506T1209.tar.gz) = f58b428e234dd52f207ffaebc4bb32a9bced7e7b3fdd7459d3ff10f8bd60ad0120d183c07bf21aba12933adc54fdbd1da46c7b2af77b262b1e8edcc7db0c8e01 +SHA512 (ugene-free-20230514T2206.tar.gz) = e940cc578c7db9364077830d7032146838fb5fcf1447a74b22f89a508ec3cb13bc7c628e71269cbeb691da5ce0ca09db3729792c70cc497f10b99d690336c73e diff --git a/ugene.spec b/ugene.spec index cb27b9f..7efc9d4 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230505 -%global gitcommit 75e21a73e8b677e0aa4d2729246b644793383e4e +%global gitdate 20230514 +%global gitcommit 41c8ea89d3e35e4a9a6aafc958bf5475db431bfc # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 85b455ff2b7ac74f36e9bc82e34c2b1f051f67ab +%global gitcommit_free f8bc70c14efe2d334d9035448735ed33d7a8dc8f %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230506 -%global tarballtime 1209 +%global tarballdate 20230514 +%global tarballtime 2206 %global use_release 0 %global use_gitbare 1 From e4d6d1dd95ee44069804b5c2eb41880cf5b0aabc Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 21 May 2023 16:39:50 +0900 Subject: [PATCH 129/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 5b58c07..ad0afc8 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230514T2206.tar.gz) = e940cc578c7db9364077830d7032146838fb5fcf1447a74b22f89a508ec3cb13bc7c628e71269cbeb691da5ce0ca09db3729792c70cc497f10b99d690336c73e +SHA512 (ugene-free-20230521T1533.tar.gz) = 3d122b39af92ec069acb1168befa7f777f74e1dbb062fea6b1f3228bf8e33cfec38395fdf0b42cb832a367071c152a4bcf3109afdbac9c1db990ffcc5b3dc5ec diff --git a/ugene.spec b/ugene.spec index 7efc9d4..0ce6dd7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230514 -%global gitcommit 41c8ea89d3e35e4a9a6aafc958bf5475db431bfc +%global gitdate 20230520 +%global gitcommit 9fde8b776ed6a19d12c5c0c4b2c3679627537047 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free f8bc70c14efe2d334d9035448735ed33d7a8dc8f +%global gitcommit_free 87c61cc62a6c34f6e0b95c08e642321ab6cfa018 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230514 -%global tarballtime 2206 +%global tarballdate 20230521 +%global tarballtime 1533 %global use_release 0 %global use_gitbare 1 From de041177820f687c21ac912303b2d106211c6319 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 23 May 2023 09:08:57 +0900 Subject: [PATCH 130/260] 47.0 entry --- sources | 2 +- ugene.spec | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/sources b/sources index ad0afc8..62161d0 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230521T1533.tar.gz) = 3d122b39af92ec069acb1168befa7f777f74e1dbb062fea6b1f3228bf8e33cfec38395fdf0b42cb832a367071c152a4bcf3109afdbac9c1db990ffcc5b3dc5ec +SHA512 (ugene-free-47.0.tar.gz) = 30a30f565cae70517e9501250ab87ae2ca204e8b76a5eb4ba1309b82ec197e33fd6779bb25cc33b9749355a940484bc4a78d24a75351290b02104b2ac6edddd1 diff --git a/ugene.spec b/ugene.spec index 0ce6dd7..67e051e 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20230521 %global tarballtime 1533 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainver 46.0 +%global mainver 47.0 %undefine prever %if 0%{?use_release} >= 1 @@ -254,6 +254,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Tue May 23 2023 Mamoru TASAKA - 47.0-1 +- 47.0 + * Fri Feb 24 2023 Mamoru TASAKA - 46.0-1 - 46.0 From 7b4539e1e9e410c1293ec2606490256f8c36cf8d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 11 Jun 2023 17:02:40 +0900 Subject: [PATCH 131/260] update to the latest git --- sources | 2 +- ugene-45.1-gcc13-header-inclusion.patch | 10 ---------- ugene.spec | 18 +++++++----------- 3 files changed, 8 insertions(+), 22 deletions(-) delete mode 100644 ugene-45.1-gcc13-header-inclusion.patch diff --git a/sources b/sources index 62161d0..8c05865 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-47.0.tar.gz) = 30a30f565cae70517e9501250ab87ae2ca204e8b76a5eb4ba1309b82ec197e33fd6779bb25cc33b9749355a940484bc4a78d24a75351290b02104b2ac6edddd1 +SHA512 (ugene-free-20230611T1636.tar.gz) = 7e3cdead83c3c9deebcad703dc4cb805c15bcaaa64996d1fd480ebfd47f8586c41710479a7e462e848c168c374835ca9d709b11c3f5f88662dcb1ab5ba53d76d diff --git a/ugene-45.1-gcc13-header-inclusion.patch b/ugene-45.1-gcc13-header-inclusion.patch deleted file mode 100644 index 893da10..0000000 --- a/ugene-45.1-gcc13-header-inclusion.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ugene-45.1/src/libs_3rdparty/breakpad/src/client/linux/handler/minidump_descriptor.h.gcc13 2022-12-31 14:29:47.000000000 +0900 -+++ ugene-45.1/src/libs_3rdparty/breakpad/src/client/linux/handler/minidump_descriptor.h 2023-01-18 20:37:30.580774335 +0900 -@@ -34,6 +34,7 @@ - #include - - #include -+#include - - #include "client/linux/handler/microdump_extra_info.h" - #include "common/using_std_string.h" diff --git a/ugene.spec b/ugene.spec index 67e051e..b2caa2a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230520 -%global gitcommit 9fde8b776ed6a19d12c5c0c4b2c3679627537047 +%global gitdate 20230611 +%global gitcommit a577b948fe9724769af9d5256a5cdff0573b16dd # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 87c61cc62a6c34f6e0b95c08e642321ab6cfa018 +%global gitcommit_free f45c7d4212d8049d8dfc1718efb48db4070c43fc %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230521 -%global tarballtime 1533 +%global tarballdate 20230611 +%global tarballtime 1636 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force @@ -70,7 +70,6 @@ Source1: create-ugene-free-tarball.sh Source2: create-%{name}-git-bare-tarball.sh # This is not installed Source10: ugene.wrapper -Patch1: ugene-45.1-gcc13-header-inclusion.patch # Currently distro-specific Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch @@ -133,9 +132,6 @@ git config user.name "%{name} Fedora maintainer" git config user.email "%{name}-maintainers@fedoraproject.org" %endif -%patch -P1 -p1 -b .gcc13 -Z - %GIT commit -m "add missing header file" -a - %patch -P102 -p1 -b .sys_mmap -Z %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a %patch -P103 -p1 -b .unwind -Z From 66a89b023a923304958e3a1a46fe2b6d0e51acc1 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 15 Jun 2023 16:28:13 +0900 Subject: [PATCH 132/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 8c05865..003366a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230611T1636.tar.gz) = 7e3cdead83c3c9deebcad703dc4cb805c15bcaaa64996d1fd480ebfd47f8586c41710479a7e462e848c168c374835ca9d709b11c3f5f88662dcb1ab5ba53d76d +SHA512 (ugene-free-20230615T1556.tar.gz) = 342ef62a5e34bde3c21b401b707dd95614869d786a000ee9c4ecfbad7c2b24511740e06c02fce6b1b911f6c02a6890353d7a579e46302839906659fd9c7350fb diff --git a/ugene.spec b/ugene.spec index b2caa2a..7146173 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230611 -%global gitcommit a577b948fe9724769af9d5256a5cdff0573b16dd +%global gitdate 20230614 +%global gitcommit f2f730851b7cedec2c0b78e4c9c7a8f4c3490577 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free f45c7d4212d8049d8dfc1718efb48db4070c43fc +%global gitcommit_free 179aeb609d8ea1751baf8d70401d139709c4d008 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230611 -%global tarballtime 1636 +%global tarballdate 20230615 +%global tarballtime 1556 %global use_release 0 %global use_gitbare 1 From eab165303c9e3e9fd65eeed5f8b315a4ae109873 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 22 Jun 2023 16:17:53 +0900 Subject: [PATCH 133/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 003366a..5e7480e 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230615T1556.tar.gz) = 342ef62a5e34bde3c21b401b707dd95614869d786a000ee9c4ecfbad7c2b24511740e06c02fce6b1b911f6c02a6890353d7a579e46302839906659fd9c7350fb +SHA512 (ugene-free-20230622T1528.tar.gz) = 7bea5ae06176d172ec1cf5a872a16fba8d0e147f02e3d0ecff652f52f75d872638a3c5a9bd0672beccbb03f4acc7aec271d839395c5e678742233ce371da540a diff --git a/ugene.spec b/ugene.spec index 7146173..130f4e3 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230614 -%global gitcommit f2f730851b7cedec2c0b78e4c9c7a8f4c3490577 +%global gitdate 20230621 +%global gitcommit 820f525248f5060d4cf67d6aa73d645f0873df63 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 179aeb609d8ea1751baf8d70401d139709c4d008 +%global gitcommit_free a96318a97e04806867d8f1ac83004dd8213b9f33 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230615 -%global tarballtime 1556 +%global tarballdate 20230622 +%global tarballtime 1528 %global use_release 0 %global use_gitbare 1 From 6bc16ea6c68eedd92f62170228c412a381c69ebb Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 23 Jun 2023 14:58:53 +0900 Subject: [PATCH 134/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 5e7480e..7674128 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230622T1528.tar.gz) = 7bea5ae06176d172ec1cf5a872a16fba8d0e147f02e3d0ecff652f52f75d872638a3c5a9bd0672beccbb03f4acc7aec271d839395c5e678742233ce371da540a +SHA512 (ugene-free-20230623T1354.tar.gz) = ecd4849c164f0ba9dc66e638872bb5ea1c7d7dd3666c63d54ef191cb3b7bc784559b3dadfc8f75e583decc8498cb49c1dcfa0b5678d1776b8313d532ad3faea9 diff --git a/ugene.spec b/ugene.spec index 130f4e3..d9b5541 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230621 -%global gitcommit 820f525248f5060d4cf67d6aa73d645f0873df63 +%global gitdate 20230622 +%global gitcommit f45c49270bf073770ba62863ca0dc4bdbe3a3f68 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free a96318a97e04806867d8f1ac83004dd8213b9f33 +%global gitcommit_free 05f408b26c2049d07af3a41a2a30882c4b11449d %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230622 -%global tarballtime 1528 +%global tarballdate 20230623 +%global tarballtime 1354 %global use_release 0 %global use_gitbare 1 From 941e7c93a218999c56d9edaac1cd2cb6942ccf8b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 1 Jul 2023 23:37:18 +0900 Subject: [PATCH 135/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 7674128..d2f0dbf 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230623T1354.tar.gz) = ecd4849c164f0ba9dc66e638872bb5ea1c7d7dd3666c63d54ef191cb3b7bc784559b3dadfc8f75e583decc8498cb49c1dcfa0b5678d1776b8313d532ad3faea9 +SHA512 (ugene-free-20230701T1614.tar.gz) = 0b2cef4f6d4be8c3775e4c1808d5bf83628be20dcbe4fda0aacddb8d65dc7a8749fd961e7602d36c0f0adde22e33d40fe734266d6733217722174304ce8f0d5f diff --git a/ugene.spec b/ugene.spec index d9b5541..f6fc7cb 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230622 -%global gitcommit f45c49270bf073770ba62863ca0dc4bdbe3a3f68 +%global gitdate 20230630 +%global gitcommit df80dd535f5ede59949d7101617a76a7da22710e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 05f408b26c2049d07af3a41a2a30882c4b11449d +%global gitcommit_free 745efeb28e0bb83f8eb447bd27e4d9cd322945f7 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230623 -%global tarballtime 1354 +%global tarballdate 20230701 +%global tarballtime 1614 %global use_release 0 %global use_gitbare 1 From 1572d052944d05f9d14c9932d9bfd866743773f2 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 4 Jul 2023 15:33:34 +0900 Subject: [PATCH 136/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index d2f0dbf..07189ae 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230701T1614.tar.gz) = 0b2cef4f6d4be8c3775e4c1808d5bf83628be20dcbe4fda0aacddb8d65dc7a8749fd961e7602d36c0f0adde22e33d40fe734266d6733217722174304ce8f0d5f +SHA512 (ugene-free-20230704T1504.tar.gz) = ccc929d8853f10ecba459b57c8673f5a39dfeb51a78fd5f6a5c2f1d801cc8e383f36b9625e99ddc2341e088db41b01540bf863d2bcf0dd63c630d97f93e927b8 diff --git a/ugene.spec b/ugene.spec index f6fc7cb..6eaee40 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230630 -%global gitcommit df80dd535f5ede59949d7101617a76a7da22710e +%global gitdate 20230704 +%global gitcommit 83be83513fe830cfa4fc6ef67018c4f8ac15b305 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 745efeb28e0bb83f8eb447bd27e4d9cd322945f7 +%global gitcommit_free de4685aaa4d2e54996d6c855f78e032c1ccee558 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230701 -%global tarballtime 1614 +%global tarballdate 20230704 +%global tarballtime 1504 %global use_release 0 %global use_gitbare 1 From b908b5d7f2016b73d41b671a5775f2e8032c094b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 7 Jul 2023 15:14:36 +0900 Subject: [PATCH 137/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 07189ae..829d85c 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230704T1504.tar.gz) = ccc929d8853f10ecba459b57c8673f5a39dfeb51a78fd5f6a5c2f1d801cc8e383f36b9625e99ddc2341e088db41b01540bf863d2bcf0dd63c630d97f93e927b8 +SHA512 (ugene-free-20230707T1441.tar.gz) = a5fa71dfd9b7266d584415eb5c6b46da636c024ae6db601b9c2da43477c85ca8c95c4a5ce56b555e069f22ced1ab6dcce7dd20eb27f209b440ed791ba959cbc7 diff --git a/ugene.spec b/ugene.spec index 6eaee40..4b999cf 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230704 -%global gitcommit 83be83513fe830cfa4fc6ef67018c4f8ac15b305 +%global gitdate 20230706 +%global gitcommit 16b5bc4250097dfb92c10f4cd71a97414002017f # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free de4685aaa4d2e54996d6c855f78e032c1ccee558 +%global gitcommit_free bf63fe9a70315d30a9600bde0f6adeb110069548 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230704 -%global tarballtime 1504 +%global tarballdate 20230707 +%global tarballtime 1441 %global use_release 0 %global use_gitbare 1 From 5ec76a10294af761c01531989e0d816f0fdb0098 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 14 Jul 2023 11:07:23 +0900 Subject: [PATCH 138/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 829d85c..6107bbf 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230707T1441.tar.gz) = a5fa71dfd9b7266d584415eb5c6b46da636c024ae6db601b9c2da43477c85ca8c95c4a5ce56b555e069f22ced1ab6dcce7dd20eb27f209b440ed791ba959cbc7 +SHA512 (ugene-free-20230714T1033.tar.gz) = 1acf5b279bbca18e98a070be63e8f39d36ab932d007387224dad49897a4a068ffd78136889c7984f529211b898c080580de2027d9e91712a85318022eae5be06 diff --git a/ugene.spec b/ugene.spec index 4b999cf..8cfde34 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230706 -%global gitcommit 16b5bc4250097dfb92c10f4cd71a97414002017f +%global gitdate 20230712 +%global gitcommit 5f3edceb3e0c3dfe74d70b8a74d57f522508efce # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free bf63fe9a70315d30a9600bde0f6adeb110069548 +%global gitcommit_free e2cfcbf5bb8af2ed7f580a431dab70f052b9748e %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230707 -%global tarballtime 1441 +%global tarballdate 20230714 +%global tarballtime 1033 %global use_release 0 %global use_gitbare 1 From 8b65bbba79561e2ffece73969952079b5f352e7c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 20 Jul 2023 16:02:03 +0900 Subject: [PATCH 139/260] update to the latest git --- sources | 2 +- ...t-plgins-smith_waterman-nonsse2-arch.patch | 107 ------------------ ugene-43.x-wrong-elif-SendReportDialog.patch | 17 --- ...t-plgins-smith_waterman-nonsse2-arch.patch | 30 +++++ ...7.x-plugins_3rdparty-hmm2-nosse-arch.patch | 19 ---- ugene.spec | 17 ++- 6 files changed, 38 insertions(+), 154 deletions(-) delete mode 100644 ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch delete mode 100644 ugene-43.x-wrong-elif-SendReportDialog.patch create mode 100644 ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch rename ugene-46.x-plugins_3rdparty-hmm2-nosse-arch.patch => ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch (62%) diff --git a/sources b/sources index 6107bbf..1aa874f 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230714T1033.tar.gz) = 1acf5b279bbca18e98a070be63e8f39d36ab932d007387224dad49897a4a068ffd78136889c7984f529211b898c080580de2027d9e91712a85318022eae5be06 +SHA512 (ugene-free-20230720T1414.tar.gz) = dd734dc2f63b42ef2425c952844797274e44b83eb62a71616f77d2864c7f445232fdf29c5a143e1601944bb6689caec6bf28328a0d40b1856d851b9f006a9601 diff --git a/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch b/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch deleted file mode 100644 index f482645..0000000 --- a/ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch +++ /dev/null @@ -1,107 +0,0 @@ ---- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp.sse_2 2021-11-11 15:42:19.590500062 +0900 -+++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp 2021-11-11 15:42:26.384496818 +0900 -@@ -90,13 +90,15 @@ - swar->registerFactory(new SWTaskFactory(SW_classic), QString("Classic 2")); // ADV search register - par->registerAlgorithm(new SWPairwiseAlignmentAlgorithm()); - -+#if defined (__SSE2__) - coreLog.trace("Registering SSE2 SW implementation"); - swar->registerFactory(new SWTaskFactory(SW_sse2), QString("SSE2")); - par->getAlgorithm("Smith-Waterman") - ->addAlgorithmRealization( - new PairwiseAlignmentSmithWatermanTaskFactory(SW_sse2), - new PairwiseAlignmentSmithWatermanGUIExtensionFactory(SW_sse2), - "SSE2"); -+#endif - } - - QList SWAlgorithmTests::createTestFactories() { ---- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp.sse_2 2021-11-11 15:42:19.590500062 +0900 -+++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp 2021-11-11 15:46:26.960369309 +0900 -@@ -146,6 +146,7 @@ - sWatermanConfig.sqnc.left(c.chunkSize * c.nThreads), - sWatermanConfig.resultView); - break; -+#ifdef __SSE2__ - case SW_sse2: - neededRam = SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(sWatermanConfig.ptrn, - sWatermanConfig.sqnc.left(c.chunkSize * c.nThreads), -@@ -154,6 +155,7 @@ - minScore, - maxScore, - sWatermanConfig.resultView); -+#endif - break; - default: - assert(0); -@@ -182,7 +184,12 @@ - - SmithWatermanAlgorithm* sw = nullptr; - if (algType == SW_sse2) { -+#if defined(__SSE2__) - sw = new SmithWatermanAlgorithmSSE2; -+#else -+ coreLog.error("SSE2 was not enabled in this build"); -+ return; -+#endif - } else { - assert(algType == SW_classic); - sw = new SmithWatermanAlgorithm; -@@ -458,7 +465,11 @@ - - SmithWatermanAlgorithm* sw = nullptr; - if (algType == SW_sse2) { -+#if defined(__SSE2__) - sw = new SmithWatermanAlgorithmSSE2; -+#else -+ coreLog.error("SSE2 was not enabled in this build"); -+#endif - } else { - assert(algType == SW_classic); - sw = new SmithWatermanAlgorithm; -@@ -582,6 +593,7 @@ - sqnc->left(c.chunkSize * c.nThreads), - SmithWatermanSettings::MULTIPLE_ALIGNMENT); - break; -+#ifdef __SSE2__ - case SW_sse2: - neededRam = SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(*ptrn, - sqnc->left(c.chunkSize * c.nThreads), -@@ -590,6 +602,7 @@ - minScore, - maxScore, - SmithWatermanSettings::MULTIPLE_ALIGNMENT); -+#endif - break; - default: - assert(0); ---- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.sse_2 2021-11-11 15:42:19.591500062 +0900 -+++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp 2021-11-11 15:42:26.385496818 +0900 -@@ -23,6 +23,7 @@ - * MA 02110-1301, USA. - */ - -+#if defined(__SSE2__) - #include - #include - -@@ -1214,3 +1215,4 @@ - } - - } // namespace U2 -+#endif ---- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2 2021-11-11 15:42:19.592500061 +0900 -+++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h 2021-11-11 15:42:26.385496818 +0900 -@@ -21,6 +21,7 @@ - - #pragma once - -+#if defined(__SSE2__) - #include - - #include "SmithWatermanAlgorithm.h" -@@ -52,3 +53,4 @@ - }; - - } // namespace U2 -+#endif diff --git a/ugene-43.x-wrong-elif-SendReportDialog.patch b/ugene-43.x-wrong-elif-SendReportDialog.patch deleted file mode 100644 index 85bc8df..0000000 --- a/ugene-43.x-wrong-elif-SendReportDialog.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- ugene-43.0/src/ugenem/src/SendReportDialog.cpp.elif 2022-08-17 15:55:45.936686547 +0900 -+++ ugene-43.0/src/ugenem/src/SendReportDialog.cpp 2022-08-17 20:56:02.123046050 +0900 -@@ -402,11 +402,11 @@ - QString ReportSender::getArchSuffix() const { - #ifdef Q_PROCESSOR_X86_64 - return " x64"; --#elif Q_PROCESSOR_X86_32 -+#elif defined(Q_PROCESSOR_X86_32) - return " x86"; --#elif Q_PROCESSOR_ARM_64 -+#elif defined(Q_PROCESSOR_ARM_64) - return " arm-64"; --#elif Q_PROCESSOR_ARM_32 -+#elif defined(Q_PROCESSOR_ARM_32) - return " arm-32"; - #else - return " unknown-arch"; diff --git a/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch b/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch new file mode 100644 index 0000000..7ba07ff --- /dev/null +++ b/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch @@ -0,0 +1,30 @@ +--- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.sse_2 2021-11-11 15:42:19.591500062 +0900 ++++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp 2021-11-11 15:42:26.385496818 +0900 +@@ -23,6 +23,7 @@ + * MA 02110-1301, USA. + */ + ++#if defined(__SSE2__) + #include + #include + +@@ -1214,3 +1215,4 @@ + } + + } // namespace U2 ++#endif +--- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2 2021-11-11 15:42:19.592500061 +0900 ++++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h 2021-11-11 15:42:26.385496818 +0900 +@@ -21,6 +21,7 @@ + + #pragma once + ++#if defined(__SSE2__) + #include + + #include "SmithWatermanAlgorithm.h" +@@ -52,3 +53,4 @@ + }; + + } // namespace U2 ++#endif diff --git a/ugene-46.x-plugins_3rdparty-hmm2-nosse-arch.patch b/ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch similarity index 62% rename from ugene-46.x-plugins_3rdparty-hmm2-nosse-arch.patch rename to ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch index 32a238a..974f41c 100644 --- a/ugene-46.x-plugins_3rdparty-hmm2-nosse-arch.patch +++ b/ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch @@ -10,25 +10,6 @@ algoCombo->addItem(tr("Conservative"), HMMSearchAlgo_Conservative); okButton = buttonBox->button(QDialogButtonBox::Ok); ---- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp.sse 2021-10-11 15:41:23.000000000 +0900 -+++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp 2021-11-09 01:34:30.052988784 +0900 -@@ -56,9 +56,15 @@ - tophit_s* dhit = AllocTophits(200); // domain hits: 200=lumpsize - - int nseq = 0; // number of sequences searched -+#if defined(__SSE2__) - if (s.alg == HMMSearchAlgo_SSEOptimized) { - main_loop_opt(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si, sseScoring); -- } else if (s.alg == HMMSearchAlgo_Conservative) { -+ } -+#else -+ if (0) { -+ } -+#endif -+ else if (s.alg == HMMSearchAlgo_Conservative) { - main_loop_serial(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si); - } else { - assert(false && "bad hmmsearch algorithm selected"); --- ugene-42.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp.sse 2022-03-09 15:37:14.586340751 +0900 +++ ugene-42.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp 2022-03-09 15:47:23.559077800 +0900 @@ -1,4 +1,5 @@ diff --git a/ugene.spec b/ugene.spec index 8cfde34..b34a6fb 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230712 -%global gitcommit 5f3edceb3e0c3dfe74d70b8a74d57f522508efce +%global gitdate 20230719 +%global gitcommit 00c1f7ddcf2a1475c50e125e14c9787d5a0d0c77 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free e2cfcbf5bb8af2ed7f580a431dab70f052b9748e +%global gitcommit_free 756ed5696df2208e9081b32ac4d45ab3d42f4ef6 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230714 -%global tarballtime 1033 +%global tarballdate 20230720 +%global tarballtime 1414 %global use_release 0 %global use_gitbare 1 @@ -73,11 +73,10 @@ Source10: ugene.wrapper # Currently distro-specific Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch -Patch104: ugene-46.x-plugins_3rdparty-hmm2-nosse-arch.patch +Patch104: ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch -Patch106: ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch +Patch106: ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch -Patch108: ugene-43.x-wrong-elif-SendReportDialog.patch BuildRequires: make BuildRequires: gcc-c++ @@ -144,8 +143,6 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %GIT commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a %patch -P107 -p1 -b .char_bigen -Z %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a -%patch -P108 -p1 -b .elif -Z - %GIT commit -m "ugenem/src/SendReportDialog.cpp: fix wrong elif usage" -a sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d' From 044f203a080ddf05b1cee3d8ac4dc148aef6570b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 20 Jul 2023 17:10:59 +0900 Subject: [PATCH 140/260] partially revert the previous patch change --- ...-47.x-git-plgins-smith_waterman-nonsse2-arch.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch b/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch index 7ba07ff..363552f 100644 --- a/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch +++ b/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch @@ -13,6 +13,17 @@ } // namespace U2 +#endif +--- ugene-47.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp.sse 2023-07-20 15:51:42.159166614 +0900 ++++ ugene-47.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp 2023-07-20 17:06:31.144953038 +0900 +@@ -8,7 +8,7 @@ + + #include "uhmmsearch_opt.h" + +-#if Q_PROCESSOR_X86 ++#if defined(__SSE2__) + # include "uhmmsearch_sse.h" + # define UGENE_HAS_SSE + #endif --- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2 2021-11-11 15:42:19.592500061 +0900 +++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h 2021-11-11 15:42:26.385496818 +0900 @@ -21,6 +21,7 @@ From 8eb625b8ad86b2262d300d859d7707df372df8af Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 21 Jul 2023 00:14:18 +0900 Subject: [PATCH 141/260] fix i686 build with sse detection --- ...-47.x-git-plgins-smith_waterman-nonsse2-arch.patch | 11 ----------- ugene-47.x-has-sse-i686.patch | 10 ++++++++++ ugene.spec | 3 +++ 3 files changed, 13 insertions(+), 11 deletions(-) create mode 100644 ugene-47.x-has-sse-i686.patch diff --git a/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch b/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch index 363552f..7ba07ff 100644 --- a/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch +++ b/ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch @@ -13,17 +13,6 @@ } // namespace U2 +#endif ---- ugene-47.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp.sse 2023-07-20 15:51:42.159166614 +0900 -+++ ugene-47.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp 2023-07-20 17:06:31.144953038 +0900 -@@ -8,7 +8,7 @@ - - #include "uhmmsearch_opt.h" - --#if Q_PROCESSOR_X86 -+#if defined(__SSE2__) - # include "uhmmsearch_sse.h" - # define UGENE_HAS_SSE - #endif --- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2 2021-11-11 15:42:19.592500061 +0900 +++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h 2021-11-11 15:42:26.385496818 +0900 @@ -21,6 +21,7 @@ diff --git a/ugene-47.x-has-sse-i686.patch b/ugene-47.x-has-sse-i686.patch new file mode 100644 index 0000000..e65a89d --- /dev/null +++ b/ugene-47.x-has-sse-i686.patch @@ -0,0 +1,10 @@ +--- ugene-47.x/src/ugene_globals.pri.i386 2023-07-20 19:37:10.106204731 +0900 ++++ ugene-47.x/src/ugene_globals.pri 2023-07-20 22:31:43.266627766 +0900 +@@ -168,6 +168,7 @@ defineTest( target_platform_has_sse ) { + contains(QMAKE_TARGET.arch, x86_64) : return (true) + # This check works on Linux & Mac. + contains(QMAKE_HOST.arch, x86_64) : return (true) ++ contains(QMAKE_HOST.arch, i686) : return (true) + return (false) + } + diff --git a/ugene.spec b/ugene.spec index b34a6fb..e416d4d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -77,6 +77,7 @@ Patch104: ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch Patch106: ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch +Patch108: ugene-47.x-has-sse-i686.patch BuildRequires: make BuildRequires: gcc-c++ @@ -143,6 +144,8 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %GIT commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a %patch -P107 -p1 -b .char_bigen -Z %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a +%patch -P108 -p1 -b .sse_i686 -Z + %GIT commit -m "ugene_globals.pri: tell sse2 available also on i686" -a sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d' From 35817ddf4d73efa4e1b18f11d45d1471eab7319c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 21 Jul 2023 19:38:27 +0900 Subject: [PATCH 142/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 1aa874f..4dbebf1 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230720T1414.tar.gz) = dd734dc2f63b42ef2425c952844797274e44b83eb62a71616f77d2864c7f445232fdf29c5a143e1601944bb6689caec6bf28328a0d40b1856d851b9f006a9601 +SHA512 (ugene-free-20230721T1532.tar.gz) = 8d6f2f0f47d7ea546f98aed9efc131aa9e8b0af1ee2c6b2f6956a2371ef8577552d398d2ef9bfbaca83df4e5dc397a6f9631ffe8c4df85c17ebb9c5ca79ac0cb diff --git a/ugene.spec b/ugene.spec index e416d4d..37d1dba 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230719 -%global gitcommit 00c1f7ddcf2a1475c50e125e14c9787d5a0d0c77 +%global gitdate 20230721 +%global gitcommit 67f58be3ff9da7602b833defd751f5785b3dead4 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 756ed5696df2208e9081b32ac4d45ab3d42f4ef6 +%global gitcommit_free f5c68e237adab50aa1165a2f66e84c4846cbc9b7 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230720 -%global tarballtime 1414 +%global tarballdate 20230721 +%global tarballtime 1532 %global use_release 0 %global use_gitbare 1 From 729c50a8709e3895c07eabe0fc90cdc5096d4428 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 23 Jul 2023 00:05:49 +0900 Subject: [PATCH 143/260] Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 67e051e..b998b16 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -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 @@ -254,6 +254,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sat Jul 22 2023 Mamoru TASAKA - 47.0-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild + * Tue May 23 2023 Mamoru TASAKA - 47.0-1 - 47.0 From 980d5ac546ff3a3803b43e463caa87afdc0b8e99 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 25 Jul 2023 14:54:21 +0900 Subject: [PATCH 144/260] update to the latest git --- sources | 2 +- ugene.spec | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/sources b/sources index 4dbebf1..6fb5583 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230721T1532.tar.gz) = 8d6f2f0f47d7ea546f98aed9efc131aa9e8b0af1ee2c6b2f6956a2371ef8577552d398d2ef9bfbaca83df4e5dc397a6f9631ffe8c4df85c17ebb9c5ca79ac0cb +SHA512 (ugene-free-20230725T1402.tar.gz) = 24d16ccce7789a728ecfd05bc79d995ad5c4cce6c4ff920744cf6d2488318c04ad6795af3cea846def6d07d1f6cd6619532628ded05f95d21d95bf0f547b147c diff --git a/ugene.spec b/ugene.spec index 5ce358a..e390ee4 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230721 -%global gitcommit 67f58be3ff9da7602b833defd751f5785b3dead4 +%global gitdate 20230724 +%global gitcommit 4b9c50e38359e9423498196be6a6bc98be9c9cc3 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free f5c68e237adab50aa1165a2f66e84c4846cbc9b7 +%global gitcommit_free 17741c6239201cc279954ba81805b6315151d5d6 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230721 -%global tarballtime 1532 +%global tarballdate 20230725 +%global tarballtime 1402 %global use_release 0 %global use_gitbare 1 @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 2%{?dist} +Release: 1%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 From 94e8e53fcb2e6ffc4d23602063b4ffadc7dad71e Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 28 Jul 2023 11:19:40 +0900 Subject: [PATCH 145/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 6fb5583..4417ec1 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230725T1402.tar.gz) = 24d16ccce7789a728ecfd05bc79d995ad5c4cce6c4ff920744cf6d2488318c04ad6795af3cea846def6d07d1f6cd6619532628ded05f95d21d95bf0f547b147c +SHA512 (ugene-free-20230728T1047.tar.gz) = e9ed5f4c7711776a9941380c58548ce291e1db2c4870bb82262e4eb7c5f02a6cd99385f1052a32499c8b33cc58d9c9d68f7036e666807bde75d3d537605e379e diff --git a/ugene.spec b/ugene.spec index e390ee4..2780a99 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230724 -%global gitcommit 4b9c50e38359e9423498196be6a6bc98be9c9cc3 +%global gitdate 20230727 +%global gitcommit 3a66e4475878186414e46d624f4775a7f0cdc788 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 17741c6239201cc279954ba81805b6315151d5d6 +%global gitcommit_free 218617199f2eeb311fc2471d56737ff227a67901 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230725 -%global tarballtime 1402 +%global tarballdate 20230728 +%global tarballtime 1047 %global use_release 0 %global use_gitbare 1 From d996f88e3bff72cdcc66f5a8b6052668c425394b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 30 Jul 2023 00:08:29 +0900 Subject: [PATCH 146/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 4417ec1..8fcdb38 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230728T1047.tar.gz) = e9ed5f4c7711776a9941380c58548ce291e1db2c4870bb82262e4eb7c5f02a6cd99385f1052a32499c8b33cc58d9c9d68f7036e666807bde75d3d537605e379e +SHA512 (ugene-free-20230729T2237.tar.gz) = 8f30b97064a69bdbc9b640cea3bed8564b90cf649feed03745d80c688a015b20044a916ff7e82803c63dc056d7c3fe6c7f3f0283015da4d5a8b6a403c26cc637 diff --git a/ugene.spec b/ugene.spec index 2780a99..f77b105 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230727 -%global gitcommit 3a66e4475878186414e46d624f4775a7f0cdc788 +%global gitdate 20230728 +%global gitcommit 96e658305dade1d3dedf8774939e6be36f481e6b # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 218617199f2eeb311fc2471d56737ff227a67901 +%global gitcommit_free 1e4b4018578904539d528fbfae9bbcc2f3cb6fc8 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230728 -%global tarballtime 1047 +%global tarballdate 20230729 +%global tarballtime 2237 %global use_release 0 %global use_gitbare 1 From 7cf5d78c452ff40e3954e86cfbcc4afbb5e9d8aa Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 3 Aug 2023 14:52:32 +0900 Subject: [PATCH 147/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 8fcdb38..aaf15ed 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230729T2237.tar.gz) = 8f30b97064a69bdbc9b640cea3bed8564b90cf649feed03745d80c688a015b20044a916ff7e82803c63dc056d7c3fe6c7f3f0283015da4d5a8b6a403c26cc637 +SHA512 (ugene-free-20230803T1426.tar.gz) = 1f9a09bdc352a43e4735441e8ec52dbe920d6f497d208e46fc27feec10b9ae19c512b0ba50c2247abab379e69d0c08bb532d2b1c61ae2e5384c66abacb80e597 diff --git a/ugene.spec b/ugene.spec index f77b105..604346f 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230728 -%global gitcommit 96e658305dade1d3dedf8774939e6be36f481e6b +%global gitdate 20230803 +%global gitcommit 34a24aca9ea3091f98f13501c38acaecf6e136df # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 1e4b4018578904539d528fbfae9bbcc2f3cb6fc8 +%global gitcommit_free 34a24aca9ea3091f98f13501c38acaecf6e136df %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230729 -%global tarballtime 2237 +%global tarballdate 20230803 +%global tarballtime 1426 %global use_release 0 %global use_gitbare 1 From b7ac7b733465564661e491cd08371145229f7425 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 6 Aug 2023 21:45:56 +0900 Subject: [PATCH 148/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index aaf15ed..13c0888 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230803T1426.tar.gz) = 1f9a09bdc352a43e4735441e8ec52dbe920d6f497d208e46fc27feec10b9ae19c512b0ba50c2247abab379e69d0c08bb532d2b1c61ae2e5384c66abacb80e597 +SHA512 (ugene-free-20230806T2104.tar.gz) = 7222d2f4ef0c92102aead693a42da3c2cbfc50314f6516f3ac070b8ca23474f91f262bec47c0541cfa75e4c47e919ba824978e95dda02ecf29960b4750edc04c diff --git a/ugene.spec b/ugene.spec index 604346f..43f43dd 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230803 -%global gitcommit 34a24aca9ea3091f98f13501c38acaecf6e136df +%global gitdate 20230804 +%global gitcommit ce30f96426e3332a885b7221bef3aa7a57c7db7e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 34a24aca9ea3091f98f13501c38acaecf6e136df +%global gitcommit_free 26f9d2942059aed043475ccae3934d2b4c45270f %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230803 -%global tarballtime 1426 +%global tarballdate 20230806 +%global tarballtime 2104 %global use_release 0 %global use_gitbare 1 From 05559c3c64395ae6f42638c8bce588f9643e615f Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 8 Aug 2023 17:22:34 +0900 Subject: [PATCH 149/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 13c0888..a11c46d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230806T2104.tar.gz) = 7222d2f4ef0c92102aead693a42da3c2cbfc50314f6516f3ac070b8ca23474f91f262bec47c0541cfa75e4c47e919ba824978e95dda02ecf29960b4750edc04c +SHA512 (ugene-free-20230808T1655.tar.gz) = ef97c7a24647d95e6940bba11eda2b43bd3a068cddb1ce020ea6a472d93c6ffe7cbfa61e803c36d7bb59323f9ca8f1cac69984513f970a5dadf21bb8f3fbe639 diff --git a/ugene.spec b/ugene.spec index 43f43dd..f31ae8b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230804 -%global gitcommit ce30f96426e3332a885b7221bef3aa7a57c7db7e +%global gitdate 20230807 +%global gitcommit ee09d6707a5a4b50cffa8858b21d78092f9aa310 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 26f9d2942059aed043475ccae3934d2b4c45270f +%global gitcommit_free 99237dea8ed4120ecf4c2a58d70ccfd458f57967 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230806 -%global tarballtime 2104 +%global tarballdate 20230808 +%global tarballtime 1655 %global use_release 0 %global use_gitbare 1 From 36724ee5ea0b98dfffd5222656794b34ce2788a2 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 10 Aug 2023 08:30:22 +0900 Subject: [PATCH 150/260] 48.0 --- sources | 2 +- ugene.spec | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/sources b/sources index a11c46d..e5f0f73 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230808T1655.tar.gz) = ef97c7a24647d95e6940bba11eda2b43bd3a068cddb1ce020ea6a472d93c6ffe7cbfa61e803c36d7bb59323f9ca8f1cac69984513f970a5dadf21bb8f3fbe639 +SHA512 (ugene-free-48.0.tar.gz) = 0bf6cbaae90ecfceae0d5f1fdfd9e8b0c8557fef0270b0d7050d25f5b0a0972e7a04e4cc19fee336614b9e3c0e650f21a1b5b33ccbacc6329755b6bbd6b84fe8 diff --git a/ugene.spec b/ugene.spec index f31ae8b..232f989 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20230808 %global tarballtime 1655 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainver 47.0 +%global mainver 48.0 %undefine prever %if 0%{?use_release} >= 1 @@ -250,6 +250,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Thu Aug 10 2023 Mamoru TASAKA - 48.0-1 +- 48.0 + * Sat Jul 22 2023 Mamoru TASAKA - 47.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild From 52697c745928e869735bff2c0df84c7bf24b8b66 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 18 Aug 2023 22:34:31 +0900 Subject: [PATCH 151/260] update to the latest git --- sources | 2 +- ugene.spec | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/sources b/sources index e5f0f73..1e573a7 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-48.0.tar.gz) = 0bf6cbaae90ecfceae0d5f1fdfd9e8b0c8557fef0270b0d7050d25f5b0a0972e7a04e4cc19fee336614b9e3c0e650f21a1b5b33ccbacc6329755b6bbd6b84fe8 +SHA512 (ugene-free-20230818T1831.tar.gz) = 7784bd25696f7bf76775f1a9f27aab7c82e6bf90cbb6f24aff0cdfae207a5fc019cf4636c1ea866038a57153584fbd458af1a1662079b4718122e94c8b95ce2b diff --git a/ugene.spec b/ugene.spec index 232f989..30db5a3 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230807 -%global gitcommit ee09d6707a5a4b50cffa8858b21d78092f9aa310 +%global gitdate 20230817 +%global gitcommit be9ee5485a087d15a05e4ef9e7cd869c276c6e73 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 99237dea8ed4120ecf4c2a58d70ccfd458f57967 +%global gitcommit_free b18de69aef36a5c3b62b3f533f498044c3c176a8 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230808 -%global tarballtime 1655 +%global tarballdate 20230818 +%global tarballtime 1831 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From 755401cc31a3d04dab806c3ce3f535e80027d82d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 24 Aug 2023 14:25:39 +0900 Subject: [PATCH 152/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 1e573a7..5b8de64 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230818T1831.tar.gz) = 7784bd25696f7bf76775f1a9f27aab7c82e6bf90cbb6f24aff0cdfae207a5fc019cf4636c1ea866038a57153584fbd458af1a1662079b4718122e94c8b95ce2b +SHA512 (ugene-free-20230823T1951.tar.gz) = 616d369d5dc246cf5e8f7efe01794bad9a810537cc3f9341e131e325ca702a0c56fdd669ccd949b177eba52a6b9488b698a446dd51e7ae1ed76bc4201f4cf90e diff --git a/ugene.spec b/ugene.spec index 30db5a3..aa68518 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230817 -%global gitcommit be9ee5485a087d15a05e4ef9e7cd869c276c6e73 +%global gitdate 20230821 +%global gitcommit b7272ab3ce2f5b07a881278382aa8b279e73045d # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b18de69aef36a5c3b62b3f533f498044c3c176a8 +%global gitcommit_free 13f7d6eea8837f3b7e7664296375ca706171a5ff %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230818 -%global tarballtime 1831 +%global tarballdate 20230823 +%global tarballtime 1951 %global use_release 0 %global use_gitbare 1 From f8ee1f325a5dac93ad864c1e639143d9b206fb30 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 29 Aug 2023 00:02:40 +0900 Subject: [PATCH 153/260] update to the latest git --- ugene.spec | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/ugene.spec b/ugene.spec index aa68518..95c3617 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230821 -%global gitcommit b7272ab3ce2f5b07a881278382aa8b279e73045d +%global gitdate 20230827 +%global gitcommit e37ce9d78858d268af508cb793a80297e116b5b2 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 13f7d6eea8837f3b7e7664296375ca706171a5ff +%global gitcommit_free e37ce9d78858d268af508cb793a80297e116b5b2 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230823 -%global tarballtime 1951 +%global tarballdate 20230828 +%global tarballtime 2340 %global use_release 0 %global use_gitbare 1 From 881a64a83841c7d8b9ec12fefee062ac5e31d9be Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 29 Aug 2023 08:30:43 +0900 Subject: [PATCH 154/260] update to the latest git --- sources | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sources b/sources index 5b8de64..a398aa8 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230823T1951.tar.gz) = 616d369d5dc246cf5e8f7efe01794bad9a810537cc3f9341e131e325ca702a0c56fdd669ccd949b177eba52a6b9488b698a446dd51e7ae1ed76bc4201f4cf90e +SHA512 (ugene-free-20230828T2340.tar.gz) = 75ef85620335dcb40d80eb0086c5360477b7816348adc4b2066f157733b1f801939ff7cf7081758c893691956b75fbfb15240c0d1c62e5d08eb5b395371df4ff From a8437906c25afa5f8b5520a6d096a8bfde7947f1 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 4 Sep 2023 15:29:15 +0900 Subject: [PATCH 155/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index a398aa8..077d67c 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230828T2340.tar.gz) = 75ef85620335dcb40d80eb0086c5360477b7816348adc4b2066f157733b1f801939ff7cf7081758c893691956b75fbfb15240c0d1c62e5d08eb5b395371df4ff +SHA512 (ugene-free-20230904T1053.tar.gz) = 702ec1dbdee44405b46a5f285ea185e967d45e7042964bce5f7a697ae7864ffcb3fcd9175368c3e10182efb7bf324ae92737cd0942cca663222106855ce73792 diff --git a/ugene.spec b/ugene.spec index 95c3617..da27473 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230827 -%global gitcommit e37ce9d78858d268af508cb793a80297e116b5b2 +%global gitdate 20230903 +%global gitcommit 3dd4779ff42843fd7c653643840c8ae23c784646 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free e37ce9d78858d268af508cb793a80297e116b5b2 +%global gitcommit_free 5b1c13afdeac24ae9af8f7d93da33ee183270879 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230828 -%global tarballtime 2340 +%global tarballdate 20230904 +%global tarballtime 1053 %global use_release 0 %global use_gitbare 1 From 4815a13c494ef006bcfd88956bfdecc29f91f54e Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 5 Sep 2023 22:44:54 +0900 Subject: [PATCH 156/260] 48.1 --- sources | 2 +- ugene.spec | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/sources b/sources index 077d67c..05f80c3 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230904T1053.tar.gz) = 702ec1dbdee44405b46a5f285ea185e967d45e7042964bce5f7a697ae7864ffcb3fcd9175368c3e10182efb7bf324ae92737cd0942cca663222106855ce73792 +SHA512 (ugene-free-48.1.tar.gz) = dca7746e78dfa64f6557c17b0c2e0d1edf7bab50bba6c4dc245ba976b854b86d77c3594f8b59bf5d8a541df73f8f806217947ce90dc96dc29f95d353aabee5d9 diff --git a/ugene.spec b/ugene.spec index da27473..2e0d87b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20230904 %global tarballtime 1053 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainver 48.0 +%global mainver 48.1 %undefine prever %if 0%{?use_release} >= 1 @@ -250,6 +250,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Tue Sep 5 2023 Mamoru TASAKA - 48.1-1 +- 48.1 + * Thu Aug 10 2023 Mamoru TASAKA - 48.0-1 - 48.0 From eeed9fc5874d2c490b58ff60870f759230a066a1 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 8 Sep 2023 11:04:16 +0900 Subject: [PATCH 157/260] update to the latest git --- sources | 2 +- ugene.spec | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/sources b/sources index 05f80c3..86b6632 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-48.1.tar.gz) = dca7746e78dfa64f6557c17b0c2e0d1edf7bab50bba6c4dc245ba976b854b86d77c3594f8b59bf5d8a541df73f8f806217947ce90dc96dc29f95d353aabee5d9 +SHA512 (ugene-free-20230908T1018.tar.gz) = 4ba898f397de84236158ee570eda08c3fbac5f9e190b77418cf0021242378024c53f956554128fd482e07b28310d964a65724090e32f23bc38d8d40fd018a6c8 diff --git a/ugene.spec b/ugene.spec index 2e0d87b..880b6f8 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230903 -%global gitcommit 3dd4779ff42843fd7c653643840c8ae23c784646 +%global gitdate 20230907 +%global gitcommit 92abaf707d38eda2a252c99ce0fc03fed0b5d51f # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 5b1c13afdeac24ae9af8f7d93da33ee183270879 +%global gitcommit_free 935bae5f39c870309a8b93e795f97f2ab18abc3b %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230904 -%global tarballtime 1053 +%global tarballdate 20230908 +%global tarballtime 1018 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From 5cd9c71aa43c82d3535846f726a0117e64d4e855 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 11 Sep 2023 15:55:28 +0900 Subject: [PATCH 158/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 86b6632..9de68cd 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230908T1018.tar.gz) = 4ba898f397de84236158ee570eda08c3fbac5f9e190b77418cf0021242378024c53f956554128fd482e07b28310d964a65724090e32f23bc38d8d40fd018a6c8 +SHA512 (ugene-free-20230911T1510.tar.gz) = 3c7b98baf6a81386860e1b7254c8a7f733f9aeb2924405ab37bf089b492f1052b55675ab9c7bca1f183a824c7464684f11d3eac980fa3c1eda04b72f043a6d8a diff --git a/ugene.spec b/ugene.spec index 880b6f8..1695902 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230907 -%global gitcommit 92abaf707d38eda2a252c99ce0fc03fed0b5d51f +%global gitdate 20230908 +%global gitcommit c74f5cb89726176e276d5e2141121d25a576175b # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 935bae5f39c870309a8b93e795f97f2ab18abc3b +%global gitcommit_free 43e9140481c40878aba5aa62c1632a22b1200922 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230908 -%global tarballtime 1018 +%global tarballdate 20230911 +%global tarballtime 1510 %global use_release 0 %global use_gitbare 1 From 9d9bdb2ff5de017bc54d1a94ac372a065077636d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 18 Sep 2023 16:47:52 +0900 Subject: [PATCH 159/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 9de68cd..a5d892c 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230911T1510.tar.gz) = 3c7b98baf6a81386860e1b7254c8a7f733f9aeb2924405ab37bf089b492f1052b55675ab9c7bca1f183a824c7464684f11d3eac980fa3c1eda04b72f043a6d8a +SHA512 (ugene-free-20230918T1537.tar.gz) = 7ce4b0c6d1040647e6adcde40cb591c7ece29f0441014926f6e0a7850e8b969ebae88ee6af0748daf740b456705185f41d395bc0cfef005ec5eecf6df9547ce1 diff --git a/ugene.spec b/ugene.spec index 1695902..aea63ed 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230908 -%global gitcommit c74f5cb89726176e276d5e2141121d25a576175b +%global gitdate 20230915 +%global gitcommit 0f0fc71b9193434c67c1eb39eda28f8a7bd3361e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 43e9140481c40878aba5aa62c1632a22b1200922 +%global gitcommit_free 0e2f85b3f4bc37c236419b32da6fe9db9346cd40 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230911 -%global tarballtime 1510 +%global tarballdate 20230918 +%global tarballtime 1537 %global use_release 0 %global use_gitbare 1 From de7268eee85e33cadb91b06eae0f993dd0c42f0f Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 1 Oct 2023 21:28:08 +0900 Subject: [PATCH 160/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index a5d892c..51281b8 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20230918T1537.tar.gz) = 7ce4b0c6d1040647e6adcde40cb591c7ece29f0441014926f6e0a7850e8b969ebae88ee6af0748daf740b456705185f41d395bc0cfef005ec5eecf6df9547ce1 +SHA512 (ugene-free-20231001T1544.tar.gz) = 7defdc2992e4d4776a4f2cd4a4744a45fafd51f4122104bde20e7f0c54adb0ed52f7750d0458310c8854ac7b508d3189114b3e29ba224b38b1b93cc515ab0325 diff --git a/ugene.spec b/ugene.spec index aea63ed..f840f22 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230915 -%global gitcommit 0f0fc71b9193434c67c1eb39eda28f8a7bd3361e +%global gitdate 20230929 +%global gitcommit bf32c1c1da0ce1034898baed15e761bbe9741b70 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 0e2f85b3f4bc37c236419b32da6fe9db9346cd40 +%global gitcommit_free 9172c383c364563a019a9dc8c4b0fae2ad7b6ddc %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20230918 -%global tarballtime 1537 +%global tarballdate 20231001 +%global tarballtime 1544 %global use_release 0 %global use_gitbare 1 From b0007f969fa291167159b8afccd2d20f97e79a0d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 11 Oct 2023 16:24:47 +0900 Subject: [PATCH 161/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 51281b8..ee99309 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231001T1544.tar.gz) = 7defdc2992e4d4776a4f2cd4a4744a45fafd51f4122104bde20e7f0c54adb0ed52f7750d0458310c8854ac7b508d3189114b3e29ba224b38b1b93cc515ab0325 +SHA512 (ugene-free-20231011T1525.tar.gz) = b7144cf5118b46b7a993c17ce791559ca91c7b920735249c6a89760470f07869463efbbc76f2eea24cc592c9457974c5d58ef1417f98014163ecb388971ae7a9 diff --git a/ugene.spec b/ugene.spec index f840f22..d7c404a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20230929 -%global gitcommit bf32c1c1da0ce1034898baed15e761bbe9741b70 +%global gitdate 20231010 +%global gitcommit 9b895736d9aee9344dbbee72a959e6ddb67f43fe # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 9172c383c364563a019a9dc8c4b0fae2ad7b6ddc +%global gitcommit_free 801900326840da2ebac00c6afa22c108978c6537 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231001 -%global tarballtime 1544 +%global tarballdate 20231011 +%global tarballtime 1525 %global use_release 0 %global use_gitbare 1 From fcc925cc0e15b1b825628517778a68bd6184c4ef Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 15 Oct 2023 09:47:22 +0900 Subject: [PATCH 162/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index ee99309..451f95f 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231011T1525.tar.gz) = b7144cf5118b46b7a993c17ce791559ca91c7b920735249c6a89760470f07869463efbbc76f2eea24cc592c9457974c5d58ef1417f98014163ecb388971ae7a9 +SHA512 (ugene-free-20231015T0819.tar.gz) = 57a7f745b9b255e7ddf86218b961eb5da8690e58480601d4c4fd522366355737386745374088f5d72c6bb668394b0b346087f76b13ea48bb1280fe3b3863e285 diff --git a/ugene.spec b/ugene.spec index d7c404a..1cc9a5e 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231010 -%global gitcommit 9b895736d9aee9344dbbee72a959e6ddb67f43fe +%global gitdate 20231013 +%global gitcommit fef5ab95330b263657bf1ef13cfe3b0ce88afd08 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 801900326840da2ebac00c6afa22c108978c6537 +%global gitcommit_free 16f6906107da90873108546c9ef9bc673a489d04 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231011 -%global tarballtime 1525 +%global tarballdate 20231015 +%global tarballtime 0819 %global use_release 0 %global use_gitbare 1 From f750ff5bd34dc6bced19544777672cce31bd37ed Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 22 Oct 2023 09:46:58 +0900 Subject: [PATCH 163/260] update to the latest git --- ugene.spec | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/ugene.spec b/ugene.spec index 1cc9a5e..b2acd81 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231013 -%global gitcommit fef5ab95330b263657bf1ef13cfe3b0ce88afd08 +%global gitdate 20231017 +%global gitcommit 2b480a44f0e35c2b2dbfd2b6bf796d3174f1c059 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 16f6906107da90873108546c9ef9bc673a489d04 +%global gitcommit_free a9023c66b5bf484218bc1371813a5c35c03e6fbb %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231015 -%global tarballtime 0819 +%global tarballdate 20231022 +%global tarballtime 0928 %global use_release 0 %global use_gitbare 1 From e0c1791b8173fdd3d58dbb2e475ca0d45af3adf2 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 22 Oct 2023 10:00:38 +0900 Subject: [PATCH 164/260] update to the latest git --- sources | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sources b/sources index 451f95f..d8c5e60 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231015T0819.tar.gz) = 57a7f745b9b255e7ddf86218b961eb5da8690e58480601d4c4fd522366355737386745374088f5d72c6bb668394b0b346087f76b13ea48bb1280fe3b3863e285 +SHA512 (ugene-free-20231022T0928.tar.gz) = 85e15258a7e06f19849002b2e1254c0b4eb078b09c4dda5ca4ebff1ecc35bc7303df247cc4b91ba10a285c458328e06a8beed78314f0776717d9536c44654875 From 2333145b91502f9e34261fcbf2d699cfe083659e Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 27 Oct 2023 11:05:23 +0900 Subject: [PATCH 165/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index d8c5e60..e4c3a64 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231022T0928.tar.gz) = 85e15258a7e06f19849002b2e1254c0b4eb078b09c4dda5ca4ebff1ecc35bc7303df247cc4b91ba10a285c458328e06a8beed78314f0776717d9536c44654875 +SHA512 (ugene-free-20231027T1031.tar.gz) = 9505232fd5c27c91b4f8e35e34e76618736096f037c68d22125180d8313e400d64d09806b6ae83b68c9e7c1e8a87deee58234eed3b1b7ebddf2727fea3e15777 diff --git a/ugene.spec b/ugene.spec index b2acd81..100b803 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231017 -%global gitcommit 2b480a44f0e35c2b2dbfd2b6bf796d3174f1c059 +%global gitdate 20231027 +%global gitcommit 5aa19ba5e0578475aa8f22700c1a326454ff24dc # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free a9023c66b5bf484218bc1371813a5c35c03e6fbb +%global gitcommit_free 9515232d9e8c10e18c3cb9bebf62797a24dbc429 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231022 -%global tarballtime 0928 +%global tarballdate 20231027 +%global tarballtime 1031 %global use_release 0 %global use_gitbare 1 From cefb0c0e8bdd413a8c9c071a5bb138cd1e79f895 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 31 Oct 2023 16:53:10 +0900 Subject: [PATCH 166/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index e4c3a64..0cd6c91 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231027T1031.tar.gz) = 9505232fd5c27c91b4f8e35e34e76618736096f037c68d22125180d8313e400d64d09806b6ae83b68c9e7c1e8a87deee58234eed3b1b7ebddf2727fea3e15777 +SHA512 (ugene-free-20231031T1534.tar.gz) = e703ac5434426b3048bd140700bfb91264148444d930bf1029bbef751347ba376fefd3493f52625a9f533748759f64a135076d8f77ca4546249c3592734b6584 diff --git a/ugene.spec b/ugene.spec index 100b803..645715d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231027 -%global gitcommit 5aa19ba5e0578475aa8f22700c1a326454ff24dc +%global gitdate 20231031 +%global gitcommit 87dd62625694dfd22401af6055505fb867775258 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 9515232d9e8c10e18c3cb9bebf62797a24dbc429 +%global gitcommit_free bec1c1f7a31b8f102c6e6fef46fc70f9a8e94f4e %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231027 -%global tarballtime 1031 +%global tarballdate 20231031 +%global tarballtime 1534 %global use_release 0 %global use_gitbare 1 From a879fd5a1f9a401e0d58a2569b94777dc2ea9a7a Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 4 Nov 2023 23:07:10 +0900 Subject: [PATCH 167/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0cd6c91..91dfe72 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231031T1534.tar.gz) = e703ac5434426b3048bd140700bfb91264148444d930bf1029bbef751347ba376fefd3493f52625a9f533748759f64a135076d8f77ca4546249c3592734b6584 +SHA512 (ugene-free-20231104T2226.tar.gz) = 682f9978a367534bd298c875b2d77d87882d9f22f9105d7f3a6d7e16f9f92d476f81702187dd56d93e29fbf83fb6adf20a9c1d5abe8fe89767810d1e52e2b374 diff --git a/ugene.spec b/ugene.spec index 645715d..159127a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231031 -%global gitcommit 87dd62625694dfd22401af6055505fb867775258 +%global gitdate 20231102 +%global gitcommit 0a205e0d660000d6c3a5638ce2104239baf64098 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free bec1c1f7a31b8f102c6e6fef46fc70f9a8e94f4e +%global gitcommit_free 03df674a79cd1afa05447599529999249ff6ecf8 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231031 -%global tarballtime 1534 +%global tarballdate 20231104 +%global tarballtime 2226 %global use_release 0 %global use_gitbare 1 From 5eb9caa09b9e4f998a221898f678bc038239a714 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 6 Nov 2023 09:16:03 +0900 Subject: [PATCH 168/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 91dfe72..7620531 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231104T2226.tar.gz) = 682f9978a367534bd298c875b2d77d87882d9f22f9105d7f3a6d7e16f9f92d476f81702187dd56d93e29fbf83fb6adf20a9c1d5abe8fe89767810d1e52e2b374 +SHA512 (ugene-free-20231106T0814.tar.gz) = 2fe6bd40c850e56e1d4dcf0960445e697f5d4c4b5b54d3426256a650b7250cf9350c9f7bf7966a121e0f22d95a2be1860e825b5f6ca12c622208b27de1637103 diff --git a/ugene.spec b/ugene.spec index 159127a..2085b1a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231102 -%global gitcommit 0a205e0d660000d6c3a5638ce2104239baf64098 +%global gitdate 20231106 +%global gitcommit 10eda8827eccc32a7c6222b738ae937e2fd81665 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 03df674a79cd1afa05447599529999249ff6ecf8 +%global gitcommit_free fcb3cae9cdfae65c794d0ad46c16a96f015c2404 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231104 -%global tarballtime 2226 +%global tarballdate 20231106 +%global tarballtime 0814 %global use_release 0 %global use_gitbare 1 From 91a789b5f5d9e514ce2e7921fd42227aeb0138a8 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 9 Nov 2023 15:28:03 +0900 Subject: [PATCH 169/260] 48.1 --- sources | 2 +- ugene.spec | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/sources b/sources index 7620531..a4ebabd 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231106T0814.tar.gz) = 2fe6bd40c850e56e1d4dcf0960445e697f5d4c4b5b54d3426256a650b7250cf9350c9f7bf7966a121e0f22d95a2be1860e825b5f6ca12c622208b27de1637103 +SHA512 (ugene-free-49.0.tar.gz) = a8e5c428bead833c3016db8346cf50cc70c0d33c6137e8a43a6773800e8eb7388b06942fd21710d10bcb4c871e680d8de973313a860517fd3155379868d57b65 diff --git a/ugene.spec b/ugene.spec index 2085b1a..8a8dffd 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20231106 %global tarballtime 0814 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainver 48.1 +%global mainver 49.0 %undefine prever %if 0%{?use_release} >= 1 @@ -250,6 +250,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Thu Nov 9 2023 Mamoru TASAKA - 49.0-1 +- 49.0 + * Tue Sep 5 2023 Mamoru TASAKA - 48.1-1 - 48.1 From 74c1d260d34b0c4b9f70b986798dbaf452bdbc04 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 28 Nov 2023 08:48:19 +0900 Subject: [PATCH 170/260] 49.1 --- sources | 2 +- ugene.spec | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/sources b/sources index a4ebabd..d9ee342 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-49.0.tar.gz) = a8e5c428bead833c3016db8346cf50cc70c0d33c6137e8a43a6773800e8eb7388b06942fd21710d10bcb4c871e680d8de973313a860517fd3155379868d57b65 +SHA512 (ugene-free-49.1.tar.gz) = c75f20053879ee347b28c31ae4447fb154676adb0947cc9a6e28c2f2664b9f45a28c3c1353abab8ff25e0773f4f9b0cc94c2fe2788862a72a50cb21f778466bf diff --git a/ugene.spec b/ugene.spec index 8a8dffd..cc3e210 100644 --- a/ugene.spec +++ b/ugene.spec @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainver 49.0 +%global mainver 49.1 %undefine prever %if 0%{?use_release} >= 1 @@ -250,6 +250,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Tue Nov 28 2023 Mamoru TASAKA - 49.1-1 +- 49.1 + * Thu Nov 9 2023 Mamoru TASAKA - 49.0-1 - 49.0 From 5f6471ef693c3b552b7b07e8df8cbead6516247a Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 13 Dec 2023 10:35:15 +0900 Subject: [PATCH 171/260] update to the latest git --- sources | 2 +- ugene.spec | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/sources b/sources index d9ee342..89cbee0 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-49.1.tar.gz) = c75f20053879ee347b28c31ae4447fb154676adb0947cc9a6e28c2f2664b9f45a28c3c1353abab8ff25e0773f4f9b0cc94c2fe2788862a72a50cb21f778466bf +SHA512 (ugene-free-20231213T0946.tar.gz) = 8960fef3407d03a44b0a0cbc96d81b36473ac8909ef51cfac81a63c4467c0e862f697ffdce5dd6c4f4d452f6ad26787bf82aa498f6aea8248dc96dd521122c81 diff --git a/ugene.spec b/ugene.spec index cc3e210..dbe1d0a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231106 -%global gitcommit 10eda8827eccc32a7c6222b738ae937e2fd81665 +%global gitdate 20231212 +%global gitcommit ef5d6bf87443c102aa35ca430c6033e43b08aab5 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free fcb3cae9cdfae65c794d0ad46c16a96f015c2404 +%global gitcommit_free b848be79494e369c0784cbb8f8edf9a85cf9a1be %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231106 -%global tarballtime 0814 +%global tarballdate 20231213 +%global tarballtime 0946 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From 3d118d89370ee3caebfae33c1236c8b02bd8a640 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 15 Dec 2023 11:57:12 +0900 Subject: [PATCH 172/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 89cbee0..4638e8a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231213T0946.tar.gz) = 8960fef3407d03a44b0a0cbc96d81b36473ac8909ef51cfac81a63c4467c0e862f697ffdce5dd6c4f4d452f6ad26787bf82aa498f6aea8248dc96dd521122c81 +SHA512 (ugene-free-20231215T1055.tar.gz) = 3df5457004cf3c3390fc245c35615d3bb295cc9bd7e819dca983b2a627bc4238f452e9eca78705165717558b14554f0ef54850ccb379451a74fc25a055b448f8 diff --git a/ugene.spec b/ugene.spec index dbe1d0a..41a9aaf 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231212 -%global gitcommit ef5d6bf87443c102aa35ca430c6033e43b08aab5 +%global gitdate 20231215 +%global gitcommit b70c69a6f9d81e760b9dcb7cb652d62dce8c9888 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b848be79494e369c0784cbb8f8edf9a85cf9a1be +%global gitcommit_free 50ab12e8a6adb3b97c1fafbed0bde596caa9e4f4 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231213 -%global tarballtime 0946 +%global tarballdate 20231215 +%global tarballtime 1055 %global use_release 0 %global use_gitbare 1 From db77410dcfa47d946feb86688341ebeef5aeb9a2 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 18 Dec 2023 16:44:14 +0900 Subject: [PATCH 173/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 4638e8a..7f9afb1 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231215T1055.tar.gz) = 3df5457004cf3c3390fc245c35615d3bb295cc9bd7e819dca983b2a627bc4238f452e9eca78705165717558b14554f0ef54850ccb379451a74fc25a055b448f8 +SHA512 (ugene-free-20231217T1954.tar.gz) = 7007a4397602624704bd3c78c95af20c73e09dd734bfd5944c5985f4683b3b6fd3703e170937a8267e21ff9d49cb2b1505184e6cfe0ca89bddeab762169d6dd5 diff --git a/ugene.spec b/ugene.spec index 41a9aaf..8f262ac 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231215 -%global gitcommit b70c69a6f9d81e760b9dcb7cb652d62dce8c9888 +%global gitdate 20231216 +%global gitcommit 569b50aec0217b03ad36717ee5f55631596d3391 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 50ab12e8a6adb3b97c1fafbed0bde596caa9e4f4 +%global gitcommit_free b3e6e421843e1aef9f90d259ccfa82a04f89e9be %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231215 -%global tarballtime 1055 +%global tarballdate 20231217 +%global tarballtime 1954 %global use_release 0 %global use_gitbare 1 From 230b1d88877312b072e684862de8d55e5762d724 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 21 Dec 2023 13:20:08 +0900 Subject: [PATCH 174/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 7f9afb1..1107174 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231217T1954.tar.gz) = 7007a4397602624704bd3c78c95af20c73e09dd734bfd5944c5985f4683b3b6fd3703e170937a8267e21ff9d49cb2b1505184e6cfe0ca89bddeab762169d6dd5 +SHA512 (ugene-free-20231221T1139.tar.gz) = e971a1700994e3a225d77705ef4afcf72a6c927aa9102fe7ab26ab3418f1a59b344dd3eeaa3c2c4c94269b694d43d4420d0c7f3f1cff298fc157cfb974c6aeaf diff --git a/ugene.spec b/ugene.spec index 8f262ac..d2a3152 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231216 -%global gitcommit 569b50aec0217b03ad36717ee5f55631596d3391 +%global gitdate 20231221 +%global gitcommit e7efecae3b57fa5ddb86c108096c0a70aff2cc15 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b3e6e421843e1aef9f90d259ccfa82a04f89e9be +%global gitcommit_free 1a4a0dc599e061b1bfd382d4789609328ffe06b0 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231217 -%global tarballtime 1954 +%global tarballdate 20231221 +%global tarballtime 1139 %global use_release 0 %global use_gitbare 1 From ec5a6d2c7744950a7ebb413ba47871efd0803028 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 1 Jan 2024 23:45:13 +0900 Subject: [PATCH 175/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 1107174..8490052 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20231221T1139.tar.gz) = e971a1700994e3a225d77705ef4afcf72a6c927aa9102fe7ab26ab3418f1a59b344dd3eeaa3c2c4c94269b694d43d4420d0c7f3f1cff298fc157cfb974c6aeaf +SHA512 (ugene-free-20240101T2204.tar.gz) = c288fd54d4543c273e46e0f4a7b01961321a766df40e1ea32bd6cce8967deba06a48e6d2e24d7223b4acb9361fea105d30047711f4892612932ddf91dd7d0451 diff --git a/ugene.spec b/ugene.spec index d2a3152..35e9e4c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20231221 -%global gitcommit e7efecae3b57fa5ddb86c108096c0a70aff2cc15 +%global gitdate 20240101 +%global gitcommit 7a67274346683fe95a0886753825f24646178ec6 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 1a4a0dc599e061b1bfd382d4789609328ffe06b0 +%global gitcommit_free 81c02a8a15bfa81f2f15102bd640fb157956aee3 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20231221 -%global tarballtime 1139 +%global tarballdate 20240101 +%global tarballtime 2204 %global use_release 0 %global use_gitbare 1 From efa35a9971dee1bb494d911499e3a8a4b18a9cba Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 9 Jan 2024 23:36:25 +0900 Subject: [PATCH 176/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 8490052..eb05587 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240101T2204.tar.gz) = c288fd54d4543c273e46e0f4a7b01961321a766df40e1ea32bd6cce8967deba06a48e6d2e24d7223b4acb9361fea105d30047711f4892612932ddf91dd7d0451 +SHA512 (ugene-free-20240109T2203.tar.gz) = 40ba084cd8589bc3b6ae490447439bb4d268383e973e66890c0851a7f454bd2f5a727d3cb39e1298761a768c16053c3eecf56b6d561b2d2cb1460267753793d9 diff --git a/ugene.spec b/ugene.spec index 35e9e4c..07aab27 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240101 -%global gitcommit 7a67274346683fe95a0886753825f24646178ec6 +%global gitdate 20240107 +%global gitcommit 496dd093c387980007e846f3d37f8b366fbdbc09 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 81c02a8a15bfa81f2f15102bd640fb157956aee3 +%global gitcommit_free cc4f6466a61429c5c1f987251f75efbe5c14cb92 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240101 -%global tarballtime 2204 +%global tarballdate 20240109 +%global tarballtime 2203 %global use_release 0 %global use_gitbare 1 From a6f23b1788d9cc5411a51668f33041b2dfdd647a Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 22 Jan 2024 18:15:55 +0900 Subject: [PATCH 177/260] Fix -Wnarrowing on non x86(-64) arch detected by gcc14 --- ugene-49.1-narrowing-for-unsigned-char.patch | 22 ++++++++++++++++++++ ugene.spec | 9 ++++++-- 2 files changed, 29 insertions(+), 2 deletions(-) create mode 100644 ugene-49.1-narrowing-for-unsigned-char.patch diff --git a/ugene-49.1-narrowing-for-unsigned-char.patch b/ugene-49.1-narrowing-for-unsigned-char.patch new file mode 100644 index 0000000..a37bc35 --- /dev/null +++ b/ugene-49.1-narrowing-for-unsigned-char.patch @@ -0,0 +1,22 @@ +--- ugene-49.1/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h.orig 2023-11-26 02:17:11.000000000 +0900 ++++ ugene-49.1/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h 2024-01-22 16:42:22.536722206 +0900 +@@ -37,7 +37,7 @@ namespace BALL + { + namespace __private + { +- extern const char BALL_EXPORT neighbour_table_[27][3]; ++ extern const signed char BALL_EXPORT neighbour_table_[27][3]; + } + + template class HashGrid3; +--- ugene-49.1/src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp.orig 2023-11-26 02:17:11.000000000 +0900 ++++ ugene-49.1/src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp 2024-01-22 16:42:28.199724474 +0900 +@@ -9,7 +9,7 @@ namespace BALL + { + namespace __private + { +- const char neighbour_table_[27][3] = ++ const signed char neighbour_table_[27][3] = + { + { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 }, + { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 }, diff --git a/ugene.spec b/ugene.spec index cc3e210..dda96db 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -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 @@ -70,6 +70,7 @@ Source1: create-ugene-free-tarball.sh Source2: create-%{name}-git-bare-tarball.sh # This is not installed Source10: ugene.wrapper +Patch1: ugene-49.1-narrowing-for-unsigned-char.patch # Currently distro-specific Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch @@ -131,7 +132,8 @@ git checkout -b %{mainver}-fedora %{gitcommit_free} git config user.name "%{name} Fedora maintainer" git config user.email "%{name}-maintainers@fedoraproject.org" %endif - +%patch -P1 -p1 -b .narrow + %GIT commit -m "Fix narrowing on arch where default char is unsigned" -a %patch -P102 -p1 -b .sys_mmap -Z %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a %patch -P103 -p1 -b .unwind -Z @@ -250,6 +252,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Mon Jan 22 2024 Mamoru TASAKA - 49.1-2 +- Fix -Wnarrowing on non x86(-64) arch detected by gcc14 + * Tue Nov 28 2023 Mamoru TASAKA - 49.1-1 - 49.1 From b261956febf2c99aedb22a83214018b64e6f9ec0 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 26 Jan 2024 12:59:01 +0900 Subject: [PATCH 178/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index eb05587..222e7aa 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240109T2203.tar.gz) = 40ba084cd8589bc3b6ae490447439bb4d268383e973e66890c0851a7f454bd2f5a727d3cb39e1298761a768c16053c3eecf56b6d561b2d2cb1460267753793d9 +SHA512 (ugene-free-20240126T1045.tar.gz) = 091a7eefcff0f719769a011a1a9d1feaa9d1d9323dd2cf5b4fb036715b3240cc922f0d148215fb7dce1e239e260519799fa2e08e88bc95d5b5fdb43a2975c2f4 diff --git a/ugene.spec b/ugene.spec index 3fb704b..6bfddac 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240107 -%global gitcommit 496dd093c387980007e846f3d37f8b366fbdbc09 +%global gitdate 20240126 +%global gitcommit 5fb77632805bf70a5a778aa2de651a6d43e2d13e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free cc4f6466a61429c5c1f987251f75efbe5c14cb92 +%global gitcommit_free 042fc80c4982271da9f52c7d9ad5d70d2d4dc3e3 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240109 -%global tarballtime 2203 +%global tarballdate 20240126 +%global tarballtime 1045 %global use_release 0 %global use_gitbare 1 From 9851c1ed9921e50bc20f0d3e05b55447b37f4b8e Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 27 Jan 2024 07:01:46 +0000 Subject: [PATCH 179/260] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index dda96db..048bfb5 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -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 @@ -252,6 +252,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sat Jan 27 2024 Fedora Release Engineering - 49.1-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + * Mon Jan 22 2024 Mamoru TASAKA - 49.1-2 - Fix -Wnarrowing on non x86(-64) arch detected by gcc14 From d291fb6850fb5b70bf00d8a8fedd6d27c813ea79 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 2 Feb 2024 14:37:22 +0900 Subject: [PATCH 180/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 222e7aa..986a352 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240126T1045.tar.gz) = 091a7eefcff0f719769a011a1a9d1feaa9d1d9323dd2cf5b4fb036715b3240cc922f0d148215fb7dce1e239e260519799fa2e08e88bc95d5b5fdb43a2975c2f4 +SHA512 (ugene-free-20240202T1315.tar.gz) = e2a6bfe987fb0e60d82fde59d849d622435d4ffce0437e5153508da49613028f46a83da2589f9178a4609d14419850f207155dc843cc5a6887a57f7fa15eac39 diff --git a/ugene.spec b/ugene.spec index 6bfddac..7d128f7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240126 -%global gitcommit 5fb77632805bf70a5a778aa2de651a6d43e2d13e +%global gitdate 20240201 +%global gitcommit c075ec9cf860739253e12688620f480e843a20ac # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 042fc80c4982271da9f52c7d9ad5d70d2d4dc3e3 +%global gitcommit_free 8465fc4e1ccfe6094b125462bfecc56435540ba4 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240126 -%global tarballtime 1045 +%global tarballdate 20240202 +%global tarballtime 1315 %global use_release 0 %global use_gitbare 1 From 8e3dafc34290d9b2544fd6b96a0f36efb40fbddb Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 6 Feb 2024 15:50:01 +0900 Subject: [PATCH 181/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 986a352..483e85b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240202T1315.tar.gz) = e2a6bfe987fb0e60d82fde59d849d622435d4ffce0437e5153508da49613028f46a83da2589f9178a4609d14419850f207155dc843cc5a6887a57f7fa15eac39 +SHA512 (ugene-free-20240206T1153.tar.gz) = 98a975d7cdceb87a45da1f330cecb4073beeba48033dbc38ab6e3152062a4ebb063629c50ca1c8daeef38dbc2450256a183d9e9abfe03b1f822e6c3f198bafc5 diff --git a/ugene.spec b/ugene.spec index 1b1ebf0..692d23f 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240201 -%global gitcommit c075ec9cf860739253e12688620f480e843a20ac +%global gitdate 20240206 +%global gitcommit 2f85b9143373e291ea19af34d15b98554ba3e76d # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 8465fc4e1ccfe6094b125462bfecc56435540ba4 +%global gitcommit_free e92e63d13cfdc37160f2b61f3028da2e85dce8aa %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240202 -%global tarballtime 1315 +%global tarballdate 20240206 +%global tarballtime 1153 %global use_release 0 %global use_gitbare 1 From c2bf7de4f1aed786d5b377c68bfbb371b6687a66 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 13 Feb 2024 19:41:35 +0900 Subject: [PATCH 182/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 483e85b..9eb4a84 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240206T1153.tar.gz) = 98a975d7cdceb87a45da1f330cecb4073beeba48033dbc38ab6e3152062a4ebb063629c50ca1c8daeef38dbc2450256a183d9e9abfe03b1f822e6c3f198bafc5 +SHA512 (ugene-free-20240213T1625.tar.gz) = 7ba61dde9a6959564e0da801bebfb07147fe9062633493df93cfe10d5fe98bc08ea0190411cdf552c5631d7916d79970cbc1ea325f505895a34adeb21633e812 diff --git a/ugene.spec b/ugene.spec index 692d23f..4beb108 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240206 -%global gitcommit 2f85b9143373e291ea19af34d15b98554ba3e76d +%global gitdate 20240213 +%global gitcommit 6e264b4a15ab13e1052f8328e5624b871e5d1f6d # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free e92e63d13cfdc37160f2b61f3028da2e85dce8aa +%global gitcommit_free 755d12ab5f3014d940d4e29c1cf6d6ce7ce13454 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240206 -%global tarballtime 1153 +%global tarballdate 20240213 +%global tarballtime 1625 %global use_release 0 %global use_gitbare 1 From 2186b2f694013b75ee0602921afffe71f81e7d67 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 25 Feb 2024 15:28:53 +0900 Subject: [PATCH 183/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 9eb4a84..1dd1dd0 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240213T1625.tar.gz) = 7ba61dde9a6959564e0da801bebfb07147fe9062633493df93cfe10d5fe98bc08ea0190411cdf552c5631d7916d79970cbc1ea325f505895a34adeb21633e812 +SHA512 (ugene-free-20240225T1437.tar.gz) = 81c4640a8ba0ebedcfcf14461a32f8ebcb0a130e6e6108ce3e509ffe48caa0ef39b6773c586fc554f8d9103f6b685cc27e601d984c23d13d3244f994c57c4416 diff --git a/ugene.spec b/ugene.spec index 4beb108..0ef5556 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240213 -%global gitcommit 6e264b4a15ab13e1052f8328e5624b871e5d1f6d +%global gitdate 20240225 +%global gitcommit 8a689b22611de2a18b762978c3f76328bc5f135b # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 755d12ab5f3014d940d4e29c1cf6d6ce7ce13454 +%global gitcommit_free b8ef5ddef24ded8a6f40e78c058970e6ac5e4cdf %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240213 -%global tarballtime 1625 +%global tarballdate 20240225 +%global tarballtime 1437 %global use_release 0 %global use_gitbare 1 From e84216a481caca0f49347ddce7235142990fb216 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 4 Mar 2024 22:35:00 +0900 Subject: [PATCH 184/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 1dd1dd0..53fbaf2 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240225T1437.tar.gz) = 81c4640a8ba0ebedcfcf14461a32f8ebcb0a130e6e6108ce3e509ffe48caa0ef39b6773c586fc554f8d9103f6b685cc27e601d984c23d13d3244f994c57c4416 +SHA512 (ugene-free-20240304T2143.tar.gz) = ff84b2d90bc326989ba5e114f56b61c48d840b18dd96693c9aa2376c2c1bc510b8fcf19f206fa5a9ce38e23ff560cd0e8600c1cb634ec99e989b6702b894a3ca diff --git a/ugene.spec b/ugene.spec index 0ef5556..4b49b38 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240225 -%global gitcommit 8a689b22611de2a18b762978c3f76328bc5f135b +%global gitdate 20240304 +%global gitcommit 82f11c4230fbdd9433eafa1a8127691f916b5c4a # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b8ef5ddef24ded8a6f40e78c058970e6ac5e4cdf +%global gitcommit_free 4173ae5f90b1ae917e108899a10a443071e9c836 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240225 -%global tarballtime 1437 +%global tarballdate 20240304 +%global tarballtime 2143 %global use_release 0 %global use_gitbare 1 From a0aab3a0f35bea138ffaab01ba95ce52e6859f0d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 10 Mar 2024 16:34:14 +0900 Subject: [PATCH 185/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 53fbaf2..d109ef7 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240304T2143.tar.gz) = ff84b2d90bc326989ba5e114f56b61c48d840b18dd96693c9aa2376c2c1bc510b8fcf19f206fa5a9ce38e23ff560cd0e8600c1cb634ec99e989b6702b894a3ca +SHA512 (ugene-free-20240310T1522.tar.gz) = 3c109f2c4f61fa4b15352e317c7a31f7fc02d6a197448e70dd7da7284c6a9e04b8e17e1d98c9353aa2912b3f65d015b85acec0b15735edcd666b3e792b5609dc diff --git a/ugene.spec b/ugene.spec index 4b49b38..869b973 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240304 -%global gitcommit 82f11c4230fbdd9433eafa1a8127691f916b5c4a +%global gitdate 20240309 +%global gitcommit e637ea7ac3553b7385ff2c5a9428afe074609146 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 4173ae5f90b1ae917e108899a10a443071e9c836 +%global gitcommit_free 44902ca6c638b2e24a24b307718b565fcb248979 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240304 -%global tarballtime 2143 +%global tarballdate 20240310 +%global tarballtime 1522 %global use_release 0 %global use_gitbare 1 From 9a2d46dc9c12ef26b4b4501e842c20efd5c316bb Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 12 Mar 2024 17:48:37 +0900 Subject: [PATCH 186/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index d109ef7..361199d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240310T1522.tar.gz) = 3c109f2c4f61fa4b15352e317c7a31f7fc02d6a197448e70dd7da7284c6a9e04b8e17e1d98c9353aa2912b3f65d015b85acec0b15735edcd666b3e792b5609dc +SHA512 (ugene-free-20240312T1249.tar.gz) = 04b9dbb061dea4088d3c81cd2fc9e56c15a3132f31e3aeef793354045770bd13dadc87adc08701be0421f0e09c26ff0e52a7fed71dcdfa42a5fb0a2b984b24ae diff --git a/ugene.spec b/ugene.spec index 869b973..3663ae2 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240309 -%global gitcommit e637ea7ac3553b7385ff2c5a9428afe074609146 +%global gitdate 20240311 +%global gitcommit 87d32f0eda28324c90001fc40b26edab2aa66e8d # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 44902ca6c638b2e24a24b307718b565fcb248979 +%global gitcommit_free d8d7ed47cdbcd7c09438872c1a393e8a0b1384db %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240310 -%global tarballtime 1522 +%global tarballdate 20240312 +%global tarballtime 1249 %global use_release 0 %global use_gitbare 1 From c2482b8599bd9ba33d93af93e9a9d4244f97ddb6 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 18 Mar 2024 16:22:04 +0900 Subject: [PATCH 187/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 361199d..d270998 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240312T1249.tar.gz) = 04b9dbb061dea4088d3c81cd2fc9e56c15a3132f31e3aeef793354045770bd13dadc87adc08701be0421f0e09c26ff0e52a7fed71dcdfa42a5fb0a2b984b24ae +SHA512 (ugene-free-20240318T1534.tar.gz) = 0ce863ca1e1bad6d194cbdc4b313197063116bc381976e73a24354e3e273c03ee4029fe675004a352bcf193ed41b2c68411d192993ea483b25d1c197daf14509 diff --git a/ugene.spec b/ugene.spec index 3663ae2..a743f0d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240311 -%global gitcommit 87d32f0eda28324c90001fc40b26edab2aa66e8d +%global gitdate 20240317 +%global gitcommit 4d46748b03e7cc138d833e2c0efe5f77e2e8053c # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free d8d7ed47cdbcd7c09438872c1a393e8a0b1384db +%global gitcommit_free e76eff5303ba3fa85739fd3bb6f761372b68d2b5 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240312 -%global tarballtime 1249 +%global tarballdate 20240318 +%global tarballtime 1534 %global use_release 0 %global use_gitbare 1 From b166a38c1d9faba164870b905f98c3be57c22271 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 23 Mar 2024 18:01:21 +0900 Subject: [PATCH 188/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index d270998..33196dd 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240318T1534.tar.gz) = 0ce863ca1e1bad6d194cbdc4b313197063116bc381976e73a24354e3e273c03ee4029fe675004a352bcf193ed41b2c68411d192993ea483b25d1c197daf14509 +SHA512 (ugene-free-20240323T1553.tar.gz) = 59beee14f8f2aa02b907886d09becbbd6b3dd5a048bec831b2d47af7ea8e36bac793d1e1e310ec9eedefd03e35777e77474d8d9815a435b7fdc85bdaaad411f4 diff --git a/ugene.spec b/ugene.spec index a743f0d..cbf2e8d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240317 -%global gitcommit 4d46748b03e7cc138d833e2c0efe5f77e2e8053c +%global gitdate 20240322 +%global gitcommit f6fa5acb06be58f1a3435f65425bb300b38bc606 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free e76eff5303ba3fa85739fd3bb6f761372b68d2b5 +%global gitcommit_free 75f645b5d3f755de2236f7df75c5da131fa6ef0f %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240318 -%global tarballtime 1534 +%global tarballdate 20240323 +%global tarballtime 1553 %global use_release 0 %global use_gitbare 1 From 21c95b4d023bc9f5dc2d87ea38b5ca793bff47b3 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 9 Apr 2024 15:57:56 +0900 Subject: [PATCH 189/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 33196dd..ca76500 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240323T1553.tar.gz) = 59beee14f8f2aa02b907886d09becbbd6b3dd5a048bec831b2d47af7ea8e36bac793d1e1e310ec9eedefd03e35777e77474d8d9815a435b7fdc85bdaaad411f4 +SHA512 (ugene-free-20240409T1411.tar.gz) = d1bc83d5c1d2b3d720380ff098a101830afd4c14d28844477ec72b8c323b39df3c2e0d7c77fc3e7d1a3a8abfb6ed277c72869aca513ead3e1b88cf8d08530a21 diff --git a/ugene.spec b/ugene.spec index cbf2e8d..848e0db 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240322 -%global gitcommit f6fa5acb06be58f1a3435f65425bb300b38bc606 +%global gitdate 20240408 +%global gitcommit da37cf518b5846da57b41a67977dac5b36671f06 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 75f645b5d3f755de2236f7df75c5da131fa6ef0f +%global gitcommit_free 54752e747f4f26bcd840c016c2bb0c7fe240152e %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240323 -%global tarballtime 1553 +%global tarballdate 20240409 +%global tarballtime 1411 %global use_release 0 %global use_gitbare 1 From e237be39018816ae6a034e3687ee92d182e18c45 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 15 Apr 2024 08:22:58 +0900 Subject: [PATCH 190/260] update to 50.0 --- sources | 2 +- ugene.spec | 11 +++++++---- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/sources b/sources index ca76500..89974d1 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240409T1411.tar.gz) = d1bc83d5c1d2b3d720380ff098a101830afd4c14d28844477ec72b8c323b39df3c2e0d7c77fc3e7d1a3a8abfb6ed277c72869aca513ead3e1b88cf8d08530a21 +SHA512 (ugene-free-50.0.tar.gz) = 8cb3ab28423cdbde8ff26b66ec3f2b9aba0384f7b417cccbc6ef9b72d812fff659730aa96bf19b636ba2b0c0a1b3d0b7c0382e8834cccda56edf14195b563677 diff --git a/ugene.spec b/ugene.spec index 848e0db..9973f94 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20240409 %global tarballtime 1411 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainver 49.1 +%global mainver 50.0 %undefine prever %if 0%{?use_release} >= 1 @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 3%{?dist} +Release: 1%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -252,6 +252,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sun Apr 14 2024 Mamoru TASAKA - 50.0-1 +- 50.0 + * Sat Jan 27 2024 Fedora Release Engineering - 49.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild From 2454c7c86995416018c6ea591467b08d48972f3e Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 5 May 2024 17:41:23 +0900 Subject: [PATCH 191/260] update to the latest git --- sources | 2 +- ugene.spec | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/sources b/sources index 89974d1..b9e5efe 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-50.0.tar.gz) = 8cb3ab28423cdbde8ff26b66ec3f2b9aba0384f7b417cccbc6ef9b72d812fff659730aa96bf19b636ba2b0c0a1b3d0b7c0382e8834cccda56edf14195b563677 +SHA512 (ugene-free-20240505T1704.tar.gz) = a5b34012544ef36b8252d12ea195ba87b49cfa6bf744c91869b77aef4bd0877f7bf6adb82950912bd204a84ce8711f7609c55ff175ddb2640092d0708c74b629 diff --git a/ugene.spec b/ugene.spec index 9973f94..62717a5 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240408 -%global gitcommit da37cf518b5846da57b41a67977dac5b36671f06 +%global gitdate 20240426 +%global gitcommit d51cdfabc89e1f89d66df2ef73fc9014ffa3bd21 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 54752e747f4f26bcd840c016c2bb0c7fe240152e +%global gitcommit_free f256852aceb40a07f4700aab25865876f5bededb %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240409 -%global tarballtime 1411 +%global tarballdate 20240505 +%global tarballtime 1704 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From 05d1c9fb69c6d0689376d4e44e4a83de216e42a2 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 24 May 2024 11:07:18 +0900 Subject: [PATCH 192/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index b9e5efe..677f2cb 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240505T1704.tar.gz) = a5b34012544ef36b8252d12ea195ba87b49cfa6bf744c91869b77aef4bd0877f7bf6adb82950912bd204a84ce8711f7609c55ff175ddb2640092d0708c74b629 +SHA512 (ugene-free-20240524T1034.tar.gz) = 6d85078af85ee003671b17f553d10703116801c5a529e27dedf6cbe106aa55a85c96d465c6645bced4b0e193c9b571014b06d66c5c1913aceac0a99dacec4831 diff --git a/ugene.spec b/ugene.spec index 62717a5..bfd9c47 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240426 -%global gitcommit d51cdfabc89e1f89d66df2ef73fc9014ffa3bd21 +%global gitdate 20240523 +%global gitcommit fa3ad176121425f420580cde302160c2af233dfb # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free f256852aceb40a07f4700aab25865876f5bededb +%global gitcommit_free f4d5595d7527c3aad9ffec03a1f7e126034e40b3 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240505 -%global tarballtime 1704 +%global tarballdate 20240524 +%global tarballtime 1034 %global use_release 0 %global use_gitbare 1 From 497fc4e9f481cc6fb7d18e3a4e8a4e83bb9358c9 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 31 May 2024 14:41:34 +0900 Subject: [PATCH 193/260] update to the latest git --- sources | 2 +- ugene-40.1-qbswap-bigendian-workaround.patch | 6 +++--- ugene.spec | 10 +++++----- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/sources b/sources index 677f2cb..2eb25fd 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240524T1034.tar.gz) = 6d85078af85ee003671b17f553d10703116801c5a529e27dedf6cbe106aa55a85c96d465c6645bced4b0e193c9b571014b06d66c5c1913aceac0a99dacec4831 +SHA512 (ugene-free-20240531T1347.tar.gz) = 8d56fcc796f7aa8f4057475dc07a7f44c97658568a1af11b5da1425d1e1668f8acc1e20a11566482aee5b5c6905ca94f63f80b8e1a0dbc42eeb7d59ce2daa431 diff --git a/ugene-40.1-qbswap-bigendian-workaround.patch b/ugene-40.1-qbswap-bigendian-workaround.patch index 813d7a8..baa1c50 100644 --- a/ugene-40.1-qbswap-bigendian-workaround.patch +++ b/ugene-40.1-qbswap-bigendian-workaround.patch @@ -40,6 +40,6 @@ +#endif +QT_END_NAMESPACE + - namespace U2 { - - static quint8 cigarOp2samtools(U2CigarOp op, U2OpStatus& os) { + extern "C" { + #include "samtools_core/htslib/cram/cram_samtools.h" + } diff --git a/ugene.spec b/ugene.spec index bfd9c47..5f3d50c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240523 -%global gitcommit fa3ad176121425f420580cde302160c2af233dfb +%global gitdate 20240530 +%global gitcommit f40147dc8c0a23bbdd5c07ecdc949f7cb5be933c # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free f4d5595d7527c3aad9ffec03a1f7e126034e40b3 +%global gitcommit_free 3b57f2d3edeb4ca854462bbf2a2ef580f8e8a000 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240524 -%global tarballtime 1034 +%global tarballdate 20240531 +%global tarballtime 1347 %global use_release 0 %global use_gitbare 1 From ce28635cefa44b79e8f2f6bc2365662c5786aee3 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 31 May 2024 17:32:38 +0900 Subject: [PATCH 194/260] some neon impl function not available yet --- ugene-50.x-aarch64-neon-impl-not-yet.patch | 26 ++++++++++++++++++++++ ugene.spec | 5 ++++- 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 ugene-50.x-aarch64-neon-impl-not-yet.patch diff --git a/ugene-50.x-aarch64-neon-impl-not-yet.patch b/ugene-50.x-aarch64-neon-impl-not-yet.patch new file mode 100644 index 0000000..d21b04b --- /dev/null +++ b/ugene-50.x-aarch64-neon-impl-not-yet.patch @@ -0,0 +1,26 @@ +diff --git a/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c b/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c +index be907d85b..820d43cf0 100644 +--- a/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c ++++ b/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c +@@ -1068,8 +1068,8 @@ unsigned char *(*rans_enc_func(int do_simd, int order)) + if (do_simd) { + if ((rans_cpu & RANS_CPU_ENC_NEON) && have_neon()) + return order & 1 +- ? rans_compress_O1_32x16_neon +- : rans_compress_O0_32x16_neon; ++ ? rans_compress_O1_32x16 ++ : rans_compress_O0_32x16; + else + return order & 1 + ? rans_compress_O1_32x16 +@@ -1091,8 +1091,8 @@ unsigned char *(*rans_dec_func(int do_simd, int order)) + if (do_simd) { + if ((rans_cpu & RANS_CPU_DEC_NEON) && have_neon()) + return order & 1 +- ? rans_uncompress_O1_32x16_neon +- : rans_uncompress_O0_32x16_neon; ++ ? rans_uncompress_O1_32x16 ++ : rans_uncompress_O0_32x16; + else + return order & 1 + ? rans_uncompress_O1_32x16 diff --git a/ugene.spec b/ugene.spec index 5f3d50c..b24c195 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -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 @@ -79,6 +79,7 @@ Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch Patch106: ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch Patch108: ugene-47.x-has-sse-i686.patch +Patch109: ugene-50.x-aarch64-neon-impl-not-yet.patch BuildRequires: make BuildRequires: gcc-c++ @@ -148,6 +149,8 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a %patch -P108 -p1 -b .sse_i686 -Z %GIT commit -m "ugene_globals.pri: tell sse2 available also on i686" -a +%patch -P109 -p1 -b .neon -Z + %GIT commit -m "neon impl not yet available" -a sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d' From f8eefc8cc36e5c9e92ecadbd7181542bb4c9e16d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 4 Jun 2024 16:23:17 +0900 Subject: [PATCH 195/260] update to the latest git --- sources | 2 +- ugene.spec | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/sources b/sources index 2eb25fd..cb4c53d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240531T1347.tar.gz) = 8d56fcc796f7aa8f4057475dc07a7f44c97658568a1af11b5da1425d1e1668f8acc1e20a11566482aee5b5c6905ca94f63f80b8e1a0dbc42eeb7d59ce2daa431 +SHA512 (ugene-free-20240604T1511.tar.gz) = de3cfa86c203b961be9385ce9b4e6ec7e93a3107d3e4125fa666d0cbad8b934a471c5d056623d3bf349818be16db2adc52c0805f68fb5f303ce137e7ea3b6b5c diff --git a/ugene.spec b/ugene.spec index b24c195..7e4a0e9 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240530 -%global gitcommit f40147dc8c0a23bbdd5c07ecdc949f7cb5be933c +%global gitdate 20240603 +%global gitcommit 8eaad78c5b05c295eb006cda8633f5f93dd22560 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 3b57f2d3edeb4ca854462bbf2a2ef580f8e8a000 +%global gitcommit_free 5df21a6f5bf35a15ee396940f741900614229678 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240531 -%global tarballtime 1347 +%global tarballdate 20240604 +%global tarballtime 1511 %global use_release 0 %global use_gitbare 1 @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 2%{?dist} +Release: 1%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 From 5bd0998da09a0df101b4b92374fde42e6451a4fe Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 7 Jun 2024 14:58:38 +0900 Subject: [PATCH 196/260] update to the latest git --- sources | 2 +- ugene.spec | 12 +++++++----- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/sources b/sources index cb4c53d..30b887b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240604T1511.tar.gz) = de3cfa86c203b961be9385ce9b4e6ec7e93a3107d3e4125fa666d0cbad8b934a471c5d056623d3bf349818be16db2adc52c0805f68fb5f303ce137e7ea3b6b5c +SHA512 (ugene-free-20240607T1352.tar.gz) = de4cef5bcd207fb002eea9bdcc2dcf215eff24bd545189b2abb863c24fa3ca4c2a70897cd2914e240f6bb8ebe2d70b131bb36880b8930f9d13d6ba9779b96cde diff --git a/ugene.spec b/ugene.spec index 7e4a0e9..32dfd6b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240603 -%global gitcommit 8eaad78c5b05c295eb006cda8633f5f93dd22560 +%global gitdate 20240605 +%global gitcommit 4881a4cd478cc6dd1593e43d7bb1a58e6fc484e3 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 5df21a6f5bf35a15ee396940f741900614229678 +%global gitcommit_free fa97d5df3549c6074254a4bbe0599fa335a6955e %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240604 -%global tarballtime 1511 +%global tarballdate 20240607 +%global tarballtime 1352 %global use_release 0 %global use_gitbare 1 @@ -149,8 +149,10 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a %patch -P108 -p1 -b .sse_i686 -Z %GIT commit -m "ugene_globals.pri: tell sse2 available also on i686" -a +%if 1 %patch -P109 -p1 -b .neon -Z %GIT commit -m "neon impl not yet available" -a +%endif sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d' From b0f232c01d652da77900e2f788a1556d22f78b53 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 10 Jun 2024 16:00:49 +0900 Subject: [PATCH 197/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 30b887b..7a48e3b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240607T1352.tar.gz) = de4cef5bcd207fb002eea9bdcc2dcf215eff24bd545189b2abb863c24fa3ca4c2a70897cd2914e240f6bb8ebe2d70b131bb36880b8930f9d13d6ba9779b96cde +SHA512 (ugene-free-20240610T1517.tar.gz) = a05a3170b762d7433983193517a3d30e9c1209f9e3cf244d14acc98c144b6690a077bd18cd0157d96eb88465619fa312bf0b82ea9a706bc09b1ffb9df99d7f1c diff --git a/ugene.spec b/ugene.spec index 32dfd6b..6237cfe 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240605 -%global gitcommit 4881a4cd478cc6dd1593e43d7bb1a58e6fc484e3 +%global gitdate 20240607 +%global gitcommit eeff18c895fdac40ff2645e56c7944889033cf60 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free fa97d5df3549c6074254a4bbe0599fa335a6955e +%global gitcommit_free 88af66bb877dfc13c673b15be6239e365497b24c %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240607 -%global tarballtime 1352 +%global tarballdate 20240610 +%global tarballtime 1517 %global use_release 0 %global use_gitbare 1 From 82f85bbc215a6a21a990ba004011c6e3f9dfdaa0 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 13 Jun 2024 13:56:13 +0900 Subject: [PATCH 198/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 7a48e3b..0742b61 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240610T1517.tar.gz) = a05a3170b762d7433983193517a3d30e9c1209f9e3cf244d14acc98c144b6690a077bd18cd0157d96eb88465619fa312bf0b82ea9a706bc09b1ffb9df99d7f1c +SHA512 (ugene-free-20240613T1218.tar.gz) = 95431c59d6abf96f66d67b4c0ca2b4484886891db9406cf086c20b225ef9442e26cdc461b42a7417be0e5154ec27f4ae57e832d7fd3a4029c15c3631b5e50de2 diff --git a/ugene.spec b/ugene.spec index 6237cfe..8c28fee 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240607 -%global gitcommit eeff18c895fdac40ff2645e56c7944889033cf60 +%global gitdate 20240610 +%global gitcommit aa06452ba49a6d5cc8e528f2083dfd6be10cf097 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 88af66bb877dfc13c673b15be6239e365497b24c +%global gitcommit_free a6262504c64791665fb34d5cd1b3a3ae8059fa94 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240610 -%global tarballtime 1517 +%global tarballdate 20240613 +%global tarballtime 1218 %global use_release 0 %global use_gitbare 1 From 3aa129ea34f8a27717eb0013642814faab5e53ef Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 17 Jun 2024 18:31:15 +0900 Subject: [PATCH 199/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0742b61..3b4fd22 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240613T1218.tar.gz) = 95431c59d6abf96f66d67b4c0ca2b4484886891db9406cf086c20b225ef9442e26cdc461b42a7417be0e5154ec27f4ae57e832d7fd3a4029c15c3631b5e50de2 +SHA512 (ugene-free-20240617T1740.tar.gz) = db51a7f7b717b04063f83cd430f4dc7ff303d88d18c6df79fb04b6325c8bf9d68caf29350fb60e7f32bb43829ded84f4442d5a4277db18d02a46070c5968eda8 diff --git a/ugene.spec b/ugene.spec index 8c28fee..109c24d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240610 -%global gitcommit aa06452ba49a6d5cc8e528f2083dfd6be10cf097 +%global gitdate 20240613 +%global gitcommit 2580e2fca6f5be28cb899082724d1fb4ad25c124 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free a6262504c64791665fb34d5cd1b3a3ae8059fa94 +%global gitcommit_free 220f9dcbe8690b71aa0df9efef0967893337b1ca %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240613 -%global tarballtime 1218 +%global tarballdate 20240617 +%global tarballtime 1740 %global use_release 0 %global use_gitbare 1 From 7bae355a27490ea106265e7e84ee209ee73f62c1 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 24 Jun 2024 16:16:25 +0900 Subject: [PATCH 200/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0742b61..19e6a85 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240613T1218.tar.gz) = 95431c59d6abf96f66d67b4c0ca2b4484886891db9406cf086c20b225ef9442e26cdc461b42a7417be0e5154ec27f4ae57e832d7fd3a4029c15c3631b5e50de2 +SHA512 (ugene-free-20240623T2223.tar.gz) = cf28370e6d83edf2aff2ab783257c224b5038438e41f01dd78ac998f51d85bfb6373b2069de524a42d6f052f2fb1b89afb6fcbaee3831d08639bb74fa15db6ff diff --git a/ugene.spec b/ugene.spec index 8c28fee..d4b2496 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240610 -%global gitcommit aa06452ba49a6d5cc8e528f2083dfd6be10cf097 +%global gitdate 20240620 +%global gitcommit 00898d6d5d7bea7baa513c0cf1d67a585241bcd4 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free a6262504c64791665fb34d5cd1b3a3ae8059fa94 +%global gitcommit_free b5fbee476045b8116a8c903144da66ad3c45ac4c %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240613 -%global tarballtime 1218 +%global tarballdate 20240623 +%global tarballtime 2223 %global use_release 0 %global use_gitbare 1 From 1fc6d3eb7142784e07afa82eb6633c337b824f9d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 26 Jun 2024 17:38:30 +0900 Subject: [PATCH 201/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 19e6a85..0759375 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240623T2223.tar.gz) = cf28370e6d83edf2aff2ab783257c224b5038438e41f01dd78ac998f51d85bfb6373b2069de524a42d6f052f2fb1b89afb6fcbaee3831d08639bb74fa15db6ff +SHA512 (ugene-free-20240626T1650.tar.gz) = afbc564ef378279796398d9fd0e8052c802b2d604bb758e72954e87fdfa114067a4870b4d2751b31468bcb1eed89be43e1d8083ef1249806302f549faf04b1d0 diff --git a/ugene.spec b/ugene.spec index d4b2496..b89e67e 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240620 -%global gitcommit 00898d6d5d7bea7baa513c0cf1d67a585241bcd4 +%global gitdate 20240625 +%global gitcommit 704de1551d710044a21e84bee54d4441f85d14a5 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b5fbee476045b8116a8c903144da66ad3c45ac4c +%global gitcommit_free 580eeba1cd11a2fae1caf96148d7be2107a5598d %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240623 -%global tarballtime 2223 +%global tarballdate 20240626 +%global tarballtime 1650 %global use_release 0 %global use_gitbare 1 From 2ac2787f6d518bc86c1abff1e9904039d24f5595 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 2 Jul 2024 16:38:42 +0900 Subject: [PATCH 202/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0759375..9390b7b 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240626T1650.tar.gz) = afbc564ef378279796398d9fd0e8052c802b2d604bb758e72954e87fdfa114067a4870b4d2751b31468bcb1eed89be43e1d8083ef1249806302f549faf04b1d0 +SHA512 (ugene-free-20240702T1557.tar.gz) = 03c1e6322e70f9e110993a5ff0562a069e92fcf05fe7769fa212d6be621aca99522ae0aed96848ea90e6f9d90419d22fe7b18f6f707c0d998fa934a286dcb505 diff --git a/ugene.spec b/ugene.spec index b89e67e..5cbb9d3 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240625 -%global gitcommit 704de1551d710044a21e84bee54d4441f85d14a5 +%global gitdate 20240701 +%global gitcommit b160206e0f7565dc79c0818220f6220356628841 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 580eeba1cd11a2fae1caf96148d7be2107a5598d +%global gitcommit_free 354608cb759ef3965638e49ea29b4e5d52e24452 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240626 -%global tarballtime 1650 +%global tarballdate 20240702 +%global tarballtime 1557 %global use_release 0 %global use_gitbare 1 From 873e7f79516b7780bb99cf17aa80819759448e2f Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 5 Jul 2024 11:34:40 +0900 Subject: [PATCH 203/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 9390b7b..7e042e0 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240702T1557.tar.gz) = 03c1e6322e70f9e110993a5ff0562a069e92fcf05fe7769fa212d6be621aca99522ae0aed96848ea90e6f9d90419d22fe7b18f6f707c0d998fa934a286dcb505 +SHA512 (ugene-free-20240705T1048.tar.gz) = eb8ffac0b4634fcea1feb9639cee22ca28be9d916071cd4f15451df7c739a0c35c35f0e74a9dcbbae699baef2a8509b448f3786de149b794b600fa0612c43a2a diff --git a/ugene.spec b/ugene.spec index 5cbb9d3..bec0d3c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240701 -%global gitcommit b160206e0f7565dc79c0818220f6220356628841 +%global gitdate 20240704 +%global gitcommit e4a7e77258f166b4fcb7a657daff7602482aed00 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 354608cb759ef3965638e49ea29b4e5d52e24452 +%global gitcommit_free 8890c28eb0aa92c3250c2904cf8dfb61d18f2a20 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240702 -%global tarballtime 1557 +%global tarballdate 20240705 +%global tarballtime 1048 %global use_release 0 %global use_gitbare 1 From 705db5a996f43c880f8528b6bf4245a237ecf9d5 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 10 Jul 2024 17:14:41 +0900 Subject: [PATCH 204/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 7e042e0..5a89b72 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240705T1048.tar.gz) = eb8ffac0b4634fcea1feb9639cee22ca28be9d916071cd4f15451df7c739a0c35c35f0e74a9dcbbae699baef2a8509b448f3786de149b794b600fa0612c43a2a +SHA512 (ugene-free-20240710T1629.tar.gz) = 12767fee2631a4af47a7a3918019704c7c9741b44d04239ac89f5dd1e73ad788b523b8a1c96626e2b6a68eaa1d48afc8cd9a4520da8de250ad48f3809581bc42 diff --git a/ugene.spec b/ugene.spec index bec0d3c..24168c5 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240704 -%global gitcommit e4a7e77258f166b4fcb7a657daff7602482aed00 +%global gitdate 20240706 +%global gitcommit 7ba6e02643489776969e38cdac9d8f5cd47db0e3 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 8890c28eb0aa92c3250c2904cf8dfb61d18f2a20 +%global gitcommit_free 41b5f67d399ad5c4d1ba3071d9781ae2ea3df58e %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240705 -%global tarballtime 1048 +%global tarballdate 20240710 +%global tarballtime 1629 %global use_release 0 %global use_gitbare 1 From efc3eb70a26ee0532493eb90023ffb696da56511 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 20 Jul 2024 08:10:48 +0000 Subject: [PATCH 205/260] Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 9973f94..1d5d9c1 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -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 @@ -252,6 +252,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sat Jul 20 2024 Fedora Release Engineering - 50.0-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild + * Sun Apr 14 2024 Mamoru TASAKA - 50.0-1 - 50.0 From 685859022c4d7edeeea84d44280e758c57517aff Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 21 Jul 2024 17:06:53 +0900 Subject: [PATCH 206/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 5a89b72..d2b8153 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240710T1629.tar.gz) = 12767fee2631a4af47a7a3918019704c7c9741b44d04239ac89f5dd1e73ad788b523b8a1c96626e2b6a68eaa1d48afc8cd9a4520da8de250ad48f3809581bc42 +SHA512 (ugene-free-20240721T1636.tar.gz) = cbf6830d7b0d34545afd68c3db4a814a7b2cc984dd7161d010f9b330212dd42a1b829614970cff1464e23a2bef2fa1c8d317d43c7d9ead69538afac9cac4d9dc diff --git a/ugene.spec b/ugene.spec index 24168c5..742bd2d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240706 -%global gitcommit 7ba6e02643489776969e38cdac9d8f5cd47db0e3 +%global gitdate 20240718 +%global gitcommit e911f113829727d9c62b1e43f2feea6499ff344f # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 41b5f67d399ad5c4d1ba3071d9781ae2ea3df58e +%global gitcommit_free a5e7f914a3d7d3b7a13f27d1b884114d8944710d %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240710 -%global tarballtime 1629 +%global tarballdate 20240721 +%global tarballtime 1636 %global use_release 0 %global use_gitbare 1 From 07c256ed4f3d21431e262b5a5ad7bc7d914b9f4c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 24 Jul 2024 17:08:51 +0900 Subject: [PATCH 207/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index d2b8153..c61c7c6 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240721T1636.tar.gz) = cbf6830d7b0d34545afd68c3db4a814a7b2cc984dd7161d010f9b330212dd42a1b829614970cff1464e23a2bef2fa1c8d317d43c7d9ead69538afac9cac4d9dc +SHA512 (ugene-free-20240724T1627.tar.gz) = e4c87ca2c3707d23efba364ab7d56291e7a370c71068a9a99c643cf51dc7307e5c0006f9a885f4d1e6e2ab22d4dac7d69eb93939210dbcf8561779624227e481 diff --git a/ugene.spec b/ugene.spec index 742bd2d..fb9028c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240718 -%global gitcommit e911f113829727d9c62b1e43f2feea6499ff344f +%global gitdate 20240722 +%global gitcommit 4efbef1200549751aec16f14430878b8f06b053e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free a5e7f914a3d7d3b7a13f27d1b884114d8944710d +%global gitcommit_free e0e6570348212b8d18d7516e89853a20c37fbd7d %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240721 -%global tarballtime 1636 +%global tarballdate 20240724 +%global tarballtime 1627 %global use_release 0 %global use_gitbare 1 From b930ec0f57aed837f1f24e2bd2cb7730bc4952bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miroslav=20Such=C3=BD?= Date: Wed, 7 Aug 2024 10:18:52 +0200 Subject: [PATCH 208/260] convert license to SPDX This is part of https://fedoraproject.org/wiki/Changes/SPDX_Licenses_Phase_4 --- ugene.spec | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/ugene.spec b/ugene.spec index 1d5d9c1..413a71b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,12 +50,13 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -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 -License: GPLv2+ and GPLv2 +# Automatically converted from old format: GPLv2+ and GPLv2 - review is highly recommended. +License: GPL-2.0-or-later AND GPL-2.0-only URL: http://ugene.net %if 0%{?use_release} >= 1 #Source0: https://github.com/ugeneunipro/ugene/archive/%{mainver}.tar.gz/#/%{name}-%{mainver}.tar.gz @@ -252,6 +253,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Wed Aug 7 2024 Miroslav Suchý - 50.0-3 +- convert license to SPDX + * Sat Jul 20 2024 Fedora Release Engineering - 50.0-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild From a6944edee3ddf427ed046cf25841db8a36e4f82d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 13 Aug 2024 15:30:59 +0900 Subject: [PATCH 209/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index c61c7c6..60e1550 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240724T1627.tar.gz) = e4c87ca2c3707d23efba364ab7d56291e7a370c71068a9a99c643cf51dc7307e5c0006f9a885f4d1e6e2ab22d4dac7d69eb93939210dbcf8561779624227e481 +SHA512 (ugene-free-20240813T1459.tar.gz) = e756b360a63cfb859e6afc782e1906353446cb3ccfec9af04d66b4585569d325692bf733c3c3dd31ad1fac86934e3b00bf1ac230ab0a23e905d322453e3546e9 diff --git a/ugene.spec b/ugene.spec index fb9028c..1ace19c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240722 -%global gitcommit 4efbef1200549751aec16f14430878b8f06b053e +%global gitdate 20240813 +%global gitcommit 4f3f00b0bea1bdd99c9dedcc2931137cf3ce59ba # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free e0e6570348212b8d18d7516e89853a20c37fbd7d +%global gitcommit_free 157d5244a59319965f23bec9338fabb81e3469d8 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240724 -%global tarballtime 1627 +%global tarballdate 20240813 +%global tarballtime 1459 %global use_release 0 %global use_gitbare 1 From f84995cfab5f20a7b138d9e06aff9e07e215ca9b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 13 Aug 2024 15:54:42 +0900 Subject: [PATCH 210/260] update BR --- ugene.spec | 2 ++ 1 file changed, 2 insertions(+) diff --git a/ugene.spec b/ugene.spec index 1ace19c..645b5d2 100644 --- a/ugene.spec +++ b/ugene.spec @@ -92,12 +92,14 @@ BuildRequires: %{_bindir}/git BuildRequires: cmake(Qt5Core) BuildRequires: cmake(Qt5Gui) BuildRequires: cmake(Qt5Network) +BuildRequies: cmake(Qt5NetworkAuth) BuildRequires: cmake(Qt5PrintSupport) BuildRequires: cmake(Qt5Script) BuildRequires: cmake(Qt5ScriptTools) BuildRequires: cmake(Qt5Sql) BuildRequires: cmake(Qt5Svg) BuildRequires: cmake(Qt5Test) +BuildRequires: cmake(Qt5WebSockets) BuildRequires: cmake(Qt5Widgets) BuildRequires: cmake(Qt5Xml) From 55838d513e60ed288f492714e72173c5ff150e8f Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 13 Aug 2024 15:57:20 +0900 Subject: [PATCH 211/260] fix typo --- ugene.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 645b5d2..0a5bdde 100644 --- a/ugene.spec +++ b/ugene.spec @@ -92,7 +92,7 @@ BuildRequires: %{_bindir}/git BuildRequires: cmake(Qt5Core) BuildRequires: cmake(Qt5Gui) BuildRequires: cmake(Qt5Network) -BuildRequies: cmake(Qt5NetworkAuth) +BuildRequires: cmake(Qt5NetworkAuth) BuildRequires: cmake(Qt5PrintSupport) BuildRequires: cmake(Qt5Script) BuildRequires: cmake(Qt5ScriptTools) From 714a7a9e352087b8fe04ac0f33dbbf876023e49d Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 16 Aug 2024 10:42:50 +0900 Subject: [PATCH 212/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 60e1550..836f257 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240813T1459.tar.gz) = e756b360a63cfb859e6afc782e1906353446cb3ccfec9af04d66b4585569d325692bf733c3c3dd31ad1fac86934e3b00bf1ac230ab0a23e905d322453e3546e9 +SHA512 (ugene-free-20240816T1013.tar.gz) = d381d8f62427d35613738ae38f2ac6a560270d908fab42eebb2dd635d77a5a9b6311fa6ddf64c49126680cbe3816d96ad27c09ddddb1839773dae9cadce6d7a0 diff --git a/ugene.spec b/ugene.spec index 0a5bdde..1a9f49c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240813 -%global gitcommit 4f3f00b0bea1bdd99c9dedcc2931137cf3ce59ba +%global gitdate 20240814 +%global gitcommit 0da602221be9160f84faf53c99f35bb26a11d8c5 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 157d5244a59319965f23bec9338fabb81e3469d8 +%global gitcommit_free f40f2d83d33c5564eda2a6e73b295b5f62d00cdb %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240813 -%global tarballtime 1459 +%global tarballdate 20240816 +%global tarballtime 1013 %global use_release 0 %global use_gitbare 1 From 0629626dd169064a8d4912b3a3038cbd262b3737 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 2 Sep 2024 15:58:16 +0900 Subject: [PATCH 213/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 836f257..8916d9f 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240816T1013.tar.gz) = d381d8f62427d35613738ae38f2ac6a560270d908fab42eebb2dd635d77a5a9b6311fa6ddf64c49126680cbe3816d96ad27c09ddddb1839773dae9cadce6d7a0 +SHA512 (ugene-free-20240902T1513.tar.gz) = b8caa1c1ccf670724041c9d6fc29984b0fadab005e36969a81edee5af0d88bf119838aeb3b2c5da70d4079a639d919016f15a1f18d8d2907de19382c0addb7c1 diff --git a/ugene.spec b/ugene.spec index 1a9f49c..db474e8 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240814 -%global gitcommit 0da602221be9160f84faf53c99f35bb26a11d8c5 +%global gitdate 20240830 +%global gitcommit cff1c2a52a64c901d70e089e83d90eac38361ca5 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free f40f2d83d33c5564eda2a6e73b295b5f62d00cdb +%global gitcommit_free ccd03e86863580e7e6eea3a1d30aebd4d401233b %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240816 -%global tarballtime 1013 +%global tarballdate 20240902 +%global tarballtime 1513 %global use_release 0 %global use_gitbare 1 From 21d3778fa103eb785656f1ba26f6805099f6ed41 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 26 Sep 2024 14:45:15 +0900 Subject: [PATCH 214/260] Update to 51.0 --- sources | 2 +- ugene.spec | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/sources b/sources index 8916d9f..a32c736 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20240902T1513.tar.gz) = b8caa1c1ccf670724041c9d6fc29984b0fadab005e36969a81edee5af0d88bf119838aeb3b2c5da70d4079a639d919016f15a1f18d8d2907de19382c0addb7c1 +SHA512 (ugene-free-51.0.tar.gz) = 7c85c618baf1fbf5c60f566046bc19c48cf3e6690c562a557e3d39a9db0cae7bd890dc823604d1f2208b904615d4ed27d9c9e448720e646c89f6345f10114f6f diff --git a/ugene.spec b/ugene.spec index db474e8..4abaa1c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20240902 %global tarballtime 1513 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainver 50.0 +%global mainver 51.0 %undefine prever %if 0%{?use_release} >= 1 From 52fd4077b5a4b27a046e07b1359b30c2e8c01716 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 26 Sep 2024 14:47:18 +0900 Subject: [PATCH 215/260] Update changelog, release --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index 712170a..6ec016f 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 3%{?dist} +Release: 1%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -260,6 +260,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Thu Sep 26 2024 Mamoru TASAKA - 51.0-1 +- 51.0 + * Wed Aug 7 2024 Miroslav Suchý - 50.0-3 - convert license to SPDX From 2e2377e7c734bdf3cd9b35bca7cfb75ecbba4167 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 8 Oct 2024 15:08:32 +0900 Subject: [PATCH 216/260] update to the latest git --- sources | 2 +- ugene.spec | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/sources b/sources index a32c736..0d61ee9 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-51.0.tar.gz) = 7c85c618baf1fbf5c60f566046bc19c48cf3e6690c562a557e3d39a9db0cae7bd890dc823604d1f2208b904615d4ed27d9c9e448720e646c89f6345f10114f6f +SHA512 (ugene-free-20241008T1432.tar.gz) = 3618db17f0dc0f677d8dd4b1c468a89d932af82884ef7bddebf624e7adafb886aa2aa1f7ea8658b333d90b1577bab67925e2adb9f4ae67eef86be58da2f61d10 diff --git a/ugene.spec b/ugene.spec index 6ec016f..ee50ea1 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20240830 -%global gitcommit cff1c2a52a64c901d70e089e83d90eac38361ca5 +%global gitdate 20241008 +%global gitcommit e4e0e32c31aa7d33e66bb320f861933c52575ce6 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free ccd03e86863580e7e6eea3a1d30aebd4d401233b +%global gitcommit_free 2d783e5f608e18556195838fac6ef7ff24a7b025 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20240902 -%global tarballtime 1513 +%global tarballdate 20241008 +%global tarballtime 1432 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From 73de175f2e895b83733e6bd2defc464a6e2506d8 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 24 Oct 2024 21:41:10 +0900 Subject: [PATCH 217/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0d61ee9..47706f6 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20241008T1432.tar.gz) = 3618db17f0dc0f677d8dd4b1c468a89d932af82884ef7bddebf624e7adafb886aa2aa1f7ea8658b333d90b1577bab67925e2adb9f4ae67eef86be58da2f61d10 +SHA512 (ugene-free-20241024T1541.tar.gz) = fc74cac6de77b1cd8e3b5b1ff6d718f47843d92382dc1bbb5a285ac70f949549886041af3111eb7ff155f411fc7cb2142580e226e071071ae3d1fba6b4697468 diff --git a/ugene.spec b/ugene.spec index ee50ea1..74280ed 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20241008 -%global gitcommit e4e0e32c31aa7d33e66bb320f861933c52575ce6 +%global gitdate 20241021 +%global gitcommit 858bd7b48d8e92ddb8d0183e5888069740375d9b # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 2d783e5f608e18556195838fac6ef7ff24a7b025 +%global gitcommit_free dd7696949ebbe7d26e431672c7a286e7d10fd824 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20241008 -%global tarballtime 1432 +%global tarballdate 20241024 +%global tarballtime 1541 %global use_release 0 %global use_gitbare 1 From aa2239ac1bd7367d290ee576afd7821cf714683c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 10 Nov 2024 16:48:30 +0900 Subject: [PATCH 218/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 47706f6..6aeb11c 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20241024T1541.tar.gz) = fc74cac6de77b1cd8e3b5b1ff6d718f47843d92382dc1bbb5a285ac70f949549886041af3111eb7ff155f411fc7cb2142580e226e071071ae3d1fba6b4697468 +SHA512 (ugene-free-20241110T1550.tar.gz) = 1b78028905c2546c0872ef23954b13b81a5f731515374ce8012ba30a35a0d46e45aae456ec86287249dab5c3165fb941c2e88597cc2187b75a4354eab75f339b diff --git a/ugene.spec b/ugene.spec index 74280ed..d4a9b85 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20241021 -%global gitcommit 858bd7b48d8e92ddb8d0183e5888069740375d9b +%global gitdate 20241109 +%global gitcommit e926c9f8b56412b12c2a03717976a06c522d9515 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free dd7696949ebbe7d26e431672c7a286e7d10fd824 +%global gitcommit_free 52feab15592f50ab894a9c2d888c4472e2624eb8 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20241024 -%global tarballtime 1541 +%global tarballdate 20241110 +%global tarballtime 1550 %global use_release 0 %global use_gitbare 1 From 3e616e840aa430c9e8c674a577fc8179a815fd55 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 5 Dec 2024 16:47:48 +0900 Subject: [PATCH 219/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 6aeb11c..0d2bd8d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20241110T1550.tar.gz) = 1b78028905c2546c0872ef23954b13b81a5f731515374ce8012ba30a35a0d46e45aae456ec86287249dab5c3165fb941c2e88597cc2187b75a4354eab75f339b +SHA512 (ugene-free-20241205T1611.tar.gz) = 9634f4049701d8712f245a3663433b10b0bf0fa7e671bc4012079655f1940c4eb63946ef0f6823d23464a2b52204c2fa68fe88b1a28170a592d522371a84da81 diff --git a/ugene.spec b/ugene.spec index d4a9b85..642a48c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20241109 -%global gitcommit e926c9f8b56412b12c2a03717976a06c522d9515 +%global gitdate 20241128 +%global gitcommit 7e84cfc59a4f258891149f4c5bef6cc8004311a7 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 52feab15592f50ab894a9c2d888c4472e2624eb8 +%global gitcommit_free b26886a6bcb99fb499b30122f9d5f38b0052b1a5 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20241110 -%global tarballtime 1550 +%global tarballdate 20241205 +%global tarballtime 1611 %global use_release 0 %global use_gitbare 1 From 7e6cf8fdd01291b86a33dbf2d0f1a51a3230c5d5 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 24 Dec 2024 15:11:50 +0900 Subject: [PATCH 220/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0d2bd8d..165e4c2 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20241205T1611.tar.gz) = 9634f4049701d8712f245a3663433b10b0bf0fa7e671bc4012079655f1940c4eb63946ef0f6823d23464a2b52204c2fa68fe88b1a28170a592d522371a84da81 +SHA512 (ugene-free-20241224T1434.tar.gz) = eca43125003e640ac0bfd11e89b29e7f4980a44d2976adc2e57ca2b46fae966f7df41867f67fb2fabc7cf3f58ce1f0e67def4343c4f1470e24c13027c8ddbf73 diff --git a/ugene.spec b/ugene.spec index 642a48c..73a2736 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20241128 -%global gitcommit 7e84cfc59a4f258891149f4c5bef6cc8004311a7 +%global gitdate 20241220 +%global gitcommit 49b755e66f8b850129d78e878ca16a031c55cf43 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b26886a6bcb99fb499b30122f9d5f38b0052b1a5 +%global gitcommit_free 242ce5e1b4cebe32828c65265d8d48ad902a0608 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20241205 -%global tarballtime 1611 +%global tarballdate 20241224 +%global tarballtime 1434 %global use_release 0 %global use_gitbare 1 From 8d26bb442b67fae9862fcd24e2be6df254a4246a Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 17 Jan 2025 19:57:13 +0900 Subject: [PATCH 221/260] Support C23 strict function prototype --- ugene-51.0-c23-function-proto.patch | 11 +++++++++++ ugene.spec | 8 +++++++- 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 ugene-51.0-c23-function-proto.patch diff --git a/ugene-51.0-c23-function-proto.patch b/ugene-51.0-c23-function-proto.patch new file mode 100644 index 0000000..8eece07 --- /dev/null +++ b/ugene-51.0-c23-function-proto.patch @@ -0,0 +1,11 @@ +--- ugene-51.0/src/plugins_3rdparty/primer3/src/primer3_core/read_boulder.c.debug 2024-09-22 03:28:25.000000000 +0900 ++++ ugene-51.0/src/plugins_3rdparty/primer3/src/primer3_core/read_boulder.c 2025-01-17 18:49:24.635201074 +0900 +@@ -104,7 +104,7 @@ static const char *pr_program_name = "TM + * undeclared functions; only those with non-int return types.) + */ + #ifndef __cplusplus +-extern double strtod(); ++extern double strtod(const char *, char **); + #endif + + /* diff --git a/ugene.spec b/ugene.spec index 6ec016f..58dadd3 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -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 @@ -72,6 +72,7 @@ Source2: create-%{name}-git-bare-tarball.sh # This is not installed Source10: ugene.wrapper Patch1: ugene-49.1-narrowing-for-unsigned-char.patch +Patch2: ugene-51.0-c23-function-proto.patch # Currently distro-specific Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch @@ -138,6 +139,8 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %endif %patch -P1 -p1 -b .narrow %GIT commit -m "Fix narrowing on arch where default char is unsigned" -a +%patch -P2 -p1 -b .c23 + %GIT comit -m "Fix for C23 strict function prototype" -a %patch -P102 -p1 -b .sys_mmap -Z %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a %patch -P103 -p1 -b .unwind -Z @@ -260,6 +263,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Fri Jan 17 2025 Mamoru TASAKA - 51.0-2 +- Support C23 strict function prototype + * Thu Sep 26 2024 Mamoru TASAKA - 51.0-1 - 51.0 From 9076fe71f599286c6b6f9a0567dc72acedf15dc0 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 24 Jan 2025 10:59:37 +0900 Subject: [PATCH 222/260] update to the latest git --- sources | 2 +- ugene.spec | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/sources b/sources index 165e4c2..3c3ec7d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20241224T1434.tar.gz) = eca43125003e640ac0bfd11e89b29e7f4980a44d2976adc2e57ca2b46fae966f7df41867f67fb2fabc7cf3f58ce1f0e67def4343c4f1470e24c13027c8ddbf73 +SHA512 (ugene-free-20250124T1006.tar.gz) = 22d1a59b7d6a74e5dd69d2b51501d252e2c19ad3175f6ac525ac2974ce5407d53783f17562b63c4948518a024dd116897f267211002d1b700d6e31ecbb184172 diff --git a/ugene.spec b/ugene.spec index dc6654f..132d6b9 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20241220 -%global gitcommit 49b755e66f8b850129d78e878ca16a031c55cf43 +%global gitdate 20250122 +%global gitcommit 9c788569aa7e36b0f07a850ec4f8755d7f6f25b4 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 242ce5e1b4cebe32828c65265d8d48ad902a0608 +%global gitcommit_free 354100d3f0c6bf05acb796baff8b1860f61cb9d0 %else # currently 41.0 branch %global gitdate 20211117 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20241224 -%global tarballtime 1434 +%global tarballdate 20250124 +%global tarballtime 1006 %global use_release 0 %global use_gitbare 1 @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 2%{?dist} +Release: 1%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -140,7 +140,7 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %patch -P1 -p1 -b .narrow %GIT commit -m "Fix narrowing on arch where default char is unsigned" -a %patch -P2 -p1 -b .c23 - %GIT comit -m "Fix for C23 strict function prototype" -a + %GIT commit -m "Fix for C23 strict function prototype" -a %patch -P102 -p1 -b .sys_mmap -Z %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a %patch -P103 -p1 -b .unwind -Z From 6406c940037aeedebb1bd0232f882050f9f33157 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 24 Jan 2025 16:32:56 +0900 Subject: [PATCH 223/260] 52.0 --- sources | 2 +- ugene.spec | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/sources b/sources index 3c3ec7d..8f7e7c8 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250124T1006.tar.gz) = 22d1a59b7d6a74e5dd69d2b51501d252e2c19ad3175f6ac525ac2974ce5407d53783f17562b63c4948518a024dd116897f267211002d1b700d6e31ecbb184172 +SHA512 (ugene-free-52.0.tar.gz) = c624380f2631c20e3fc66f98915755835e07b099dc4fc0e944df292bf88f352c497063e097ef859b0273ec790d323eaa2d1348fc6d9d76003ec5d4a12e9c7eb2 diff --git a/ugene.spec b/ugene.spec index 132d6b9..a242433 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20250124 %global tarballtime 1006 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainver 51.0 +%global mainver 52.0 %undefine prever %if 0%{?use_release} >= 1 @@ -263,6 +263,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Fri Jan 24 2025 Mamoru TASAKA - 52.0-1 +- 52.0 + * Fri Jan 17 2025 Mamoru TASAKA - 51.0-2 - Support C23 strict function prototype From 169e715cb3622c847e198a143dedc2e2be54b53f Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 13 Mar 2025 11:35:08 +0900 Subject: [PATCH 224/260] update to the latest git --- sources | 2 +- ugene.spec | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/sources b/sources index 8f7e7c8..c7a68fd 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-52.0.tar.gz) = c624380f2631c20e3fc66f98915755835e07b099dc4fc0e944df292bf88f352c497063e097ef859b0273ec790d323eaa2d1348fc6d9d76003ec5d4a12e9c7eb2 +SHA512 (ugene-free-20250313T1027.tar.gz) = 257dae7127100fcfbba037e505f58e0ea3a755d1ed61d77776268162e6db3cf19ece32335e76ac3b7fbfda2604a9bd2b80f5a40dc7a15d5ab1ce5230c7383655 diff --git a/ugene.spec b/ugene.spec index a242433..d47e5c7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -8,21 +8,21 @@ %global gitcommit_free 354100d3f0c6bf05acb796baff8b1860f61cb9d0 %else # currently 41.0 branch -%global gitdate 20211117 -%global gitcommit 2d776cc668bc5019452e25ecc330c88093e75c48 +%global gitdate 20250313 +%global gitcommit c0dffab5a15e01c026f80cf0a7033b08112a355f # New git commit with non-free part using "git filter-branch" -%global gitcommit_free f995e33068c5959c1bab249cd04ed3776e9b2d96 +%global gitcommit_free b0631c54cc0603a88793ed5d6ee02dec196b823e %endif %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250124 -%global tarballtime 1006 +%global tarballdate 20250313 +%global tarballtime 1027 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From a34e5374556d156c9c1493dcd6a5c0d4235dfd72 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 21 Mar 2025 15:14:06 +0900 Subject: [PATCH 225/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index c7a68fd..74fbb39 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250313T1027.tar.gz) = 257dae7127100fcfbba037e505f58e0ea3a755d1ed61d77776268162e6db3cf19ece32335e76ac3b7fbfda2604a9bd2b80f5a40dc7a15d5ab1ce5230c7383655 +SHA512 (ugene-free-20250321T1416.tar.gz) = db6b4ca2bcf40b9c575991d3e445283cb64e33d1c110928f539ddaac57916ec0ab3e030bfbc4ebeb059f919662dfdcb882fd5ac7409be8b0484b01be903fc015 diff --git a/ugene.spec b/ugene.spec index d47e5c7..a8ce0e4 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250122 -%global gitcommit 9c788569aa7e36b0f07a850ec4f8755d7f6f25b4 +%global gitdate 20250313 +%global gitcommit 747e30c19e446975835022ddb40240e780a01423 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 354100d3f0c6bf05acb796baff8b1860f61cb9d0 +%global gitcommit_free 26ee85f61df8a2591b371e19c491d3c3c00fc3f9 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250313 -%global tarballtime 1027 +%global tarballdate 20250321 +%global tarballtime 1416 %global use_release 0 %global use_gitbare 1 From 828a752507f1aac067f0dcb4bc9cb2cf226dbedf Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 17 Apr 2025 15:25:22 +0900 Subject: [PATCH 226/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 74fbb39..6e52315 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250321T1416.tar.gz) = db6b4ca2bcf40b9c575991d3e445283cb64e33d1c110928f539ddaac57916ec0ab3e030bfbc4ebeb059f919662dfdcb882fd5ac7409be8b0484b01be903fc015 +SHA512 (ugene-free-20250417T1434.tar.gz) = a3ea1b3ac746ea3cc2aae3ef52d6a4177642dd3aa2f87ace3d89c94cc3e0e221fb90caa4cd3d4e17f2ac8f52c2c3d8d2e3d7ded923c32465e6dd61c678319bba diff --git a/ugene.spec b/ugene.spec index a8ce0e4..2f641d9 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250313 -%global gitcommit 747e30c19e446975835022ddb40240e780a01423 +%global gitdate 20250415 +%global gitcommit 5f4b1fa07f7a83eb2a12c10cbc4ec0df2578254f # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 26ee85f61df8a2591b371e19c491d3c3c00fc3f9 +%global gitcommit_free 2706f43528c821539ee120ac432425bc704f2fc0 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250321 -%global tarballtime 1416 +%global tarballdate 20250417 +%global tarballtime 1434 %global use_release 0 %global use_gitbare 1 From 511368c0ddf8e6a03cea510473a1d6183813d154 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 30 Apr 2025 17:54:13 +0900 Subject: [PATCH 227/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 6e52315..d39ee65 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250417T1434.tar.gz) = a3ea1b3ac746ea3cc2aae3ef52d6a4177642dd3aa2f87ace3d89c94cc3e0e221fb90caa4cd3d4e17f2ac8f52c2c3d8d2e3d7ded923c32465e6dd61c678319bba +SHA512 (ugene-free-20250430T1705.tar.gz) = 56e8c12a4fbd1de84c6db599e5d2c96f763e3bd6827325fb41b43b6a7a196b70283b10f330946b7dfde871c58b5caecf62729864ece3b0d76cc2ab9165e64555 diff --git a/ugene.spec b/ugene.spec index 2f641d9..7defb73 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250415 -%global gitcommit 5f4b1fa07f7a83eb2a12c10cbc4ec0df2578254f +%global gitdate 20250428 +%global gitcommit ea4503585b90105e7e938557122cbc43bcd8c815 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 2706f43528c821539ee120ac432425bc704f2fc0 +%global gitcommit_free 6efa8bdfb69a0a945d7f434a81d24f9c97a658e7 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250417 -%global tarballtime 1434 +%global tarballdate 20250430 +%global tarballtime 1705 %global use_release 0 %global use_gitbare 1 From 0a60726dc983e0c786801aef41a73762ca9629ca Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 8 May 2025 17:14:22 +0900 Subject: [PATCH 228/260] 52.1 --- sources | 2 +- ugene.spec | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/sources b/sources index d39ee65..71fc8d4 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250430T1705.tar.gz) = 56e8c12a4fbd1de84c6db599e5d2c96f763e3bd6827325fb41b43b6a7a196b70283b10f330946b7dfde871c58b5caecf62729864ece3b0d76cc2ab9165e64555 +SHA512 (ugene-free-52.1.tar.gz) = 649318573922d989b1c689c8d8dbf7936500f136254e7c05ae0ef361a645b1df10e6593129a0203f79321257f90aa53da9c6974ec8d23206fcbd96e9f41e601a diff --git a/ugene.spec b/ugene.spec index 7defb73..260a34d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20250430 %global tarballtime 1705 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainver 52.0 +%global mainver 52.1 %undefine prever %if 0%{?use_release} >= 1 @@ -263,6 +263,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Thu May 08 2025 Mamoru TASAKA - 52.1-1 +- 52.1 + * Fri Jan 24 2025 Mamoru TASAKA - 52.0-1 - 52.0 From b21b67fefbc9576b998ea30f8d1b3f4cdd6f46c9 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 8 May 2025 17:48:04 +0900 Subject: [PATCH 229/260] workaround --- ugene.spec | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/ugene.spec b/ugene.spec index 260a34d..b0a8829 100644 --- a/ugene.spec +++ b/ugene.spec @@ -164,10 +164,16 @@ sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d' %GIT commit -m "remove nonfree code" -a +# Workaround +sed -i src/ugene_globals.pri \ + -e '\@DEFINES.=UGENE_VERSION=@i DEFINES+=U2_APP_VERSION=\$\${UGENE_VERSION}' + %GIT commit -m "set U2_APP_VERSION as a workaround" -a + %build %if 0%{?use_gitbare} >= 1 cd %{name} %endif + %{qmake_qt5} -r \ PREFIX=%{_libdir}/%{name} \ UGENE_EXCLUDE_LIST_ENABLED=1 \ From fe487ac9298fd307db0916c204f4f600bb750f5c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 27 May 2025 15:28:05 +0900 Subject: [PATCH 230/260] update to the latest git --- sources | 2 +- ugene.spec | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/sources b/sources index 71fc8d4..a44ecb7 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-52.1.tar.gz) = 649318573922d989b1c689c8d8dbf7936500f136254e7c05ae0ef361a645b1df10e6593129a0203f79321257f90aa53da9c6974ec8d23206fcbd96e9f41e601a +SHA512 (ugene-free-20250527T1451.tar.gz) = a14e11965dc117658b278dba2a56d1eca79ee0d794e2a70fd25996366582a82e04ecabc21ef278993981ea9ecc333e3d28c256741617daf1d79ae9e9afafe3fc diff --git a/ugene.spec b/ugene.spec index b0a8829..b744086 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250428 -%global gitcommit ea4503585b90105e7e938557122cbc43bcd8c815 +%global gitdate 20250523 +%global gitcommit 4b094b4d05b6dec75baf423efc07de327e5c4a4c # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 6efa8bdfb69a0a945d7f434a81d24f9c97a658e7 +%global gitcommit_free 46784d55ce0fb8e18544bbcf7ce18ec7cd66cb49 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250430 -%global tarballtime 1705 +%global tarballdate 20250527 +%global tarballtime 1451 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From 4a670977a31f3393e9fcd03cb1d07838d358fd3b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 18 Jul 2025 16:54:55 +0900 Subject: [PATCH 231/260] Fix data files symlink --- ugene.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/ugene.spec b/ugene.spec index b0a8829..ff43dd7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 1%{?dist} +Release: 2%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -211,7 +211,7 @@ install -cpm 0755 %{SOURCE10} ./%{_bindir}/%{name} # 1-1 data files mkdir -p ./%{_datadir}/%{name}/ mv ./$LIBAPPDIR/data ./%{_datadir}/%{name} -ln -sf ../../../%{_datadir}/%{name} ./$LIBAPPDIR/data +ln -sf ../../..%{_datadir}/%{name}/data ./$LIBAPPDIR/data # 1-11 hicolor mkdir -p ./%{_datadir}/icons/hicolor/32x32/mimetypes/ @@ -269,6 +269,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Fri Jul 18 2025 Mamoru TASAKA - 52.1-2 +- Fix data files symlink + * Thu May 08 2025 Mamoru TASAKA - 52.1-1 - 52.1 From d997fe52d14ef21458ec42e665c652dbc82374f4 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 18 Jul 2025 17:00:58 +0900 Subject: [PATCH 232/260] switch to cmake --- ugene-52.x-s390x-platform-macro.patch | 27 ++++++ ugene.spec | 114 +++++++++++++++++--------- 2 files changed, 103 insertions(+), 38 deletions(-) create mode 100644 ugene-52.x-s390x-platform-macro.patch diff --git a/ugene-52.x-s390x-platform-macro.patch b/ugene-52.x-s390x-platform-macro.patch new file mode 100644 index 0000000..72ca2de --- /dev/null +++ b/ugene-52.x-s390x-platform-macro.patch @@ -0,0 +1,27 @@ +diff --git a/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h b/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h +index a4695a261..ec063f1ee 100644 +--- a/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h ++++ b/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h +@@ -407,6 +407,13 @@ + #define WTF_CPU_RISCV32 1 + #endif + ++/* CPU(IBM z system) */ ++#if defined(__s390x__) || defined(__s390__) ++#define WTF_CPU_S390X 1 ++#define WTF_CPU_BIG_ENDIAN 1 ++#endif ++ ++ + /* ==== OS() - underlying operating system; only to be used for mandated low-level services like + virtual memory, not to choose a GUI toolkit ==== */ + +@@ -960,6 +967,8 @@ + #if !defined(WTF_USE_JSVALUE64) && !defined(WTF_USE_JSVALUE32) && !defined(WTF_USE_JSVALUE32_64) + #if (CPU(X86_64) && !CPU(X32) && (OS(UNIX) || OS(WINDOWS) || OS(SOLARIS) || OS(HPUX))) || (CPU(IA64) && !CPU(IA64_32)) || CPU(ALPHA) || CPU(AIX64) || CPU(SPARC64) || CPU(MIPS64) || CPU(AARCH64) || CPU(RISCV64) + #define WTF_USE_JSVALUE64 1 ++#elif (CPU(S390X)) ++#define WTF_USE_JSVALUE64 1 + #elif CPU(ARM) || CPU(PPC64) || CPU(RISCV32) + #define WTF_USE_JSVALUE32 1 + #elif OS(WINDOWS) && COMPILER(MINGW) diff --git a/ugene.spec b/ugene.spec index e1ddfb6..05ed0c0 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -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 @@ -82,6 +82,7 @@ Patch106: ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch Patch108: ugene-47.x-has-sse-i686.patch Patch109: ugene-50.x-aarch64-neon-impl-not-yet.patch +Patch110: ugene-52.x-s390x-platform-macro.patch BuildRequires: make BuildRequires: gcc-c++ @@ -93,6 +94,7 @@ BuildRequires: %{_bindir}/git BuildRequires: cmake(Qt5Core) BuildRequires: cmake(Qt5Gui) +BuildRequires: cmake(Qt5LinguistTools) BuildRequires: cmake(Qt5Network) BuildRequires: cmake(Qt5NetworkAuth) BuildRequires: cmake(Qt5PrintSupport) @@ -159,11 +161,42 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %patch -P109 -p1 -b .neon -Z %GIT commit -m "neon impl not yet available" -a %endif +%patch -P110 -p1 -b .s390x_macro -Z + %GIT commit -m "define s390x related macro" -a + +# Kill system-provided 3rd-party libs +sed -i CMakeLists.txt \ + -e '\@add_subdirectory.*libs_3rdparty/sqlite3@d' \ + -e '\@add_subdirectory.*libs_3rdparty/zlib@d' \ + %{nil} +rm -rf src/libs_3rdparty/{sqlite3,zlib} +rm -rf src/include/3rdparty/{sqlite3,zlib} + %GIT rm -r -f src/libs_3rdparty/{sqlite3,zlib} || true + %GIT rm -r -f src/include/3rdparty/{sqlite3,zlib} || true + %GIT commit -m "kill system-provided 3rd-party libs" -a +grep -rl --exclude-dir=.git 3rdparty/zlib/zlib.h . | \ + xargs sed -i 's|3rdparty/zlib/zlib.h|zlib.h|' +grep -rl --exclude-dir=.git 3rdparty/sqlite3/sqlite3.h . | \ + xargs sed -i 's|3rdparty/sqlite3/sqlite3.h|sqlite3.h|' +find . -name CMakeLists.txt | \ + xargs sed -i \ + -e 's|zlib|z|' \ + -e 's|ugenedb|sqlite3|' \ + %{nil} + %GIT commit -m "fix system provided header path" -a sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d' %GIT commit -m "remove nonfree code" -a +# Remove -Werror +sed -i CMakeLists.txt -e '\@" -Werror=@d' + %GIT commit -m "remove -Werror" -a + +# Enable some deprecated API +sed -i CMakeLists.txt -e '\@QT_DISABLE_DEPRECATED_BEFORE=@s|0x050F00|0x050000|' + %GIT commit -m "enable some deprecated API" -a + # Workaround sed -i src/ugene_globals.pri \ -e '\@DEFINES.=UGENE_VERSION=@i DEFINES+=U2_APP_VERSION=\$\${UGENE_VERSION}' @@ -174,64 +207,67 @@ sed -i src/ugene_globals.pri \ cd %{name} %endif -%{qmake_qt5} -r \ - PREFIX=%{_libdir}/%{name} \ - UGENE_EXCLUDE_LIST_ENABLED=1 \ - UGENE_USE_SYSTEM_SQLITE=1 \ - UGENE_USE_BUNDLED_ZLIB=0 \ - UGENE_WITHOUT_NON_FREE=1 \ - %{nil} +export QT_DIR=%{_libdir}/qt5 +export LD_LIBRARY_PATH=$(pwd)/%{_vpath_builddir}/dist -%make_build -k +%cmake \ + -DCMAKE_SKIP_RPATH=TRUE \ + %{nil} +%cmake_build %install -LIBAPPDIR=%{_libdir}/%{name} - %if 0%{?use_gitbare} >= 1 cd %{name} %endif -make install \ - INSTALL_ROOT=%{buildroot} \ - INSTALL="install -p" \ - %{nil} -# Some needed files are not installed..... -mkdir -p %{buildroot}$LIBAPPDIR -cp -a src/_release/* %{buildroot}$LIBAPPDIR -rm -f %{buildroot}$LIBAPPDIR/*.a +%cmake_install -# 1. manually move files... -pushd %{buildroot} -rm -f ./$LIBAPPDIR/LICENSE* +# Install all files manually... +# 0. Documents +cp -a \ + LICENSE.3rd_party.txt \ + LICENSE.txt \ + .. + +pushd %_vpath_builddir # 1-0 bindir -mkdir -p ./%{_bindir} -install -cpm 0755 %{SOURCE10} ./%{_bindir}/%{name} +mkdir -p %{buildroot}%{_bindir} +install -cpm 0755 %{SOURCE10} %{buildroot}%{_bindir}/%{name} -# 1-1 data files -mkdir -p ./%{_datadir}/%{name}/ -mv ./$LIBAPPDIR/data ./%{_datadir}/%{name} -ln -sf ../../..%{_datadir}/%{name}/data ./$LIBAPPDIR/data +# 1-1 libraries +mkdir -p %{buildroot}%{_libdir}/%{name} +cp -a dist/* %{buildroot}%{_libdir}/%{name}/ +rm -f %{buildroot}%{_libdir}/%{name}/*.a +# Back to the top directory +popd + +# 1-2 data files +mkdir -p %{buildroot}%{_datadir}/%{name}/ +cp -a data %{buildroot}%{_datadir}/%{name} +ln -sf ../../../%{_datadir}/%{name}/data %{buildroot}%{_libdir}/%{name}/data + +pushd ./etc/shared # 1-11 hicolor -mkdir -p ./%{_datadir}/icons/hicolor/32x32/mimetypes/ -mv ./$LIBAPPDIR/application-x-ugene-ext.png ./%{_datadir}/icons/hicolor/32x32/mimetypes/ +mkdir -p %{buildroot}%{_datadir}/icons/hicolor/32x32/mimetypes/ +cp -p application-x-ugene-ext.png %{buildroot}/%{_datadir}/icons/hicolor/32x32/mimetypes/ # 1-12 mime -mkdir -p ./%{_datadir}/mime/packages -mv ./$LIBAPPDIR/application-x-ugene.xml ./%{_datadir}/mime/packages +mkdir -p %{buildroot}%{_datadir}/mime/packages +cp -p application-x-ugene.xml %{buildroot}/%{_datadir}/mime/packages # 1-13 man file -mkdir -p ./%{_mandir}/man1 -mv ./$LIBAPPDIR/%{name}.1* ./%{_mandir}/man1 +mkdir -p %{buildroot}%{_mandir}/man1 +cp -p %{name}.1* %{buildroot}/%{_mandir}/man1 # 1-14 desktop files -mkdir -p ./%{_datadir}/applications/ -mv ./$LIBAPPDIR/%{name}.desktop ./%{_datadir}/applications/ +mkdir -p %{buildroot}%{_datadir}/applications/ +cp -p %{name}.desktop %{buildroot}/%{_datadir}/applications/ # 1-15 icons -mkdir -p ./%{_datadir}/pixmaps -mv ./$LIBAPPDIR/%{name}.{png,xpm} ./%{_datadir}/pixmaps +mkdir -p %{buildroot}%{_datadir}/pixmaps +cp -p %{name}.{png,xpm} %{buildroot}%{_datadir}/pixmaps popd %check @@ -251,6 +287,8 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_libdir}/%{name}/plugins/*.plugin %{_libdir}/%{name}/plugins/lib*.so +%{_libdir}/%{name}/transl_*.qm + %{_libdir}/%{name}/%{name} %{_libdir}/%{name}/%{name}cl %{_libdir}/%{name}/%{name}m From 47cb1a8b42c065c142cab416f95841854aaad8dc Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 18 Jul 2025 19:58:55 +0900 Subject: [PATCH 233/260] Update to the latest git --- sources | 2 +- ugene-47.x-has-sse-i686.patch | 10 ---------- ugene.spec | 21 ++++++--------------- 3 files changed, 7 insertions(+), 26 deletions(-) delete mode 100644 ugene-47.x-has-sse-i686.patch diff --git a/sources b/sources index a44ecb7..8ebf376 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250527T1451.tar.gz) = a14e11965dc117658b278dba2a56d1eca79ee0d794e2a70fd25996366582a82e04ecabc21ef278993981ea9ecc333e3d28c256741617daf1d79ae9e9afafe3fc +SHA512 (ugene-free-20250718T1659.tar.gz) = 064890320d8386e161a32b649033d96b2ce3364f664471d14faa80738972086007ec0eeede303f5d843ca57f9b3263dc74ab5ac63518a5bf609c2aa50f110add diff --git a/ugene-47.x-has-sse-i686.patch b/ugene-47.x-has-sse-i686.patch deleted file mode 100644 index e65a89d..0000000 --- a/ugene-47.x-has-sse-i686.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ugene-47.x/src/ugene_globals.pri.i386 2023-07-20 19:37:10.106204731 +0900 -+++ ugene-47.x/src/ugene_globals.pri 2023-07-20 22:31:43.266627766 +0900 -@@ -168,6 +168,7 @@ defineTest( target_platform_has_sse ) { - contains(QMAKE_TARGET.arch, x86_64) : return (true) - # This check works on Linux & Mac. - contains(QMAKE_HOST.arch, x86_64) : return (true) -+ contains(QMAKE_HOST.arch, i686) : return (true) - return (false) - } - diff --git a/ugene.spec b/ugene.spec index 05ed0c0..434248a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250523 -%global gitcommit 4b094b4d05b6dec75baf423efc07de327e5c4a4c +%global gitdate 20250716 +%global gitcommit 1f8a02dc8c832375d7ea2950e4ff8deccf8bde59 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 46784d55ce0fb8e18544bbcf7ce18ec7cd66cb49 +%global gitcommit_free e3ec3e8a212c97b86cf271776e296fe12edc925d %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250527 -%global tarballtime 1451 +%global tarballdate 20250718 +%global tarballtime 1659 %global use_release 0 %global use_gitbare 1 @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 3%{?dist} +Release: 1%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -80,7 +80,6 @@ Patch104: ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch Patch105: ugene-40.1-libs_3rdparty-breakpad-arch-port.patch Patch106: ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch Patch107: ugene-40.1-qbswap-bigendian-workaround.patch -Patch108: ugene-47.x-has-sse-i686.patch Patch109: ugene-50.x-aarch64-neon-impl-not-yet.patch Patch110: ugene-52.x-s390x-platform-macro.patch @@ -155,8 +154,6 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %GIT commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a %patch -P107 -p1 -b .char_bigen -Z %GIT commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a -%patch -P108 -p1 -b .sse_i686 -Z - %GIT commit -m "ugene_globals.pri: tell sse2 available also on i686" -a %if 1 %patch -P109 -p1 -b .neon -Z %GIT commit -m "neon impl not yet available" -a @@ -186,7 +183,6 @@ find . -name CMakeLists.txt | \ %GIT commit -m "fix system provided header path" -a sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d' -sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d' %GIT commit -m "remove nonfree code" -a # Remove -Werror @@ -197,11 +193,6 @@ sed -i CMakeLists.txt -e '\@" -Werror=@d' sed -i CMakeLists.txt -e '\@QT_DISABLE_DEPRECATED_BEFORE=@s|0x050F00|0x050000|' %GIT commit -m "enable some deprecated API" -a -# Workaround -sed -i src/ugene_globals.pri \ - -e '\@DEFINES.=UGENE_VERSION=@i DEFINES+=U2_APP_VERSION=\$\${UGENE_VERSION}' - %GIT commit -m "set U2_APP_VERSION as a workaround" -a - %build %if 0%{?use_gitbare} >= 1 cd %{name} From b7c8a0eb6132016db0d14d79d52ec3aff878f748 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 25 Jul 2025 19:44:11 +0000 Subject: [PATCH 234/260] Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild --- ugene.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ugene.spec b/ugene.spec index ff43dd7..f544049 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -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 @@ -269,6 +269,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Fri Jul 25 2025 Fedora Release Engineering - 52.1-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild + * Fri Jul 18 2025 Mamoru TASAKA - 52.1-2 - Fix data files symlink From fdc494d7dda448e23b3a0293889f8e6ee2a4427e Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 31 Jul 2025 13:21:15 +0900 Subject: [PATCH 235/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 8ebf376..d6d0e9d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250718T1659.tar.gz) = 064890320d8386e161a32b649033d96b2ce3364f664471d14faa80738972086007ec0eeede303f5d843ca57f9b3263dc74ab5ac63518a5bf609c2aa50f110add +SHA512 (ugene-free-20250731T1157.tar.gz) = d2d82a0f25390d2c793267d8ea13eee122fac2eb8a6669021043cacd107ed05a2650f1c6558d2a74d825c2e5f7458451b21e7e12d0e824c0518c5de6332f8c41 diff --git a/ugene.spec b/ugene.spec index 434248a..8cf3bb2 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250716 -%global gitcommit 1f8a02dc8c832375d7ea2950e4ff8deccf8bde59 +%global gitdate 20250731 +%global gitcommit 610ba8c1ba02f7a2c7fdce4b0942e3a9447f1935 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free e3ec3e8a212c97b86cf271776e296fe12edc925d +%global gitcommit_free 578ebb0ba279ffb9cbfcc72bc2f598ba022bc5eb %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250718 -%global tarballtime 1659 +%global tarballdate 20250731 +%global tarballtime 1157 %global use_release 0 %global use_gitbare 1 From 6dfae714653aac8c921f3e9f61053dc05c80a087 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 1 Aug 2025 16:38:04 +0900 Subject: [PATCH 236/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index d6d0e9d..c68e83e 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250731T1157.tar.gz) = d2d82a0f25390d2c793267d8ea13eee122fac2eb8a6669021043cacd107ed05a2650f1c6558d2a74d825c2e5f7458451b21e7e12d0e824c0518c5de6332f8c41 +SHA512 (ugene-free-20250801T1540.tar.gz) = 3549ef2b928fd529dd5d93d90c82759a36357eca60ea983965cc71850e4e3cb4de11f6829b652329cbf0877f3a082686d3ffce2f6f5552c297cba70503453c5d diff --git a/ugene.spec b/ugene.spec index 8cf3bb2..1c2d7e6 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250731 -%global gitcommit 610ba8c1ba02f7a2c7fdce4b0942e3a9447f1935 +%global gitdate 20250801 +%global gitcommit f855fa2e27b5b262a9de5eedfa4a0d992aa7bb1a # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 578ebb0ba279ffb9cbfcc72bc2f598ba022bc5eb +%global gitcommit_free c81801ad5b129bbf61f1899c7e0e972bb0103e6c %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250731 -%global tarballtime 1157 +%global tarballdate 20250801 +%global tarballtime 1540 %global use_release 0 %global use_gitbare 1 From f2561aaba79b93b693b1680f094f888a13c4fc82 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 3 Aug 2025 22:08:37 +0900 Subject: [PATCH 237/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index c68e83e..1bcfe14 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250801T1540.tar.gz) = 3549ef2b928fd529dd5d93d90c82759a36357eca60ea983965cc71850e4e3cb4de11f6829b652329cbf0877f3a082686d3ffce2f6f5552c297cba70503453c5d +SHA512 (ugene-free-20250803T1654.tar.gz) = 3b859a78a199535878be6463165daa12d4d4421ff776ff244dd7cbcdcefe313b11edd67b6d628753a5165fb7bd3e5bc65789900cb2e693d59f534b4e4c11d851 diff --git a/ugene.spec b/ugene.spec index 1c2d7e6..d63d0fc 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250801 -%global gitcommit f855fa2e27b5b262a9de5eedfa4a0d992aa7bb1a +%global gitdate 20250803 +%global gitcommit 8d98b7e18b44d1561bb62971a1811f51277c58e6 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free c81801ad5b129bbf61f1899c7e0e972bb0103e6c +%global gitcommit_free be014319b1e944e91acee3c6bbd8ae8a2e2243bb %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250801 -%global tarballtime 1540 +%global tarballdate 20250803 +%global tarballtime 1654 %global use_release 0 %global use_gitbare 1 From 28f31382bae1ac79d3790dfc2df5b28ba034a784 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 12 Aug 2025 13:34:36 +0900 Subject: [PATCH 238/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 1bcfe14..50f42fa 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250803T1654.tar.gz) = 3b859a78a199535878be6463165daa12d4d4421ff776ff244dd7cbcdcefe313b11edd67b6d628753a5165fb7bd3e5bc65789900cb2e693d59f534b4e4c11d851 +SHA512 (ugene-free-20250812T0918.tar.gz) = c0a5f7e75f43f54d4e63136e17621acd0bb779354059a10316135bff8b686dc23c6de9974d31b56fdf6b950c9cb7d90c042c4cd46b4cdf008d838d24aeff6e4d diff --git a/ugene.spec b/ugene.spec index d63d0fc..f10ae28 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250803 -%global gitcommit 8d98b7e18b44d1561bb62971a1811f51277c58e6 +%global gitdate 20250807 +%global gitcommit f3ebe74de9489390ffd0e0e27224f5b2a69ff501 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free be014319b1e944e91acee3c6bbd8ae8a2e2243bb +%global gitcommit_free 428ae14d5b87b5d38ed9418403398264c4960bbb %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250803 -%global tarballtime 1654 +%global tarballdate 20250812 +%global tarballtime 0918 %global use_release 0 %global use_gitbare 1 From 613a207bf802b888dee0cd93e43837e4092cd836 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 14 Aug 2025 23:36:56 +0900 Subject: [PATCH 239/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 50f42fa..411354d 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250812T0918.tar.gz) = c0a5f7e75f43f54d4e63136e17621acd0bb779354059a10316135bff8b686dc23c6de9974d31b56fdf6b950c9cb7d90c042c4cd46b4cdf008d838d24aeff6e4d +SHA512 (ugene-free-20250814T2245.tar.gz) = 99a27ffe448bf76626bd73498def71581437b4eaa229d35972d4a42874764559cf0a903a50232c92e53425ee891ee7757f976abc39267d5ef365302ea424fa5a diff --git a/ugene.spec b/ugene.spec index f10ae28..f8f92fb 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250807 -%global gitcommit f3ebe74de9489390ffd0e0e27224f5b2a69ff501 +%global gitdate 20250813 +%global gitcommit aa587527d214ebf0e4d9a580afaefee1f4b36509 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 428ae14d5b87b5d38ed9418403398264c4960bbb +%global gitcommit_free a6a69d27ca2c40bb538a39941d98abbb0d3da4d9 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250812 -%global tarballtime 0918 +%global tarballdate 20250814 +%global tarballtime 2245 %global use_release 0 %global use_gitbare 1 From 1c089d97ba479c11c026b3576fe7b32262e3e4c2 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 24 Aug 2025 15:55:39 +0900 Subject: [PATCH 240/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 411354d..4c4bc19 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250814T2245.tar.gz) = 99a27ffe448bf76626bd73498def71581437b4eaa229d35972d4a42874764559cf0a903a50232c92e53425ee891ee7757f976abc39267d5ef365302ea424fa5a +SHA512 (ugene-free-20250824T1052.tar.gz) = 5cbb1b0d1e8097ac0719f99aea10a1325f1dbdf9e4ef23ad9ec6ae3ba0b49ad96e7e9a28b1c56fcad4de4723281489dc9b6c3891c9878f944d7149d17bfc82de diff --git a/ugene.spec b/ugene.spec index f8f92fb..75755a4 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250813 -%global gitcommit aa587527d214ebf0e4d9a580afaefee1f4b36509 +%global gitdate 20250822 +%global gitcommit 5cd84dbeea1125513bf70d71703b68a8dd9a4b3c # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free a6a69d27ca2c40bb538a39941d98abbb0d3da4d9 +%global gitcommit_free 5cd84dbeea1125513bf70d71703b68a8dd9a4b3c %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250814 -%global tarballtime 2245 +%global tarballdate 20250824 +%global tarballtime 1052 %global use_release 0 %global use_gitbare 1 From b39d12ab9898ca45b4436328a2f89bdd1ce02268 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 24 Aug 2025 16:42:45 +0900 Subject: [PATCH 241/260] add patch to resolve missing include --- ....x-RegionSelectorController-missing-include.patch | 12 ++++++++++++ ugene.spec | 3 +++ 2 files changed, 15 insertions(+) create mode 100644 ugene-52.1.x-RegionSelectorController-missing-include.patch diff --git a/ugene-52.1.x-RegionSelectorController-missing-include.patch b/ugene-52.1.x-RegionSelectorController-missing-include.patch new file mode 100644 index 0000000..a26e886 --- /dev/null +++ b/ugene-52.1.x-RegionSelectorController-missing-include.patch @@ -0,0 +1,12 @@ +diff --git a/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp b/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp +index 4395ce000..f052b9122 100644 +--- a/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp ++++ b/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp +@@ -23,6 +23,7 @@ + #include + + #include ++#include + + #include + #include diff --git a/ugene.spec b/ugene.spec index 75755a4..1f6f1e0 100644 --- a/ugene.spec +++ b/ugene.spec @@ -73,6 +73,7 @@ Source2: create-%{name}-git-bare-tarball.sh Source10: ugene.wrapper Patch1: ugene-49.1-narrowing-for-unsigned-char.patch Patch2: ugene-51.0-c23-function-proto.patch +Patch3: ugene-52.1.x-RegionSelectorController-missing-include.patch # Currently distro-specific Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch @@ -142,6 +143,8 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %GIT commit -m "Fix narrowing on arch where default char is unsigned" -a %patch -P2 -p1 -b .c23 %GIT commit -m "Fix for C23 strict function prototype" -a +%patch -P3 -p1 -b .include + %GIT commit -m "RegionSelectorController: add missing include" -a %patch -P102 -p1 -b .sys_mmap -Z %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a %patch -P103 -p1 -b .unwind -Z From 82fe4e28be397b6d6814bbbac70be078adc1a691 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 24 Aug 2025 20:15:23 +0900 Subject: [PATCH 242/260] Fix QComboBox::activated overloaded function usage --- ...x-RegionSelectorController-missing-include.patch | 12 ------------ ...e-52.1.x-RegionSelectorController-overload.patch | 13 +++++++++++++ ugene.spec | 4 ++-- 3 files changed, 15 insertions(+), 14 deletions(-) delete mode 100644 ugene-52.1.x-RegionSelectorController-missing-include.patch create mode 100644 ugene-52.1.x-RegionSelectorController-overload.patch diff --git a/ugene-52.1.x-RegionSelectorController-missing-include.patch b/ugene-52.1.x-RegionSelectorController-missing-include.patch deleted file mode 100644 index a26e886..0000000 --- a/ugene-52.1.x-RegionSelectorController-missing-include.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp b/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp -index 4395ce000..f052b9122 100644 ---- a/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp -+++ b/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp -@@ -23,6 +23,7 @@ - #include - - #include -+#include - - #include - #include diff --git a/ugene-52.1.x-RegionSelectorController-overload.patch b/ugene-52.1.x-RegionSelectorController-overload.patch new file mode 100644 index 0000000..ebc5ad2 --- /dev/null +++ b/ugene-52.1.x-RegionSelectorController-overload.patch @@ -0,0 +1,13 @@ +diff --git a/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp b/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp +index f052b9122..d0fdfeb0d 100644 +--- a/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp ++++ b/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp +@@ -339,7 +339,7 @@ void RegionSelectorController::connectSlots() { + + connect(gui.startLineEdit, &QLineEdit::textEdited, this, &RegionSelectorController::sl_onRegionChanged); + connect(gui.endLineEdit, &QLineEdit::textEdited, this, &RegionSelectorController::sl_onRegionChanged); +- connect(gui.presetsComboBox, &QComboBox::activated, this, &RegionSelectorController::sl_onPresetChanged); ++ connect(gui.presetsComboBox, QOverload::of(&QComboBox::activated), this, &RegionSelectorController::sl_onPresetChanged); + + if (settings.selection != nullptr) { + connect(settings.selection, SIGNAL(si_onSelectionChanged(GSelection*)), SLOT(sl_onSelectionChanged(GSelection*))); diff --git a/ugene.spec b/ugene.spec index 1f6f1e0..0aa6ca5 100644 --- a/ugene.spec +++ b/ugene.spec @@ -73,7 +73,7 @@ Source2: create-%{name}-git-bare-tarball.sh Source10: ugene.wrapper Patch1: ugene-49.1-narrowing-for-unsigned-char.patch Patch2: ugene-51.0-c23-function-proto.patch -Patch3: ugene-52.1.x-RegionSelectorController-missing-include.patch +Patch3: ugene-52.1.x-RegionSelectorController-overload.patch # Currently distro-specific Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch Patch103: ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch @@ -144,7 +144,7 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %patch -P2 -p1 -b .c23 %GIT commit -m "Fix for C23 strict function prototype" -a %patch -P3 -p1 -b .include - %GIT commit -m "RegionSelectorController: add missing include" -a + %GIT commit -m "RegionSelectorController: specify overloaded function" -a %patch -P102 -p1 -b .sys_mmap -Z %GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a %patch -P103 -p1 -b .unwind -Z From 447d9446f03932365da44d5006ee24802e2a82c4 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 28 Aug 2025 17:24:12 +0900 Subject: [PATCH 243/260] update to the latest git --- sources | 2 +- ugene-51.0-c23-function-proto.patch | 11 ----------- ugene.spec | 13 +++++-------- 3 files changed, 6 insertions(+), 20 deletions(-) delete mode 100644 ugene-51.0-c23-function-proto.patch diff --git a/sources b/sources index 4c4bc19..d875fc3 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250824T1052.tar.gz) = 5cbb1b0d1e8097ac0719f99aea10a1325f1dbdf9e4ef23ad9ec6ae3ba0b49ad96e7e9a28b1c56fcad4de4723281489dc9b6c3891c9878f944d7149d17bfc82de +SHA512 (ugene-free-20250828T1021.tar.gz) = 45176d8ee8dcf36246492a88aabf36b0cda91e12fbec0374ac6223411ce61cf5adba922d2924cd1b0b3dc0873a819bf8b2e338f7c01e921d3b12258dcba3c8a2 diff --git a/ugene-51.0-c23-function-proto.patch b/ugene-51.0-c23-function-proto.patch deleted file mode 100644 index 8eece07..0000000 --- a/ugene-51.0-c23-function-proto.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ugene-51.0/src/plugins_3rdparty/primer3/src/primer3_core/read_boulder.c.debug 2024-09-22 03:28:25.000000000 +0900 -+++ ugene-51.0/src/plugins_3rdparty/primer3/src/primer3_core/read_boulder.c 2025-01-17 18:49:24.635201074 +0900 -@@ -104,7 +104,7 @@ static const char *pr_program_name = "TM - * undeclared functions; only those with non-int return types.) - */ - #ifndef __cplusplus --extern double strtod(); -+extern double strtod(const char *, char **); - #endif - - /* diff --git a/ugene.spec b/ugene.spec index 0aa6ca5..fba6220 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250822 -%global gitcommit 5cd84dbeea1125513bf70d71703b68a8dd9a4b3c +%global gitdate 20250826 +%global gitcommit 1ad00bf6ecc5d94b0be4ac89744b0e1a167af7ee # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 5cd84dbeea1125513bf70d71703b68a8dd9a4b3c +%global gitcommit_free b2f88c8f9c9fe2009d2a009d7bb45f03085bb081 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250824 -%global tarballtime 1052 +%global tarballdate 20250828 +%global tarballtime 1021 %global use_release 0 %global use_gitbare 1 @@ -72,7 +72,6 @@ Source2: create-%{name}-git-bare-tarball.sh # This is not installed Source10: ugene.wrapper Patch1: ugene-49.1-narrowing-for-unsigned-char.patch -Patch2: ugene-51.0-c23-function-proto.patch Patch3: ugene-52.1.x-RegionSelectorController-overload.patch # Currently distro-specific Patch102: ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch @@ -141,8 +140,6 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %endif %patch -P1 -p1 -b .narrow %GIT commit -m "Fix narrowing on arch where default char is unsigned" -a -%patch -P2 -p1 -b .c23 - %GIT commit -m "Fix for C23 strict function prototype" -a %patch -P3 -p1 -b .include %GIT commit -m "RegionSelectorController: specify overloaded function" -a %patch -P102 -p1 -b .sys_mmap -Z From bdea65807be9dc1fccc1bbd0dd76d976c0acd0e0 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 31 Aug 2025 22:37:49 +0900 Subject: [PATCH 244/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index d875fc3..863bfe3 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250828T1021.tar.gz) = 45176d8ee8dcf36246492a88aabf36b0cda91e12fbec0374ac6223411ce61cf5adba922d2924cd1b0b3dc0873a819bf8b2e338f7c01e921d3b12258dcba3c8a2 +SHA512 (ugene-free-20250831T1658.tar.gz) = c9e658fd55839d5806f0c7775c89d0543de7de2e11914f797bb09a780de6de83faaaa068c9ff71a96aaf05ce3441f248f98d83b00bcf2827bb3d7c94d8c3b3b1 diff --git a/ugene.spec b/ugene.spec index fba6220..d05601b 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250826 -%global gitcommit 1ad00bf6ecc5d94b0be4ac89744b0e1a167af7ee +%global gitdate 20250828 +%global gitcommit 74abee97f9389858dc55f9163eeed688b61b9ddf # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b2f88c8f9c9fe2009d2a009d7bb45f03085bb081 +%global gitcommit_free 078e4fc08a52f43bf9de89cd8a781fcb88c2ae33 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250828 -%global tarballtime 1021 +%global tarballdate 20250831 +%global tarballtime 1658 %global use_release 0 %global use_gitbare 1 From af20b88ed06e9d8932160a4b0b17f871adc3712c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 8 Sep 2025 16:51:11 +0900 Subject: [PATCH 245/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 863bfe3..b2c38de 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250831T1658.tar.gz) = c9e658fd55839d5806f0c7775c89d0543de7de2e11914f797bb09a780de6de83faaaa068c9ff71a96aaf05ce3441f248f98d83b00bcf2827bb3d7c94d8c3b3b1 +SHA512 (ugene-free-20250908T1554.tar.gz) = 22c7d5bc5d0c70c9de41cd06ba1afb2f5db249eb12963d354e12b910545d4ef6929da73323a41553070bce0ca3a88ecd127df3bd25896d95ce6bf0d83ba943ba diff --git a/ugene.spec b/ugene.spec index d05601b..2a8f958 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250828 -%global gitcommit 74abee97f9389858dc55f9163eeed688b61b9ddf +%global gitdate 20250908 +%global gitcommit 8f62b0f9caf3145e1c3b0fe34db4e363827d4ef0 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 078e4fc08a52f43bf9de89cd8a781fcb88c2ae33 +%global gitcommit_free c9b31eab4b4742876bfba8bfca4da0b64385c5ee %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250831 -%global tarballtime 1658 +%global tarballdate 20250908 +%global tarballtime 1554 %global use_release 0 %global use_gitbare 1 From 44db947d29f9440804581f16f1976236b932da00 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 11 Sep 2025 12:05:31 +0900 Subject: [PATCH 246/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index b2c38de..f6b6146 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250908T1554.tar.gz) = 22c7d5bc5d0c70c9de41cd06ba1afb2f5db249eb12963d354e12b910545d4ef6929da73323a41553070bce0ca3a88ecd127df3bd25896d95ce6bf0d83ba943ba +SHA512 (ugene-free-20250911T1121.tar.gz) = d90ab648ac21561aa49860dafb22480b716a5bcf0db10869e645a8747fa0a5f6a4afc9181f037988d5da4e5c9cebfa9df03c68ac3ec4f7bbba9767942a70d019 diff --git a/ugene.spec b/ugene.spec index a04f069..d0f9f1f 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250908 -%global gitcommit 8f62b0f9caf3145e1c3b0fe34db4e363827d4ef0 +%global gitdate 20250910 +%global gitcommit efc2808714912866c9e4d31a4e2cb92ae8f05067 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free c9b31eab4b4742876bfba8bfca4da0b64385c5ee +%global gitcommit_free 8f605c1045160d7025f23a0f2c36e33cb2a478e5 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250908 -%global tarballtime 1554 +%global tarballdate 20250911 +%global tarballtime 1121 %global use_release 0 %global use_gitbare 1 From 8b05308bb5cd821c44323679eb73804a36ab4a8f Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 18 Sep 2025 11:58:06 +0900 Subject: [PATCH 247/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index f6b6146..9a56687 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250911T1121.tar.gz) = d90ab648ac21561aa49860dafb22480b716a5bcf0db10869e645a8747fa0a5f6a4afc9181f037988d5da4e5c9cebfa9df03c68ac3ec4f7bbba9767942a70d019 +SHA512 (ugene-free-20250918T1057.tar.gz) = 1475f884aea9f207bf9a630d565e3967f181e763426591cad2ee5828196de828588fa25530469fb37f725a4e9d2e5342f53e96af0819f22469e5824a9740defe diff --git a/ugene.spec b/ugene.spec index d0f9f1f..1b65a7d 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250910 -%global gitcommit efc2808714912866c9e4d31a4e2cb92ae8f05067 +%global gitdate 20250912 +%global gitcommit 5f7755124a09effffab54dc89b053d89eabf70e3 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 8f605c1045160d7025f23a0f2c36e33cb2a478e5 +%global gitcommit_free 0044c530132c58c249cac22979e34e305ef2bd5a %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250911 -%global tarballtime 1121 +%global tarballdate 20250918 +%global tarballtime 1057 %global use_release 0 %global use_gitbare 1 From 30e98538488016442271bec491ed77c0b1a825b0 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 25 Sep 2025 14:39:34 +0900 Subject: [PATCH 248/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 9a56687..e1af4f1 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250918T1057.tar.gz) = 1475f884aea9f207bf9a630d565e3967f181e763426591cad2ee5828196de828588fa25530469fb37f725a4e9d2e5342f53e96af0819f22469e5824a9740defe +SHA512 (ugene-free-20250924T1746.tar.gz) = b028533b5bd51aba4a19338806f08df705184bcf403a927c5c4b454863b9f540767afbd6aa9605923881aa45450ef913b9813ecf92658f2866fbd94c5fa86423 diff --git a/ugene.spec b/ugene.spec index 1b65a7d..c85c4bf 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250912 -%global gitcommit 5f7755124a09effffab54dc89b053d89eabf70e3 +%global gitdate 20250922 +%global gitcommit 671f853c44eb499139150046eec8e5ed56015b24 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 0044c530132c58c249cac22979e34e305ef2bd5a +%global gitcommit_free ec5c9c41cb53849aa4284ee06eec03495a4b85ca %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250918 -%global tarballtime 1057 +%global tarballdate 20250924 +%global tarballtime 1746 %global use_release 0 %global use_gitbare 1 From 16277f369351741bf9cb05297a8e87454c2438b0 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 2 Oct 2025 23:58:48 +0900 Subject: [PATCH 249/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index e1af4f1..ee29c98 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20250924T1746.tar.gz) = b028533b5bd51aba4a19338806f08df705184bcf403a927c5c4b454863b9f540767afbd6aa9605923881aa45450ef913b9813ecf92658f2866fbd94c5fa86423 +SHA512 (ugene-free-20251002T1713.tar.gz) = e976086c59e99beeb5089838b14efbd5b7fc9c343c1f233fe9ab0ebd8c4306e3dec5e19630912f4f61c5cf640289680e344c038ea9b838bf4e8c719cb2b2e490 diff --git a/ugene.spec b/ugene.spec index c85c4bf..0fd59c7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250922 -%global gitcommit 671f853c44eb499139150046eec8e5ed56015b24 +%global gitdate 20250930 +%global gitcommit dac76aca2e097f7ebae94191473a7f7a6249a1f7 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free ec5c9c41cb53849aa4284ee06eec03495a4b85ca +%global gitcommit_free ae5bbab2162e02a59fa802ffdac99be4e0c1cbe3 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250924 -%global tarballtime 1746 +%global tarballdate 20251002 +%global tarballtime 1713 %global use_release 0 %global use_gitbare 1 From 45c335720ff127694d8afb27cacd9478de4ae19b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 5 Oct 2025 22:40:53 +0900 Subject: [PATCH 250/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index ee29c98..0fbbfe5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20251002T1713.tar.gz) = e976086c59e99beeb5089838b14efbd5b7fc9c343c1f233fe9ab0ebd8c4306e3dec5e19630912f4f61c5cf640289680e344c038ea9b838bf4e8c719cb2b2e490 +SHA512 (ugene-free-20251005T2157.tar.gz) = 2b178e177554024d5d7e2a844dda9f2003ced67a3e50a24a63119cdcf2c27c34e2fddaeb18186b3c130a04cf262ece16bcdaa938a7a9de49a8cd0b411484debf diff --git a/ugene.spec b/ugene.spec index 0fd59c7..d1ea8f4 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20250930 -%global gitcommit dac76aca2e097f7ebae94191473a7f7a6249a1f7 +%global gitdate 20251003 +%global gitcommit ac7912ebba82e225cbb6db84331d8c8f362e0e7b # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free ae5bbab2162e02a59fa802ffdac99be4e0c1cbe3 +%global gitcommit_free 1357451fc21cc0bfa67d0b71603aba54d9f30ab7 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20251002 -%global tarballtime 1713 +%global tarballdate 20251005 +%global tarballtime 2157 %global use_release 0 %global use_gitbare 1 From dc0e7fc52c3c2b2a6a08818a9ab1d9fa9a71ea0c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 10 Oct 2025 10:16:42 +0900 Subject: [PATCH 251/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 0fbbfe5..c35c7c3 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20251005T2157.tar.gz) = 2b178e177554024d5d7e2a844dda9f2003ced67a3e50a24a63119cdcf2c27c34e2fddaeb18186b3c130a04cf262ece16bcdaa938a7a9de49a8cd0b411484debf +SHA512 (ugene-free-20251010T0733.tar.gz) = 16e958591056d50c1504e4bf8ea848886dcdb7de304c7c780491b11bfe54a068083814642acb89d1c0e0999840ee75d84268ab320292d465ba93413fc11d0bfe diff --git a/ugene.spec b/ugene.spec index d1ea8f4..15d087c 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20251003 -%global gitcommit ac7912ebba82e225cbb6db84331d8c8f362e0e7b +%global gitdate 20251009 +%global gitcommit 1ab227ab5aedd0ad0dba1070a5f2c6a4fa94037e # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 1357451fc21cc0bfa67d0b71603aba54d9f30ab7 +%global gitcommit_free 78912ce40f024e2dda9794b1c9e9507394aac172 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20251005 -%global tarballtime 2157 +%global tarballdate 20251010 +%global tarballtime 0733 %global use_release 0 %global use_gitbare 1 From d588606d0e07359a17d6667b2fb4050bf5f292bc Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 20 Oct 2025 23:04:23 +0900 Subject: [PATCH 252/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index c35c7c3..a7bea3a 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20251010T0733.tar.gz) = 16e958591056d50c1504e4bf8ea848886dcdb7de304c7c780491b11bfe54a068083814642acb89d1c0e0999840ee75d84268ab320292d465ba93413fc11d0bfe +SHA512 (ugene-free-20251020T2221.tar.gz) = 6fce97015cef1e09578997431872f8841926f06e9b0ac984b980b2ba7ffde9d38c45282f91a8117d44d03ad28bf64ae06e8e37f646560ffd96f853f9bd369d27 diff --git a/ugene.spec b/ugene.spec index 15d087c..aaba840 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20251009 -%global gitcommit 1ab227ab5aedd0ad0dba1070a5f2c6a4fa94037e +%global gitdate 20251016 +%global gitcommit c28e1a75ace460b6a6da29dac79685a62258d341 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 78912ce40f024e2dda9794b1c9e9507394aac172 +%global gitcommit_free 89e62dde587d058646f2b00dd9a18354d76a8123 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20251010 -%global tarballtime 0733 +%global tarballdate 20251020 +%global tarballtime 2221 %global use_release 0 %global use_gitbare 1 From eed5b4297022180d79d16abd3fa4a99fa65896aa Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sat, 25 Oct 2025 21:38:10 +0900 Subject: [PATCH 253/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index a7bea3a..3fd2eb5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20251020T2221.tar.gz) = 6fce97015cef1e09578997431872f8841926f06e9b0ac984b980b2ba7ffde9d38c45282f91a8117d44d03ad28bf64ae06e8e37f646560ffd96f853f9bd369d27 +SHA512 (ugene-free-20251025T1706.tar.gz) = 4496154acaaa85661c42a17c630db8731b4bc3971df48c186589711a8d21e6240b0e44bfb2cfa134960624ffe87b099b3cec5fb45e460b6fd6965daa87e50dbb diff --git a/ugene.spec b/ugene.spec index aaba840..64f0737 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20251016 -%global gitcommit c28e1a75ace460b6a6da29dac79685a62258d341 +%global gitdate 20251022 +%global gitcommit cbd7d8369c7af370470507eeddbf7725dcb5b3bc # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 89e62dde587d058646f2b00dd9a18354d76a8123 +%global gitcommit_free 7cfb4dae7ec25fb8e5de49ab6df7c2de02bde799 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20251020 -%global tarballtime 2221 +%global tarballdate 20251025 +%global tarballtime 1706 %global use_release 0 %global use_gitbare 1 From 400ad63c902e36a3db8bf83004040e4938c0e941 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Mon, 3 Nov 2025 17:22:38 +0900 Subject: [PATCH 254/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 3fd2eb5..1cb05fc 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20251025T1706.tar.gz) = 4496154acaaa85661c42a17c630db8731b4bc3971df48c186589711a8d21e6240b0e44bfb2cfa134960624ffe87b099b3cec5fb45e460b6fd6965daa87e50dbb +SHA512 (ugene-free-20251103T1601.tar.gz) = 7249250a71629bbb91b7073a6e1248e50adf42b2bda3b0946655bf863e20561dcbc2e2529379994a8c744d259e6f4ea6ce6c54de30e6c859b434fd8040db8efc diff --git a/ugene.spec b/ugene.spec index 64f0737..85f6832 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20251022 -%global gitcommit cbd7d8369c7af370470507eeddbf7725dcb5b3bc +%global gitdate 20251030 +%global gitcommit 8b2ac42f743b6ce69e5eef0a8f7aa74de59c7f22 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 7cfb4dae7ec25fb8e5de49ab6df7c2de02bde799 +%global gitcommit_free 96c79ce7b0e0a33add7ff8be28cd7bf793267c67 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20251025 -%global tarballtime 1706 +%global tarballdate 20251103 +%global tarballtime 1601 %global use_release 0 %global use_gitbare 1 From e957a9aed84fc5dda78de944e415a24773e5bb70 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 14 Nov 2025 22:13:59 +0900 Subject: [PATCH 255/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 1cb05fc..26410ce 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20251103T1601.tar.gz) = 7249250a71629bbb91b7073a6e1248e50adf42b2bda3b0946655bf863e20561dcbc2e2529379994a8c744d259e6f4ea6ce6c54de30e6c859b434fd8040db8efc +SHA512 (ugene-free-20251114T2040.tar.gz) = 37b417d34fc9d64a52ba250f289f7ec6c85b8c4b3cbc886c7bdb94e5aed66ade180b0da3a0e77b7e1211576f1a3411d9e8d34021d31dd03245dd7da938d034b3 diff --git a/ugene.spec b/ugene.spec index 85f6832..7f13193 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20251030 -%global gitcommit 8b2ac42f743b6ce69e5eef0a8f7aa74de59c7f22 +%global gitdate 20251114 +%global gitcommit 984e82ecdfdfc0692c70a43fe5a6f42443612363 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 96c79ce7b0e0a33add7ff8be28cd7bf793267c67 +%global gitcommit_free 7c1f5c5f19e543bd68d11d315ff1ade71f8ab919 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20251103 -%global tarballtime 1601 +%global tarballdate 20251114 +%global tarballtime 2040 %global use_release 0 %global use_gitbare 1 From 29153ca5731e73ec28c9f3cb2cc073e79d4d3f7e Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 20 Nov 2025 14:32:43 +0900 Subject: [PATCH 256/260] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 26410ce..3d0e10e 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20251114T2040.tar.gz) = 37b417d34fc9d64a52ba250f289f7ec6c85b8c4b3cbc886c7bdb94e5aed66ade180b0da3a0e77b7e1211576f1a3411d9e8d34021d31dd03245dd7da938d034b3 +SHA512 (ugene-free-20251120T1101.tar.gz) = cc535233f0ccdb45b7533378ee24f993b332dfc667d2849f9ce6034f0897ea2052cba62083492e9dbc2906fda71d2c06c987e864e44e6a9b9c1d8c96559775ff diff --git a/ugene.spec b/ugene.spec index 7f13193..c757e68 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20251114 -%global gitcommit 984e82ecdfdfc0692c70a43fe5a6f42443612363 +%global gitdate 20251120 +%global gitcommit c2fb4d63da1071046795d60f395ba791cfeced89 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 7c1f5c5f19e543bd68d11d315ff1ade71f8ab919 +%global gitcommit_free b219d482d0bf5ba1247c71c804b595d4bbd14e57 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,8 +18,8 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20251114 -%global tarballtime 2040 +%global tarballdate 20251120 +%global tarballtime 1101 %global use_release 0 %global use_gitbare 1 From ea92663e6f3410008467df7e64bb784dc6187434 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 30 Nov 2025 16:52:59 +0900 Subject: [PATCH 257/260] 53.0 --- sources | 2 +- ugene.spec | 11 ++++++----- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 3d0e10e..76e7d22 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20251120T1101.tar.gz) = cc535233f0ccdb45b7533378ee24f993b332dfc667d2849f9ce6034f0897ea2052cba62083492e9dbc2906fda71d2c06c987e864e44e6a9b9c1d8c96559775ff +SHA512 (ugene-free-53.0.tar.gz) = 233c857d9a0ea42005efaa53e5ba5162e76a149f01d7406a73bd9215b96c096b3c379cc3b14c7d7b83c61df5ea2435412f6d43c71aef84b23d1d683d5a172b30 diff --git a/ugene.spec b/ugene.spec index c757e68..eddfa6a 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20251120 %global tarballtime 1101 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force @@ -35,7 +35,7 @@ %global GIT git %endif -%global mainver 52.1 +%global mainver 53.0 %undefine prever %if 0%{?use_release} >= 1 @@ -124,8 +124,6 @@ is a designer for custom bioinformatics workflows. %prep %if 0%{?use_release} >= 1 %setup -q -# Umm... -sed -i.desktop ugene.pri -e '\@desktop@s|etc/share/|etc/shared/|' %endif %if 0%{?use_gitbare} >= 1 @@ -298,6 +296,9 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop %{_mandir}/man1/%{name}.1* %changelog +* Sun Nov 30 2025 Mamoru TASAKA - 53.0-1 +- 53.0 + * Fri Jul 25 2025 Fedora Release Engineering - 52.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild From 9aea5c96b77e82a576a5cb2734b8648df1272018 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 11 Dec 2025 23:24:45 +0900 Subject: [PATCH 258/260] update to the latest git --- sources | 2 +- ugene.spec | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/sources b/sources index 76e7d22..b0fa0b5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-53.0.tar.gz) = 233c857d9a0ea42005efaa53e5ba5162e76a149f01d7406a73bd9215b96c096b3c379cc3b14c7d7b83c61df5ea2435412f6d43c71aef84b23d1d683d5a172b30 +SHA512 (ugene-free-20251211T2210.tar.gz) = da2347edd06051e46bd239000ca7c6c5c96304935fd2463f34dccd2b7c0cb953308feea82e61410c884ddbee45ecc39641f41cb5e021990fc2868672ddc3f7df diff --git a/ugene.spec b/ugene.spec index eddfa6a..cf1ce88 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20251120 -%global gitcommit c2fb4d63da1071046795d60f395ba791cfeced89 +%global gitdate 20251211 +%global gitcommit b50ca792f254939978f0ffd3126e3d9ab770a10a # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free b219d482d0bf5ba1247c71c804b595d4bbd14e57 +%global gitcommit_free 7e674061492924b3dfbc884c4c9503ecab9887b2 %else # currently 41.0 branch %global gitdate 20250313 @@ -18,11 +18,11 @@ %global shortcommit %(c=%{gitcommit}; echo ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20251120 -%global tarballtime 1101 +%global tarballdate 20251211 +%global tarballtime 2210 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From f806b16a46f8491b73f566824de51e66ff0a8e51 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 12 Dec 2025 09:20:06 +0900 Subject: [PATCH 259/260] switch back to release --- ugene.spec | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ugene.spec b/ugene.spec index cf1ce88..7390734 100644 --- a/ugene.spec +++ b/ugene.spec @@ -21,8 +21,8 @@ %global tarballdate 20251211 %global tarballtime 2210 -%global use_release 0 -%global use_gitbare 1 +%global use_release 1 +%global use_gitbare 0 %if 0%{?use_gitbare} < 1 # force From df0fff2cfc4c6fc0f8502b641712fdf6661afb8a Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 12 Dec 2025 09:20:45 +0900 Subject: [PATCH 260/260] upload again --- sources | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sources b/sources index b0fa0b5..76e7d22 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20251211T2210.tar.gz) = da2347edd06051e46bd239000ca7c6c5c96304935fd2463f34dccd2b7c0cb953308feea82e61410c884ddbee45ecc39641f41cb5e021990fc2868672ddc3f7df +SHA512 (ugene-free-53.0.tar.gz) = 233c857d9a0ea42005efaa53e5ba5162e76a149f01d7406a73bd9215b96c096b3c379cc3b14c7d7b83c61df5ea2435412f6d43c71aef84b23d1d683d5a172b30