From 169e715cb3622c847e198a143dedc2e2be54b53f Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Thu, 13 Mar 2025 11:35:08 +0900 Subject: [PATCH 01/37] 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 02/37] 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 03/37] 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 04/37] 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 05/37] 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 06/37] 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 07/37] 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 ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250430 -%global tarballtime 1705 +%global tarballdate 20250527 +%global tarballtime 1451 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From 4a670977a31f3393e9fcd03cb1d07838d358fd3b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 18 Jul 2025 16:54:55 +0900 Subject: [PATCH 08/37] Fix data files symlink --- ugene.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/ugene.spec b/ugene.spec index b0a8829..ff43dd7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 1%{?dist} +Release: 2%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -211,7 +211,7 @@ install -cpm 0755 %{SOURCE10} ./%{_bindir}/%{name} # 1-1 data files mkdir -p ./%{_datadir}/%{name}/ mv ./$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 09/37] 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 10/37] 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 11/37] 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 12/37] 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 13/37] 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 14/37] 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 15/37] 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 16/37] 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 17/37] 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 18/37] 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 19/37] 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 20/37] 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 21/37] 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 22/37] 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 23/37] 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 24/37] 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 25/37] 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 26/37] 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 27/37] 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 28/37] 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 29/37] 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 30/37] 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 31/37] 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 32/37] 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 33/37] 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 34/37] 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 35/37] 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 36/37] 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 37/37] 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