From 691bc247e45c2dac480a49beaa705d38da4ea1db Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 3 Apr 2026 16:49:32 +0900 Subject: [PATCH 1/5] update to the latest git --- sources | 2 +- ugene.spec | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/sources b/sources index e17d906..bf680b7 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-53.1.tar.gz) = 5d2a1d9fac81a14fd7916c33223704aaaedfc29bd39086561202766f87cebbc7739775eccabe6a789a2381e14384bd7f8f4f7a9dfde334811190fe47dbbcc455 +SHA512 (ugene-free-20260403T1607.tar.gz) = 4fb90c6ebb0123ab7afa958c5720b71ffeff6e96ae71e80ddc9a89e53f71a813d10871142481de3a2cd5444ab0549d3ba41a9dd5171d8ac3681047eec14c85c8 diff --git a/ugene.spec b/ugene.spec index 828e81d..d8b6766 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20260228 -%global gitcommit 77338a76808d0e1b36461a94d16f0a45c83b64e9 +%global gitdate 20260402 +%global gitcommit 59163e8824b4e852f29760f782ea13609274eefc # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 6812b00935495786e28ebe901bfb8304dbee457c +%global gitcommit_free 9be7c151520500b0bebcc60bf7a0933cff1845b4 %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 20260301 -%global tarballtime 1637 +%global tarballdate 20260403 +%global tarballtime 1607 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From 13684f64efd2a36182f81a6e344f5e062ae47f9c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 5 Jul 2026 17:19:53 +0900 Subject: [PATCH 2/5] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index bf680b7..640ca99 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20260403T1607.tar.gz) = 4fb90c6ebb0123ab7afa958c5720b71ffeff6e96ae71e80ddc9a89e53f71a813d10871142481de3a2cd5444ab0549d3ba41a9dd5171d8ac3681047eec14c85c8 +SHA512 (ugene-free-20260614T2155.tar.gz) = 149a4901b696adb9db3532dba00c39a69e4931634a766a16be3d15a4ca4b0bdef2126c2af588f3a34a026a17c5c75d532113cc288237185c4fb0a56ae9f3f08c diff --git a/ugene.spec b/ugene.spec index d8b6766..04d3314 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20260402 -%global gitcommit 59163e8824b4e852f29760f782ea13609274eefc +%global gitdate 20260611 +%global gitcommit e177f75f3deebf8d659f9a24f1214aa0c61f84b0 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 9be7c151520500b0bebcc60bf7a0933cff1845b4 +%global gitcommit_free 891f1b12c7bae74d4badbdf14609ee568e239bcb %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 20260403 -%global tarballtime 1607 +%global tarballdate 20260614 +%global tarballtime 2155 %global use_release 0 %global use_gitbare 1 From b3d9f841889378a9c2b24133766903f320138a5c Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Wed, 12 Aug 2026 22:54:55 +0900 Subject: [PATCH 3/5] update to the latest git --- sources | 2 +- ugene.spec | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sources b/sources index 640ca99..917dd15 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20260614T2155.tar.gz) = 149a4901b696adb9db3532dba00c39a69e4931634a766a16be3d15a4ca4b0bdef2126c2af588f3a34a026a17c5c75d532113cc288237185c4fb0a56ae9f3f08c +SHA512 (ugene-free-20260812T1738.tar.gz) = 634d476c67553a849c6428c29289b17139ec0e5445e8a1219a9c9a8609ca731f6afc356449751dd1fcad88a87c15745875715f88d75272975cae83468b814e12 diff --git a/ugene.spec b/ugene.spec index 26c01e2..f30d7be 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20260611 -%global gitcommit e177f75f3deebf8d659f9a24f1214aa0c61f84b0 +%global gitdate 20260803 +%global gitcommit 5a73f330bcc9f654d40a27382ca132aca9cf84f3 # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 891f1b12c7bae74d4badbdf14609ee568e239bcb +%global gitcommit_free 4e4dbbc28242601a15ef35312b246d9c160b45f0 %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 20260614 -%global tarballtime 2155 +%global tarballdate 20260812 +%global tarballtime 1738 %global use_release 0 %global use_gitbare 1 From d1902730c33c46b4f2c83ab030d9cc1e806553f8 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 6 Sep 2026 15:21:02 +0900 Subject: [PATCH 4/5] update to the latest git --- sources | 2 +- ugene.spec | 41 +++++++++++++++++++++-------------------- 2 files changed, 22 insertions(+), 21 deletions(-) diff --git a/sources b/sources index 917dd15..f61ddfc 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -SHA512 (ugene-free-20260812T1738.tar.gz) = 634d476c67553a849c6428c29289b17139ec0e5445e8a1219a9c9a8609ca731f6afc356449751dd1fcad88a87c15745875715f88d75272975cae83468b814e12 +SHA512 (ugene-free-20260906T1440.tar.gz) = fc0890fc79acb337959450119b81b5178ba0f3ff3fb7502e1450d12d0e4f18a8a0586b5b6256d9d97c42f21251bbc54c97d215a23fb68d1e3fd33368fe1da37f diff --git a/ugene.spec b/ugene.spec index f30d7be..f015be8 100644 --- a/ugene.spec +++ b/ugene.spec @@ -2,10 +2,10 @@ %if 0%{?use_release_branch} < 1 # master -%global gitdate 20260803 -%global gitcommit 5a73f330bcc9f654d40a27382ca132aca9cf84f3 +%global gitdate 20260905 +%global gitcommit 0a5caecdcd44ea72e322524032ee8bc8b94f901a # New git commit with non-free part removed using "git filter-branch" -%global gitcommit_free 4e4dbbc28242601a15ef35312b246d9c160b45f0 +%global gitcommit_free 84beedcc4e5b93b227a96cc8303a4d56ac82ca64 %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 20260812 -%global tarballtime 1738 +%global tarballdate 20260906 +%global tarballtime 1440 %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 @@ -91,20 +91,21 @@ BuildRequires: desktop-file-utils BuildRequires: %{_bindir}/git %endif -BuildRequires: cmake(Qt5Core) -BuildRequires: cmake(Qt5Gui) -BuildRequires: cmake(Qt5LinguistTools) -BuildRequires: cmake(Qt5Network) -BuildRequires: 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) +BuildRequires: cmake(Qt6Core) +BuildRequires: cmake(Qt6Core5Compat) +BuildRequires: cmake(Qt6CorePrivate) +BuildRequires: cmake(Qt6Gui) +BuildRequires: cmake(Qt6LinguistTools) +BuildRequires: cmake(Qt6Network) +BuildRequires: cmake(Qt6NetworkAuth) +BuildRequires: cmake(Qt6OpenGL) +BuildRequires: cmake(Qt6OpenGLWidgets) +BuildRequires: cmake(Qt6PrintSupport) +BuildRequires: cmake(Qt6Svg) +BuildRequires: cmake(Qt6Test) +BuildRequires: cmake(Qt6WebSockets) +BuildRequires: cmake(Qt6Widgets) +BuildRequires: cmake(Qt6Xml) BuildRequires: pkgconfig(gl) BuildRequires: pkgconfig(glu) From 8e82a0c71cb9057d0dcd08d3638337982302a081 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Sun, 6 Sep 2026 16:47:27 +0900 Subject: [PATCH 5/5] Fix signness for qmin on 32bit --- ugene-53.1.x-qmin-arg-signness.patch | 17 +++++++++++++++++ ugene.spec | 3 +++ 2 files changed, 20 insertions(+) create mode 100644 ugene-53.1.x-qmin-arg-signness.patch diff --git a/ugene-53.1.x-qmin-arg-signness.patch b/ugene-53.1.x-qmin-arg-signness.patch new file mode 100644 index 0000000..5e3b0f1 --- /dev/null +++ b/ugene-53.1.x-qmin-arg-signness.patch @@ -0,0 +1,17 @@ +diff --git a/src/plugins/pcr/src/InSilicoPcrTask.cpp b/src/plugins/pcr/src/InSilicoPcrTask.cpp +index c2e106cd9..a5febc83e 100644 +--- a/src/plugins/pcr/src/InSilicoPcrTask.cpp ++++ b/src/plugins/pcr/src/InSilicoPcrTask.cpp +@@ -66,10 +66,10 @@ namespace { + int getMaxError(const InSilicoPcrTaskSettings* settings, U2Strand::Direction direction) { + int res = 0; + if (direction == U2Strand::Direct) { +- res = qMin((qsizetype)settings->forwardMismatches, settings->forwardPrimer.length() - settings->perfectMatch); ++ res = qMin((qsizetype)settings->forwardMismatches, settings->forwardPrimer.length() - (qsizetype)settings->perfectMatch); + res = qMin(res, settings->forwardPrimer.length() - 1); + } else { +- res = qMin((qsizetype)settings->reverseMismatches, settings->reversePrimer.length() - settings->perfectMatch); ++ res = qMin((qsizetype)settings->reverseMismatches, settings->reversePrimer.length() - (qsizetype)settings->perfectMatch); + res = qMin(res, settings->reversePrimer.length() - 1); + } + return qMax(0, res); diff --git a/ugene.spec b/ugene.spec index f015be8..e187721 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 Patch3: ugene-52.1.x-QObject-connect-overload.patch +Patch4: ugene-53.1.x-qmin-arg-signness.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 @@ -141,6 +142,8 @@ git config user.email "%{name}-maintainers@fedoraproject.org" %GIT commit -m "Fix narrowing on arch where default char is unsigned" -a %patch -P3 -p1 -b .include %GIT commit -m "RegionSelectorController: specify overloaded function" -a +%patch -P4 -p1 -b .signness + %GIT commit -m "Fix signness for qMin argument" -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