From 188690e6e543541a0ad84660bd746a0e9bdd4a50 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 2 Sep 2022 14:25:44 +0900 Subject: [PATCH 001/182] 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 002/182] 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 003/182] 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 004/182] 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 005/182] 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 006/182] 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 007/182] 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 008/182] 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 009/182] 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 010/182] 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 011/182] 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 012/182] 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 013/182] 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 014/182] 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 015/182] 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 016/182] 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 017/182] 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 018/182] 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 019/182] 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 020/182] 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 021/182] 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 022/182] 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 023/182] 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 024/182] 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 025/182] 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 026/182] 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 027/182] 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 028/182] 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 029/182] 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 030/182] 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 031/182] 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 032/182] 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 033/182] 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 034/182] 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 035/182] 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 036/182] 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 037/182] 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 038/182] 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 039/182] 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 040/182] 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 041/182] 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 042/182] 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 043/182] 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 044/182] 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 045/182] 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 046/182] 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 047/182] 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 048/182] 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 049/182] 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 050/182] 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 051/182] 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 052/182] 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 053/182] 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 054/182] 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 055/182] 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 056/182] 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 057/182] 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 058/182] 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 059/182] 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 060/182] 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 061/182] 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 062/182] 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 063/182] 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 064/182] 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 065/182] 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 066/182] 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 067/182] 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 068/182] 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 069/182] 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 070/182] 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 071/182] 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 072/182] 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 073/182] 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 074/182] 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 075/182] 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 076/182] 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 077/182] 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 078/182] 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 079/182] 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 080/182] 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 081/182] 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 082/182] 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 083/182] 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 084/182] 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 085/182] 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 086/182] 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 087/182] 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 088/182] 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 089/182] 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 090/182] 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 091/182] 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 092/182] 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 093/182] 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 094/182] 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 095/182] 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 096/182] 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 097/182] 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 098/182] 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 099/182] 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 100/182] 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 101/182] 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 102/182] 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 103/182] 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 104/182] 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 105/182] 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 106/182] 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 107/182] 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 108/182] 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 109/182] 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 110/182] 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 111/182] 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 112/182] 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 113/182] 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 114/182] 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 115/182] 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 116/182] 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 117/182] 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 118/182] 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 119/182] 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 120/182] 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 121/182] 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 122/182] 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 123/182] 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 124/182] 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 125/182] 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 126/182] 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 127/182] 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 128/182] 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 129/182] 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 130/182] 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 131/182] 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 132/182] 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 133/182] 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 134/182] 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 135/182] 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 136/182] 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 137/182] 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 138/182] 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 139/182] 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 140/182] 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 141/182] 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 142/182] 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 143/182] 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 144/182] 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 145/182] 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 146/182] 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 147/182] 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 148/182] 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 149/182] 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 150/182] 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 151/182] 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 152/182] 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 ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250430 -%global tarballtime 1705 +%global tarballdate 20250527 +%global tarballtime 1451 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From 4a670977a31f3393e9fcd03cb1d07838d358fd3b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 18 Jul 2025 16:54:55 +0900 Subject: [PATCH 153/182] Fix data files symlink --- ugene.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/ugene.spec b/ugene.spec index b0a8829..ff43dd7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 1%{?dist} +Release: 2%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -211,7 +211,7 @@ install -cpm 0755 %{SOURCE10} ./%{_bindir}/%{name} # 1-1 data files mkdir -p ./%{_datadir}/%{name}/ mv ./$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 154/182] 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 155/182] 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 156/182] 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 157/182] 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 158/182] 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 159/182] 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 160/182] 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 161/182] 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 162/182] 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 163/182] 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 164/182] 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 165/182] 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 166/182] 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 167/182] 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 168/182] 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 169/182] 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 170/182] 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 171/182] 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 172/182] 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 173/182] 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 174/182] 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 175/182] 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 176/182] 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 177/182] 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 178/182] 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 179/182] 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 180/182] 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 181/182] 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 182/182] 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