From eeed9fc5874d2c490b58ff60870f759230a066a1 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 8 Sep 2023 11:04:16 +0900 Subject: [PATCH 001/104] 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 002/104] 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 003/104] 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 004/104] 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 005/104] 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 006/104] 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 007/104] 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 008/104] 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 009/104] 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 010/104] 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 011/104] 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 012/104] 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 013/104] 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 014/104] 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 015/104] 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 016/104] 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 017/104] 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 018/104] 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 019/104] 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 020/104] 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 021/104] 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 022/104] 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 023/104] 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 024/104] 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 025/104] 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 026/104] 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 027/104] 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 028/104] 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 029/104] 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 030/104] 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 031/104] 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 032/104] 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 033/104] 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 034/104] 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 035/104] 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 036/104] 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 037/104] 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 038/104] 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 039/104] 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 040/104] 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 041/104] 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 042/104] 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 043/104] 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 044/104] 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 045/104] 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 046/104] 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 047/104] 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 048/104] 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 049/104] 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 050/104] 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 051/104] 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 052/104] 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 053/104] 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 054/104] 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 055/104] 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 056/104] 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 057/104] 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 058/104] 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 059/104] 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 060/104] 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 061/104] 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 062/104] 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 063/104] 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 064/104] 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 065/104] 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 066/104] 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 067/104] 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 068/104] 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 069/104] 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 070/104] 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 071/104] 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 072/104] 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 073/104] 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 074/104] 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 ${c:0:7}) %global git_version %{gitdate}git%{shortcommit} -%global tarballdate 20250430 -%global tarballtime 1705 +%global tarballdate 20250527 +%global tarballtime 1451 -%global use_release 1 -%global use_gitbare 0 +%global use_release 0 +%global use_gitbare 1 %if 0%{?use_gitbare} < 1 # force From 4a670977a31f3393e9fcd03cb1d07838d358fd3b Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Fri, 18 Jul 2025 16:54:55 +0900 Subject: [PATCH 075/104] Fix data files symlink --- ugene.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/ugene.spec b/ugene.spec index b0a8829..ff43dd7 100644 --- a/ugene.spec +++ b/ugene.spec @@ -50,7 +50,7 @@ Name: ugene Summary: Integrated bioinformatics toolkit Version: %{fedoraver} -Release: 1%{?dist} +Release: 2%{?dist} #The entire source code is GPLv2+ except: #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2 @@ -211,7 +211,7 @@ install -cpm 0755 %{SOURCE10} ./%{_bindir}/%{name} # 1-1 data files mkdir -p ./%{_datadir}/%{name}/ mv ./$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 076/104] 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 077/104] 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 078/104] 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 079/104] 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 080/104] 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 081/104] 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 082/104] 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 083/104] 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 084/104] 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 085/104] 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 086/104] 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 087/104] 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 088/104] 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 089/104] 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 090/104] 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 091/104] 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 092/104] 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 093/104] 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 094/104] 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 095/104] 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 096/104] 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 097/104] 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 098/104] 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 099/104] 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 100/104] 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 101/104] 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 102/104] 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 103/104] 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 104/104] 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