From 8d35656b4a4e3a2ad6f87abb36b9fc3987d95a53 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 26 Mar 2025 00:31:47 +0000 Subject: gentoo auto-resync : 26:03:2025 - 00:31:47 --- sci-biology/Manifest.gz | Bin 19014 -> 19008 bytes sci-biology/bwa/Manifest | 6 +++--- sci-biology/bwa/bwa-0.7.17.ebuild | 4 +++- sci-biology/bwa/files/bwa-0.7.17-Makefile.patch | 4 ++++ sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch | 2 ++ 5 files changed, 12 insertions(+), 4 deletions(-) (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index 9f68854701fd..360a3f6a92b6 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest index d3a08a8cae7a..b26d28f5fc22 100644 --- a/sci-biology/bwa/Manifest +++ b/sci-biology/bwa/Manifest @@ -1,5 +1,5 @@ -AUX bwa-0.7.17-Makefile.patch 1341 BLAKE2B 21b566233ab5838174648a5316bc0c05ede4e3b6ecc1e8761556810d0c5bf5f026677fe8836ea397630f2c1d7ad45624bb6c5c26724fe1d072c9cd77889ae3c0 SHA512 0c4679d79c04ebcb8d86d7dc276cef390cd5260a08b37d7735b40d3aede634e3d98a8834154d3cf23903cf999abb00cf06661f912f6ada6d53f1242be7d1c140 -AUX bwa-0.7.17-gcc-10.patch 228 BLAKE2B c80d2fb9f1414705881178983227d762920051597edc99cca194a041b7d4dfec4d925b872448478804fbefa6881b58851e8d1a35a24b0efbc405b72f5f31cd62 SHA512 32bb9732ab9971bf26ecdaec9d512470bc970c26d1a928edb88957a4216cad1e650f0df2b69ab0214392503bbd483eade1212ed3e799393fa076b3ecdc5d5427 +AUX bwa-0.7.17-Makefile.patch 1459 BLAKE2B 1988617e713884c82b079b5e2b681cb11c9f8a58e3e05f4318dd16bd566926144eb8babc82dffe9ba9bb9ab2f66538c2931595b607a7da0a0d36a25b37582c62 SHA512 d218ff9c5960552c4a083769dc14e6c1c5682b6b419521684d17ab588fe29c43890ea4ed005269eb63d9e10c92d45edd0e8c47ef0a6a3b43f01b5eee07f29b59 +AUX bwa-0.7.17-gcc-10.patch 265 BLAKE2B ae68e743fd1d2e28d69c7bec5e3beae788fa938c65648d1c5a1f1ba395c8a0a7c4c0bb5e3e3bf6f00da7d6c2be6889b42468a05a1e54190553ca1e6fc4913b32 SHA512 157aab65cee1515b0ec9433d14c6f0c99c81d63f58f25b29e6a7c7188c3a3de36613faa1616070deda8dfa68433745adef1d80a24d84865e0ff19a94a2d3573e DIST bwa-0.7.17.tar.gz 232593 BLAKE2B fa48aad72a47547d66c767e2e2a5aadfcfc7c77c517410812230f51a2222ee66bb04383b068036b696af0a57b04b35e97bed11e3c44793aa899a8c0807f3df5e SHA512 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48 -EBUILD bwa-0.7.17.ebuild 881 BLAKE2B 3e7ffa40c7c8fc46b0ed39e5576ca0a7c1e6b6edbb1360803e3677fd7d3fa83e5d103c697c1beab095ceb6b1a66d8f971da7d206e69a6721114f8679a1d33309 SHA512 fde531dffc47c7e341cede8785e31769bb561c30d7c15c8cd1396ae5477651cc4ae04a9842edbceb9e8368dd916ea575337683194456afa248c77d2a7e6255a9 +EBUILD bwa-0.7.17.ebuild 932 BLAKE2B 51e09b73198e01e7a94a32e783339076f7e42a8959cb932823f8c1340bcde06a492c4fb0ec36b9c29f04e98b083e4e3bad935f67ee526b158adf595f1a0151eb SHA512 89339ac26a26eb918ba65036f141953770e6d90bd53ad3e5b60cc849c3cfef0b03086f867a0a07aad7742e4d18d24f73554abda77931e59dd7b736cfef60561f MISC metadata.xml 386 BLAKE2B 806a9423225c62d01adb9e64b867442b3e99c71f8847cf42d170ab2663ffa451b443a42f412eb4d6c932c1a5278873ec78e423473de76db19b51ccc296bb909b SHA512 40052cfd404f45f728a2b4dad8bac03a58557899b159aa79c9440cd95a62674be6a13df0f3f7cc20bae3c3833483c01edaabfe7b4b936a2e52810b23e139d891 diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild index e1b6dbb6184e..455cbc875ee3 100644 --- a/sci-biology/bwa/bwa-0.7.17.ebuild +++ b/sci-biology/bwa/bwa-0.7.17.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -28,6 +28,8 @@ src_configure() { # -Werror=lto-type-mismatch # https://bugs.gentoo.org/862255 # https://github.com/lh3/bwa/issues/411 + # + # Fix merged upstream. Remove on next revbump. filter-lto tc-export CC AR diff --git a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch index 944369cb75e2..cbdd136e87aa 100644 --- a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch +++ b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch @@ -1,3 +1,7 @@ +https://github.com/lh3/bwa/pull/267 + +Rejected, but small parts of it included in https://github.com/lh3/bwa/pull/263 + --- a/Makefile +++ b/Makefile @@ -1,9 +1,7 @@ diff --git a/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch index 1babb8356c4a..4d2762cef84c 100644 --- a/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch +++ b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch @@ -1,3 +1,5 @@ +https://github.com/lh3/bwa/pull/267 + --- a/rle.h +++ b/rle.h @@ -30,7 +30,7 @@ -- cgit v1.2.3