gentoo auto-resync : 29:02:2024 - 05:41:15

5 files changed, 16 insertions, 6 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 22c234b52b48..9dd890d7398e 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index 64d24373a5df..d3a08a8cae7a 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
 DIST bwa-0.7.17.tar.gz 232593 BLAKE2B fa48aad72a47547d66c767e2e2a5aadfcfc7c77c517410812230f51a2222ee66bb04383b068036b696af0a57b04b35e97bed11e3c44793aa899a8c0807f3df5e SHA512 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
-EBUILD bwa-0.7.17.ebuild 751 BLAKE2B b46e83d917a259affadb85c333c69821af7d54070409c5119e0d10c1a3e6136fd8fb8118f18b0e1525985b21d5d61fa00ecb3988403c42a4fd02eea5513eb5f7 SHA512 fb8c1d63bcb526c37795fa315dd4bbb8ffeb2bd6634f43ac82e1352416ffddddd44e38fcd7ec0a0608fd33143176618a418cbeb5b346f12e64172f071cf00d0d
+EBUILD bwa-0.7.17.ebuild 881 BLAKE2B 3e7ffa40c7c8fc46b0ed39e5576ca0a7c1e6b6edbb1360803e3677fd7d3fa83e5d103c697c1beab095ceb6b1a66d8f971da7d206e69a6721114f8679a1d33309 SHA512 fde531dffc47c7e341cede8785e31769bb561c30d7c15c8cd1396ae5477651cc4ae04a9842edbceb9e8368dd916ea575337683194456afa248c77d2a7e6255a9
 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 3da06fd74f92..e1b6dbb6184e 100644
--- a/sci-biology/bwa/bwa-0.7.17.ebuild
+++ b/sci-biology/bwa/bwa-0.7.17.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-inherit toolchain-funcs
+inherit flag-o-matic toolchain-funcs
 
 DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
 HOMEPAGE="https://github.com/lh3/bwa/"
@@ -25,6 +25,11 @@ PATCHES=(
 DOCS=( NEWS.md README-alt.md README.md )
 
 src_configure() {
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/862255
+	# https://github.com/lh3/bwa/issues/411
+	filter-lto
+
 	tc-export CC AR
 }
 
diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest
index d167e19a87ca..702b029f7ca1 100644
--- a/sci-biology/exonerate/Manifest
+++ b/sci-biology/exonerate/Manifest
@@ -1,4 +1,4 @@
 AUX exonerate-2.2.0-autotools.patch 1407 BLAKE2B b34e8c4d8301d4f416b44f4516154917943e17d30b548c7710e097706ce2c9123770d97d3ae962a268c6253a83ab60159f9285fadab1328be4ad5dc48249ee3f SHA512 f34c35228d23a8fd9402c514312c58bd877a7844487ade7f9f8d545d66c5d350f3f82f1aab1862a7b647b7f7aaaa0dbd8100d34bc0ef7d79969063c30a8558d0
 DIST exonerate-2.2.0.tar.gz 509870 BLAKE2B 58b12338ef7d819a8e33ab87d72afe807ca219581a8f35ae38951860915a676bb9ba34a481f685e970948d9272be3e5f28d6b63c14f4d5facf35c4be52530d3b SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c
-EBUILD exonerate-2.2.0-r3.ebuild 946 BLAKE2B 2e45818d3920b0ce295831122765dfd164b6612dd11a1ce72b87a52c84a73aee7b4c22f3cdb86db953900fc52182798daf73adeae1e9f3fd3cdc3b49baad15b1 SHA512 40a8ad91c8fb09103ca1ddcdc8466f08e637e2a002021dbbf2b33a35d00c649ca022cff4275c1ba42bb65cb714ca1b5e417f6683ec0d4c12bfb5e3f45061a2d0
+EBUILD exonerate-2.2.0-r3.ebuild 1116 BLAKE2B f59cc5313300713da8720cc6c9c6559dada912125649f3371647cd0866f4b6a6379b775227d00eca79a35f0e1d23f73768dff46efdecf6ed955725d06de96c42 SHA512 ff3707230bf002e3236f4ef33a95fe10c79c3bf17f14935c756205349ceef60f5e06034be636c6cc696415f7d3af535a6c0dd267928a1ee4387f8745a4524591
 MISC metadata.xml 654 BLAKE2B c84cf7eb3eed086e51e990906b2ea2645160683ba9314d2d15790e03d077714c1592bd4f305a8f3ed9109e376292118b44a1d10ea9ad1118139874a4e451bf6b SHA512 820b824d3d2a05feee023573580135fa2895832dd1b602c35253c1b8ee46aafdd0e010b5e8a77ce1805058264e3110821d27533a1dfe9d30799a5e63ea1551f1
diff --git a/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild
index 20110bdb6f1c..9d7683b6dc4d 100644
--- a/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild
+++ b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-inherit autotools toolchain-funcs
+inherit autotools flag-o-matic toolchain-funcs
 
 DESCRIPTION="Generic tool for pairwise sequence comparison"
 HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate"
@@ -27,6 +27,11 @@ src_prepare() {
 }
 
 src_configure() {
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/862264
+	# Upstream doesn't use a bug tracker, so I fired them an email about it. -- Eli
+	filter-lto
+
 	# the bootstrapping code loads AR and CC from the environment
 	tc-export CC RANLIB
 	export C4_AR="$(tc-getAR)"