gentoo auto-resync : 24:09:2024 - 01:25:19

11 files changed, 40 insertions, 17 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 3cd5396be933..20bc82a0f766 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest
index 8237f313332a..780bf8f77044 100644
--- a/sci-biology/clustalx/Manifest
+++ b/sci-biology/clustalx/Manifest
@@ -1,5 +1,5 @@
 AUX clustalx-2.1-qt5.patch 8173 BLAKE2B dca2d4f7531ac38510cc9c2aa788244293c436940d38945c906c76b7a29d395179190833517c01cbe48d450111d3f115427fb55536ab55dd01fc0617ff9e7bc2 SHA512 d8c9e9e1aade86f6ba4aa88618ace305152b819cf445119c82b4d4e56c7923e25876c83fd74c8dc91715ce484ff0ea3111b13ed7d8219c1222ad60e09b72d29e
 DIST clustalx-2.1.tar.gz 341649 BLAKE2B 43a740b278127d4745699a75479e422cc95a864bd55a9fe37eb68c0b36ae89e07848e8fdae2207ff9b3850eebc273b803df0261eefd3e7d96d8fa58c75af3adc SHA512 e8cbad783722161de6999ab01a91d555fc10db609197a8d2878f91e9d7dc998784c02d2ccb54c4936ee27b41321db6f4f37021221662f483b8b6d945b6e1c026
 DIST clustalx.png.xz 74808 BLAKE2B 3e0b7ba5d0c4e1013a1ea0146460384279e7116cccde1abdd2e34de16867d83b88c0a04fbc64524e340611fdc5a5df4dbc73f10af610a43fae65c0907b7ac25d SHA512 0907710c944fc1b883c58501cd7bc2abbc5bf171495b58dbe9829d60d7c3530c210f89a5bfafc3cec03808ae50f5c9a78ce37b9175c2e37590494e115e8e343a
-EBUILD clustalx-2.1-r3.ebuild 1336 BLAKE2B 06a333b85b40abfedc034d2a9eb4133d2e49fa2e3a7ad18920cae45444d7e2d3f9d2ec364024ff54ce2c82f502c1ac5cff03c6d71eafae28251153820c65a001 SHA512 37f141b7c69300fbd920eecd8c54532c53f059c305f7bb1ad6b051c0e3bf22c25d4a3e87871d5f1e5bb891c512427b645506cecd76a8ae2ce8dbf53daad09882
+EBUILD clustalx-2.1-r3.ebuild 1328 BLAKE2B 3f6d801ab0e9c0da759b88f4276bdb42ab82da245fa8d66c484407eac8bbde3ec2f1d06ffb7a8b938b78ed705df777d6b7af43bcd6798b8bf384be3983313c3b SHA512 fd9eefecbb698e3e2c82687163b92c4a55278c2f779b9c5d300680fba23a82e4a0b4e5550007d0231b655466ad80eaa159e918a448604bf0166342b5321c5733
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/clustalx/clustalx-2.1-r3.ebuild b/sci-biology/clustalx/clustalx-2.1-r3.ebuild
index fa956bd186e8..ae15401a3488 100644
--- a/sci-biology/clustalx/clustalx-2.1-r3.ebuild
+++ b/sci-biology/clustalx/clustalx-2.1-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -14,7 +14,6 @@ SRC_URI="
 LICENSE="GPL-3 LGPL-3"
 SLOT="0"
 KEYWORDS="amd64 ~x86"
-IUSE=""
 
 DEPEND="
 	dev-qt/qtcore:5
diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest
index 8abc6902fbba..48b42be0ae87 100644
--- a/sci-biology/embassy-esim4/Manifest
+++ b/sci-biology/embassy-esim4/Manifest
@@ -1,4 +1,4 @@
 AUX embassy-esim4-1.0.0.650_fix-build-system.patch 2944 BLAKE2B 92dacc9399084c4a53e9e95ca25962fabf115c49986ec65edc15c3586f1969556ba5053082bc5a1da746b7f33cffa31b36fefc525c91ba58c60f8c0ebfdbed0e SHA512 05fd07e2e4252b1336a96cdb771d3d58fea7e01ed954c24387e94859d77e74886dcc2e7da96ed83640915a0d146c6516c622773540eabb0d6df45587a7bf89e2
 DIST embassy-esim4-1.0.0.660.tar.gz 473261 BLAKE2B d15029b0723dd739fa9208f9b0ffd7814cbddc630ca2ff15955412f493f7983753acf82bcc8a3fc6ddfd49abe630982ead377e6941dcbff44ddc5d8ab4e7d6e5 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152
-EBUILD embassy-esim4-1.0.0.660-r1.ebuild 374 BLAKE2B a80f736ff608fb351157fcdb7bc00d5efe94baf12ab735fe6aced51d9207f46b673f05c8c1b5186f5e0a8a5e218f824e90b49cca449d98568ace07161b854593 SHA512 1991b3962967038eb2d3b0a36213be5c8f8c43bf2259b2fc2c0566f31c2d7a5341203785e2565083684537f7d4e31e02084e86d70121768fbdcf693c4e1ba324
+EBUILD embassy-esim4-1.0.0.660-r1.ebuild 544 BLAKE2B 07227133c5a691c2906ac6d7e948581113a700b4f3bc84b39b4463f2c60af23e8f08aa59dd3248857b4fd094abe8a1eac5962d76d11eda2669687c9947beca99 SHA512 a4471436bcdcb605dcab2b7e2c83288cba67918d067fa5b79f0fb1f33611200cc74993b70edb97ca160419abbe6be3f66f821539c64ae37ef55a085277a3b630
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild
index ab0fee10dc58..9da13422f06e 100644
--- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild
+++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.660-r1.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA"
 
-inherit autotools emboss-r3
+inherit autotools emboss-r3 flag-o-matic
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
@@ -16,3 +16,13 @@ src_prepare() {
 	default
 	eautoreconf
 }
+
+src_configure() {
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/862258
+	#
+	# Upstream is dead since 2013.
+	filter-lto
+
+	emboss-r3_src_configure
+}
diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest
index 13d152a70843..2da3905242d9 100644
--- a/sci-biology/embassy-mse/Manifest
+++ b/sci-biology/embassy-mse/Manifest
@@ -1,4 +1,4 @@
 AUX embassy-mse-3.0.0.650_fix-build-system.patch 3968 BLAKE2B 93a61bae2ec37053f3c014634181bae9859e68c92bb2d5fe99fda09d5f083d19a2b3c8cdcf0117d8dfc34f6d892c44f1817115f2619a47909bc26e0f766a5429 SHA512 4824292eb41cb75ca038be63a8b4985b119a80426333f42a83c9316b69bc6431355d5637d3a30e6b42307ec4cc7603e53250bda9ef3fabbd00e3885a5252e73a
 DIST embassy-mse-3.0.0.660.tar.gz 491747 BLAKE2B 7d072458577a90fc367c5b6ed72d1d36592e42b83b3a4e31126b925ddc76f1946fba14e22b7410f66eb837f686f848bdb1033f3b62084f1423543d7605c4f6b9 SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3
-EBUILD embassy-mse-3.0.0.660-r1.ebuild 570 BLAKE2B d5ec39363a6682dca1070762f22c9ba34fbc98282204b78dcb369753a394a17fd69866cbe57acc2a9e73211bdf1397abaadb1130ec2d96ddc333837e07fa89e9 SHA512 49298c9f723e5cfc03f098c971781d483f2311d62a6f077bd6897a3fde3b37e26132267110c00ba9ee9de7f894b7ee2a4cb0755afe7ed8bea19f9a47f5a9a5aa
+EBUILD embassy-mse-3.0.0.660-r1.ebuild 694 BLAKE2B 6d11c46bf630706a5d5ccbdfb9aaf2fc58d8d065e9f05fe4094c63578e280eb7cf931e75b4607b8a2e6152a33117c8d18e429519fea0d128a7d7c77328a99403 SHA512 eb5874d54c35b84629a27163094140521c0d58affeab6aa2c08300a724726ac67aa831f4d047c2e46d23fec1cabc2ead488bfe564c4ae68d58d69806651047de
 MISC metadata.xml 338 BLAKE2B acd164074e32c1d0d2b3806e491017e350b45603515e368127fe6c1d9aefd305873d9dda8ed181da325f975043411aee91bebd2d8554c31976f618f6324e9456 SHA512 8cf0ad2755a86551c8bfdde159e2c25a1048a04f0f32c37b29a526ca29233d7eb76ad1704c70194745cf167b359f23529cbba5bfeb8003b833e6f22e0d4a333e
diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild
index a806410e6366..9b71d99d9e5b 100644
--- a/sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild
+++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.660-r1.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor"
 
-inherit autotools emboss-r3
+inherit autotools emboss-r3 flag-o-matic
 
 KEYWORDS="~amd64 ~x86 ~x86-linux"
 
@@ -21,6 +21,12 @@ src_prepare() {
 }
 
 src_configure() {
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/927386
+	#
+	# Upstream is dead since 2013.
+	filter-lto
+
 	emboss-r3_src_configure --enable-curses
 }
 
diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest
index 04367b5bf202..a7de57c08446 100644
--- a/sci-biology/embassy-phylipnew/Manifest
+++ b/sci-biology/embassy-phylipnew/Manifest
@@ -1,5 +1,5 @@
 AUX embassy-phylipnew-3.69.650-fno-common.patch 16289 BLAKE2B 346f5d704be918503a80ab224e1892953a2d1d6ef642e6ced95fcb1476954e09d983bd0eef1d6afe71d2c4e043a05a99dd92748151e337ac5d3646d91008c2e9 SHA512 0ea1f10865832a44647f0888eabef1df6e5baadace9fda782f171d52eef70fc7d8ef80317d46eaeb029896b8b0b4ca0d845561ae761daf406f7c26e18ebd1341
 AUX embassy-phylipnew-3.69.650_fix-build-system.patch 3019 BLAKE2B 94bdca3ee696570f1f6c82cdc3e948d8e48621ed3537c98f681e953a0ce88fe790b2a8ef60cc836cd2d9c303348cf13b2bc27ccb411714880da98af9ff0d42c8 SHA512 3ce374ac3d2537fd307e310357c6efa8b66330475c6fd383dd83a7507fe179796cbfb4c25036b3254731467a0dd5798b9024e9b6009c905df3990a168a528a6b
 DIST embassy-phylipnew-3.69.660.tar.gz 1741298 BLAKE2B 58a2c66ffb9c447fa17462bf54d7b8e65702701d74c1f16ec6906a3acaf076ebcab30982befe6334101bc483901132069a71ffa0e2334aaee0da02a30276b7f2 SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5
-EBUILD embassy-phylipnew-3.69.660-r1.ebuild 441 BLAKE2B 773748fdfc603bd1134d4324f3e24ff49bfd2f4cf4f6a033aaa708aea2c3475f20a1467becbb3a965b07b2b77ec6dd2a1e6ae0d3f3ad1c4fe0e8ee6512b588fd SHA512 b075fe9ae13b226dba97252706cec3d5da279cf9be3225a29c7d673a21dcff4fb05d860d75a59f2b7a611c2c640df9d8c34272f72ae25f2b8be475255ff8a034
+EBUILD embassy-phylipnew-3.69.660-r1.ebuild 611 BLAKE2B cbe7382dfe72fdfef8112a2c0e1ed338579969dcafb7bce81aa8f17b17ec176ce0818ccc8a75f7a533fb5d253bf9febcc442183949f97800fadfc5bc39283f17 SHA512 3fad5d6e5df6b5f91731d3d944fee24e4d9777e2eeb8fa1e5f82e9aef0bcdfd9e6af507d0d443571b4a481abcc3266322f57acf9d9f0125fb8d754117c0d3105
 MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd
diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild
index d7dc57a64fc8..90833621fa75 100644
--- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild
+++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.660-r1.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 EBO_DESCRIPTION="The Phylogeny Inference Package"
 
-inherit autotools emboss-r3
+inherit autotools emboss-r3 flag-o-matic
 
 LICENSE+=" free-noncomm"
 
@@ -21,3 +21,13 @@ src_prepare() {
 	default
 	eautoreconf
 }
+
+src_configure() {
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/862261
+	#
+	# Upstream is dead since 2013.
+	filter-lto
+
+	emboss-r3_src_configure
+}
diff --git a/sci-biology/sim4/Manifest b/sci-biology/sim4/Manifest
index 530496d9579e..34b5d1a4e90c 100644
--- a/sci-biology/sim4/Manifest
+++ b/sci-biology/sim4/Manifest
@@ -1,4 +1,4 @@
 AUX sim4-20030921-fix-build-system.patch 491 BLAKE2B 87842374146fa44c2788ce7444480cb7be244d04f0e2f2d22bdc5cca766b4bd610b94a5d6088c58ce2005b8e7664fab6ec4b0ea598e833a34fa1edff29e413da SHA512 fdc737ccacd7cb4f7c5534af49587d7958f62dbe66a5197c38bda89af3cdd572231c10af75e8bb59120fa116f856f1ca5ba95279f9a2fe07228543588552f915
 DIST sim4-20030921.tar.gz 60814 BLAKE2B 2a6aeaf56cbec7b3d5e8cb0c0405afd3b1325977d1b68ba319347dbc38461bde9bdb028e92d8b463a593a2fdc8d72d65db27c8e30462901ce8921632201ad038 SHA512 de7ee4094830262cb7ea8ed2f4573beed96df4b12f2915f669c52fd3fa40f5a4894cd94224e575bfb2588f9a6f19c0b73a38d6209d92a1dc644639a4927aa6b5
-EBUILD sim4-20030921-r2.ebuild 526 BLAKE2B 5ce172642026a68778c15228a9ed778948805e4e7d424f0c0035d1c7a4480e45d4c0a93c308a0e5f203dcf79d102dd1b65b2d69d3122d9abf3bcf6be4ad629e6 SHA512 d6d3cc0e35c09424182357554b94d0cd2327ffeb13c78b989ad7aea503a3e2161ec1355c08d6190b934e5c731cf214f9d13cadeb127a8305a8897bd55a649de6
+EBUILD sim4-20030921-r2.ebuild 519 BLAKE2B 0264ca6f2db497ac26f201750dc29aa979b1952eb73425f811e67f4087cfab4f97addea7291bb82192aa0a20b78dd8eebe5ce0849386868ef34ddda59bf4f805 SHA512 c35e7e93f344f26e51c69542a98ddce5b7bdc41974b497cf7c32cbdc3746c0321de368736ef5ddb731a6d1a3c6413c7d9dec02fd7fe0f5647e06e70896bbe3a0
 MISC metadata.xml 1229 BLAKE2B 19108d167b885de760799921cae4723e42b5a1ed83b290a46e15e3ff79bf84feeed1f5f60e3334acd1036f9f45d1b9e01a8dfda9dc9c22a7cc5c9e8abb52ec70 SHA512 482ab89bc2a9226ab858417a7ec52eef4e36c21e8c0399174ad811f37ba8409fad1990187abb9161b54166f7691a06729835d77d51fdb0b85044b89c8e2402de
diff --git a/sci-biology/sim4/sim4-20030921-r2.ebuild b/sci-biology/sim4/sim4-20030921-r2.ebuild
index 1e1b725f7910..64c0e64d19ef 100644
--- a/sci-biology/sim4/sim4-20030921-r2.ebuild
+++ b/sci-biology/sim4/sim4-20030921-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -8,13 +8,11 @@ inherit toolchain-funcs
 DESCRIPTION="A program to align cDNA and genomic DNA"
 HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html"
 SRC_URI="mirror://gentoo/${P}.tar.gz"
+S="${WORKDIR}/${PN}.2003-09-21"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-
-S=${WORKDIR}/${PN}.2003-09-21
 
 PATCHES=( "${FILESDIR}"/${PN}-20030921-fix-build-system.patch )