From 1f43daba2fbe6f53e67c63944941dc645657c5b3 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@koprulu.sector>
Date: Thu, 11 Apr 2024 18:33:04 +0100
Subject: gentoo auto-resync : 11:04:2024 - 18:33:04

---
 sci-biology/newick-utils/Manifest                  |  2 +-
 .../newick-utils/newick-utils-1.6-r1.ebuild        | 44 -------------------
 .../newick-utils/newick-utils-1.6-r2.ebuild        | 49 ++++++++++++++++++++++
 3 files changed, 50 insertions(+), 45 deletions(-)
 delete mode 100644 sci-biology/newick-utils/newick-utils-1.6-r1.ebuild
 create mode 100644 sci-biology/newick-utils/newick-utils-1.6-r2.ebuild

(limited to 'sci-biology/newick-utils')

diff --git a/sci-biology/newick-utils/Manifest b/sci-biology/newick-utils/Manifest
index d463b4d0f506..6baf75e98b5a 100644
--- a/sci-biology/newick-utils/Manifest
+++ b/sci-biology/newick-utils/Manifest
@@ -1,5 +1,5 @@
 AUX newick-utils-1.6-deduplicate-libnw.patch 5843 BLAKE2B ce36e9b1160ccd2d41a29c28626086fc713d1bd24ce5d93b9def21780bac7275bcde87e3c39a51cfb8bc5db6f99094ab9412b25fcedbab6bac7ab14720c89eac SHA512 e189a53f97fc2a31305c1d8c52d088fe0a80031d3328fafbebdc8371d6ff030b1aa71ae008981c591519888457c345281986d0130653b60e492a19d063a957ba
 AUX newick-utils-1.6-fno-common.patch 1359 BLAKE2B ccc59ad91d69ac2268d26e6704eeafc15c65e883bf8292ddfa6f1f5e75ef368238cbb38dea7f18fdafbb390d4e916fae1184ff89d8746ae98dfd5d759be69154 SHA512 9f6e53485e5d6872393bbf6404a112a105cde6d2e8993bb0c28b73be0458ce64a438eb574b451eefad28076a63ef82b0d204e3e78e301543d320f0e7b34b7799
 DIST newick-utils-1.6.tar.gz 7518535 BLAKE2B 6b5456be6fec4311e40b19972736194a3f2eb51e8efc4a97cdcf027838459a8f22f41d10e49e7ac3e6461aa290aeed1813baeffcb5706749ebf1bf4333e28047 SHA512 1e327f9a32b5b0df097bcb63f933f9073a85f0499a2a48be122f4affca52ae1541e1a6e0cca7420447aa8fe8d10d6e76e8d89933b2f84e023d6c87b50808d96c
-EBUILD newick-utils-1.6-r1.ebuild 733 BLAKE2B 60cf97660294c13efba331d06d299ed21761446981e62832bf5d9fdb713196fa10f2713f0cd33e89c1dd31e5829decca3ce919806fbf92a5652e30cee4e10c6f SHA512 b6f9daeecf7035a145e53feeb9b70676154412dea04861f1093862fb0f943a2d3f26cb791506918f1f12596abe31680ce0a13081e88494270d295d5d5d70cf74
+EBUILD newick-utils-1.6-r2.ebuild 964 BLAKE2B f576f6563a5901644e720d28ae68376489c4dd9dbffa89127c87b15c0ae577956f52bad2068e7fb85996d739084b8f7a0193bfb543e78d9e240eb08d3aff6890 SHA512 627fb54e196c6f061dce58de9612319bed17214d8ff45eab6afa7b7b22dfb4f317a39d72d467bed4c6c0ecde03c2594d3c532f9d09a046b35f1cdcc22fdf70f1
 MISC metadata.xml 441 BLAKE2B 584487b207ee6e49f0de8862a5ad3d9834dddd5cc048e8d809c5ca6ea57b2a640b590d09a2511b4d4807d360c4bbb0dfaca61fd9bd1dd7624eebd5735de56cd4 SHA512 623e7923a1496d7a1ff8f64a51906dcc15ef4079af606eede85edbe4e7aa75c8f2b23626a2916c28077e267526558308b22da77b2df2ccfb29dea2cf251cabf2
diff --git a/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild b/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild
deleted file mode 100644
index 3dcb438832a2..000000000000
--- a/sci-biology/newick-utils/newick-utils-1.6-r1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools
-
-DESCRIPTION="Tools for processing phylogenetic trees"
-HOMEPAGE="http://cegg.unige.ch/newick_utils"
-SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="xml"
-
-DEPEND="
-	xml? ( dev-libs/libxml2 )"
-RDEPEND="
-	${DEPEND}
-	!dev-games/libnw"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-deduplicate-libnw.patch
-	"${FILESDIR}"/${P}-fno-common.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--disable-static \
-		--without-guile \
-		--without-lua \
-		$(use_with xml libxml)
-}
-
-src_install() {
-	default
-	find "${ED}" -name '*.la' -delete || die
-}
diff --git a/sci-biology/newick-utils/newick-utils-1.6-r2.ebuild b/sci-biology/newick-utils/newick-utils-1.6-r2.ebuild
new file mode 100644
index 000000000000..5d5cfa360ccb
--- /dev/null
+++ b/sci-biology/newick-utils/newick-utils-1.6-r2.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools flag-o-matic
+
+DESCRIPTION="Tools for processing phylogenetic trees"
+HOMEPAGE="https://web.archive.org/web/20120206012743/http://cegg.unige.ch/newick_utils"
+SRC_URI="https://web.archive.org/web/20120126210029if_/http://cegg.unige.ch/pub/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="xml"
+
+DEPEND="
+	xml? ( dev-libs/libxml2 )"
+RDEPEND="
+	${DEPEND}
+	!dev-games/libnw"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-deduplicate-libnw.patch
+	"${FILESDIR}"/${P}-fno-common.patch
+)
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/862279
+	# https://github.com/tjunier/newick_utils/issues/34
+	filter-lto
+
+	econf \
+		--disable-static \
+		--without-guile \
+		--without-lua \
+		$(use_with xml libxml)
+}
+
+src_install() {
+	default
+	find "${ED}" -name '*.la' -delete || die
+}
-- 
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