From 67717f5ed7e33856e34f632d5f17a5e218401c0a Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@koprulu.sector>
Date: Sun, 4 Sep 2022 04:20:30 +0100
Subject: gentoo auto-resync : 04:09:2022 - 04:20:30

---
 sci-biology/augustus/Manifest                 |  2 +-
 sci-biology/augustus/augustus-3.4.0-r1.ebuild | 48 -------------------------
 sci-biology/augustus/augustus-3.4.0-r2.ebuild | 51 +++++++++++++++++++++++++++
 3 files changed, 52 insertions(+), 49 deletions(-)
 delete mode 100644 sci-biology/augustus/augustus-3.4.0-r1.ebuild
 create mode 100644 sci-biology/augustus/augustus-3.4.0-r2.ebuild

(limited to 'sci-biology/augustus')

diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest
index a3321dccb4f8..68a832441ac2 100644
--- a/sci-biology/augustus/Manifest
+++ b/sci-biology/augustus/Manifest
@@ -2,5 +2,5 @@ AUX augustus-2.5.5-sane-build.patch 5271 BLAKE2B 1ba799aa4d9611087f1455f334dc356
 DIST augustus-3.4.0.tar.gz 221652100 BLAKE2B dfc8c98107f5a955f688f3d2976ca936faf2ef7004095f6b9d7c1902a36ca5d3c9aef59cab1b82b56cd5c2abc7b67195c5030111ed68557d53128814b1bf6bab SHA512 ca1df1016589f55527a883429edd5024cbc32c1b32036c81f9df5e0967a7d194f5b7a82109e924f380627427d9731caa478e63cad8cd804c01521aed76d8c4a6
 DIST augustus.2.5.5.tar.gz 70826249 BLAKE2B 3f3f1537c5c614f00298e1835eeb7bbe968987c3e0dee13299e1e26b4abf198d8635a93121b11722d2c90b63ff54cf153c72716d01c3ca033481bb54357b7bcf SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f
 EBUILD augustus-2.5.5.ebuild 910 BLAKE2B 5cde42582b4873dbaabe4457a4b7b4f5305b928cbfd7afc3c067cbeb3ea042e82faa56810b4f72078d57f7b0ecd4c96eaa30cfde5ef73d67c26fd05d0035d84e SHA512 03103b4d5cec5dfd46971f1a089d0c02d3cc5ecf7647ee5589e8e297b3f60689c2c763b8c8f2137becfa0e11c0e3c7977186c466085c3065f88eaf5a469bcb9c
-EBUILD augustus-3.4.0-r1.ebuild 958 BLAKE2B f5ef14e9e3d9f954eb5676365fdc9bc7f7f10d48b3b7e862fef66ca411d372259ad125fdc80f5479854b2e8ffda29520f5ae6c733f6fde7872ef7d0580958ea9 SHA512 d74481f445e88696674edf54ebf6ee765b5bca3ad9346021c39cd7308f8f875b96a9875995d537dd9542a57bac12c729a7e63ee60c78f74d6b83a2e5b86a5468
+EBUILD augustus-3.4.0-r2.ebuild 1031 BLAKE2B 45a1ddd194df245043599abe15d9a104a7857f2592441f6aec1dff942c3d4b145e56204a6a7dbb1e714943797f38a5d13259e674b4ba6585c2c4eab9caee85f4 SHA512 f2740287ddb5de53ac1ba572b35849aa527d341044dd353d83387222d9e2a2f67c85f8e0bd07e2b077227730b241153af2f5d5d8c843d1b7999dc1927a8c62a4
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/augustus/augustus-3.4.0-r1.ebuild b/sci-biology/augustus/augustus-3.4.0-r1.ebuild
deleted file mode 100644
index 56c2f49baebc..000000000000
--- a/sci-biology/augustus/augustus-3.4.0-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DOCS_BUILDER="doxygen"
-DOCS_CONFIG_NAME="doxygen.conf"
-inherit docs
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/"
-SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${P^}"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	dev-db/sqlite:3
-	dev-db/mysql++
-	dev-db/mysql-connector-c
-	dev-libs/boost:=
-	sci-biology/bamtools
-	sci-biology/samtools:0
-	sci-libs/gsl
-	sci-libs/htslib
-	sci-libs/suitesparse
-	sci-mathematics/lpsolve
-	sys-libs/zlib
-"
-DEPEND="${RDEPEND}"
-
-src_compile() {
-	default
-	docs_compile
-}
-
-src_install() {
-	einstalldocs
-	# from upstream Makefile install:
-	dodir "opt/${P}"
-	cp -a config bin scripts "${ED}/opt/${P}" || die
-	local file
-	for file in bin/*; do
-		dosym "../${P}/${file}" "/opt/${file}"
-	done
-}
diff --git a/sci-biology/augustus/augustus-3.4.0-r2.ebuild b/sci-biology/augustus/augustus-3.4.0-r2.ebuild
new file mode 100644
index 000000000000..30b3d7d0a6f8
--- /dev/null
+++ b/sci-biology/augustus/augustus-3.4.0-r2.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DOCS_BUILDER="doxygen"
+DOCS_CONFIG_NAME="doxygen.conf"
+inherit docs toolchain-funcs
+
+DESCRIPTION="Eukaryotic gene predictor"
+HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/"
+SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${P^}"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-db/sqlite:3
+	dev-db/mysql++:=
+	dev-db/mysql-connector-c:=
+	dev-libs/boost:=[zlib]
+	sci-biology/bamtools:=
+	sci-biology/samtools:0
+	sci-libs/gsl:=
+	sci-libs/htslib:=
+	sci-libs/suitesparse
+	sci-mathematics/lpsolve
+	sys-libs/zlib
+"
+DEPEND="${RDEPEND}"
+
+src_compile() {
+	tc-export CC CXX
+
+	emake LINK.cc="$(tc-getCXX)"
+
+	docs_compile
+}
+
+src_install() {
+	einstalldocs
+	# from upstream Makefile install:
+	dodir "opt/${P}"
+	cp -a config bin scripts "${ED}/opt/${P}" || die
+	local file
+	for file in bin/*; do
+		dosym "../${P}/${file}" "/opt/${file}"
+	done
+}
-- 
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