sci-biology/t-coffee: Fix building with GCC 7

Closes: https://bugs.gentoo.org/639832
Package-Manager: Portage-2.3.19, Repoman-2.3.6

1 files changed, 54 insertions, 0 deletions

diff --git a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild
new file mode 100644
index 000000000000..df1859afb208
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+MY_HASH="4466924"
+MY_PV="${PV}.${MY_HASH}"
+MY_P="${PN^^}_distribution_Version_${MY_PV}"
+
+DESCRIPTION="A multiple sequence alignment package"
+HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
+SRC_URI="http://www.tcoffee.org/Packages/Beta/Latest/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+	sci-biology/clustalw
+	sci-chemistry/tm-align"
+DEPEND=""
+
+S="${WORKDIR}/${MY_P}"
+PATCHES=(
+	"${FILESDIR}"/${P}-mayhem.patch
+	"${FILESDIR}"/${P}-set_proper_dir_permissions.patch
+	"${FILESDIR}"/${P}-cxx11.patch
+	"${FILESDIR}"/${P}-gcc7.patch
+)
+
+src_prepare() {
+	default
+	sed \
+		-e '/@/s:.*;:\t:g' \
+		-e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \
+		-i t_coffee_source/makefile || die
+}
+
+src_compile() {
+	emake \
+		V=1 \
+		CC="$(tc-getCXX)" \
+		CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \
+		-C t_coffee_source t_coffee
+}
+
+src_install() {
+	dobin t_coffee_source/t_coffee
+
+	insinto /usr/share/${PN}
+	doins -r example
+}