From 7b52bc0205bc66c7e130b7794a76b5c455395232 Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Sun, 24 Dec 2017 19:24:32 +0100
Subject: sci-biology/primer3: Fix building with GCC 7

Closes: https://bugs.gentoo.org/638604
Package-Manager: Portage-2.3.19, Repoman-2.3.6
---
 sci-biology/primer3/files/primer3-2.3.7-gcc7.patch | 17 +++++++++++++++
 sci-biology/primer3/primer3-2.3.7.ebuild           | 24 ++++++++++++++--------
 2 files changed, 32 insertions(+), 9 deletions(-)
 create mode 100644 sci-biology/primer3/files/primer3-2.3.7-gcc7.patch

(limited to 'sci-biology')

diff --git a/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch b/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch
new file mode 100644
index 00000000000..a04ee1ac3b1
--- /dev/null
+++ b/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch
@@ -0,0 +1,17 @@
+--- a/src/thal.c
++++ b/src/thal.c
+@@ -426,12 +426,12 @@
+ 	       "Illegal type");
+    o->align_end_1 = -1;
+    o->align_end_2 = -1;
+-   if ('\0' == oligo_f) {
++   if ('\0' == oligo_f[0]) {
+       strcpy(o->msg, "Empty first sequence");
+       o->temp = 0.0;
+       return;
+    }
+-   if ('\0' == oligo_r) {
++   if ('\0' == oligo_r[0]) {
+       strcpy(o->msg, "Empty second sequence");
+       o->temp = 0.0;
+       return;
diff --git a/sci-biology/primer3/primer3-2.3.7.ebuild b/sci-biology/primer3/primer3-2.3.7.ebuild
index d0dbc736368..4c6c9ce7bf4 100644
--- a/sci-biology/primer3/primer3-2.3.7.ebuild
+++ b/sci-biology/primer3/primer3-2.3.7.ebuild
@@ -1,30 +1,34 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Primer Design for PCR reactions"
 HOMEPAGE="http://primer3.sourceforge.net/"
 SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.gz"
 
-SLOT="0"
 LICENSE="GPL-2"
-IUSE=""
+SLOT="0"
 KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 
 DEPEND="dev-lang/perl"
 RDEPEND=""
 
-PATCHES=( "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch )
+PATCHES=(
+	"${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
+	"${FILESDIR}"/${PN}-2.3.7-gcc7.patch
+)
 
 src_prepare() {
 	default
 	if [[ ${CHOST} == *-darwin* ]]; then
 		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
 	fi
+}
 
+src_configure() {
 	tc-export CC CXX AR RANLIB
 }
 
@@ -32,16 +36,18 @@ src_compile() {
 	emake -C src
 }
 
-src_test () {
+src_test() {
 	emake -C test | tee "${T}"/test.log
 	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
 }
 
-src_install () {
+src_install() {
 	dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
-	dodoc src/release_notes.txt example
+
 	insinto /opt/primer3_config
-	doins -r src/primer3_config/* primer3*settings.txt
+	doins -r src/primer3_config/. primer3*settings.txt
+
+	dodoc src/release_notes.txt example
 	docinto html
 	dodoc primer3_manual.htm
 }
-- 
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