gentoo resync : 25.12.2017

5 files changed, 34 insertions, 104 deletions

diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
index 98e896ecef04..75cde6014283 100644
--- a/sci-biology/primer3/Manifest
+++ b/sci-biology/primer3/Manifest
@@ -1,8 +1,5 @@
 AUX primer3-2.3.4-buildsystem.patch 5460 BLAKE2B 1e7680501e9c4a74c599f52caa787751f74f6a4fd028d8273d00364c7d2e59c0a641d343386e6ff7598d7d0bbfa66ce80412d300646cd54d0112ce118ff8422d SHA512 52f539f52c92e5e21c3166da62813c6fa9f90fd9e0ca87d9ab67658496e13f4b5ce5c53770802cb1cdd21044244e21f09b0de2ce3c6d3db0182b3d9cbf64a037
-DIST primer3-2.3.5.tar.gz 1655871 BLAKE2B 6311a15334adc4121a62a4ff0f42f32f81e147b43742a59d6708c2e64a714c59b019433fcedebf5e88cefd2e46f4879d1f950acc0346f2da73d2567e621056f2 SHA512 e64c27eea0258af913304963254494d6c874e7776b09a14ee9a273f1a3cdfa908acf92b78affc0102f06df17effbf011181c60d97ebd0a645044df7a28b41fec
+AUX primer3-2.3.7-gcc7.patch 421 BLAKE2B 3f861ecb493ce9673cdebac9ea224a0588bd3b758d72a7ef4e41d4efb929db444a8c2808a55ead42dcb174265a926c021a89dd83dc8a1e5ba4eb5ed26280be43 SHA512 c818cd80e4762ef46e4e52acd27f4eb966d676995154b3503c98d8defb545c3dd7ea307c8946b5b5c462dd7f5dee6abc254cea59e21e2229cb779a7178dec04d
 DIST primer3-2.3.7.tar.gz 1658090 BLAKE2B 0bc9a0faa19c4ac3b48680d65b0d91a13d8bdd651ad3a0d344b4f50ce8dc510fe7a22665192751fb2c8ff6282b560daf4540a02cc70482dba0fcc344f7727e37 SHA512 f227f80d395cb682a9d65e0ac3afdcacb8385d66e721b9163fda939a9c788a7c6907273f6223782702b48d7df66ea2331114f6303fcd29e3b3c50a2717da2fa7
-DIST primer3-src-2.3.6.tar.gz 1667573 BLAKE2B 02344f1f13a639654ec040c893691c132193f81d2c64588a6ac1556f268d6768307bf12f77580aa8096f35f95401caebecfa080135bbb75bff4fac30120cc4a9 SHA512 671b420f3bc9b6b9972e19a757925ada170e5f8c0e3e8a90630a48e6cde44abc0e1e09b9ea90129f94b58f835e30440f3d91c14fb4b796fd94eb478b2ca28ead
-EBUILD primer3-2.3.5.ebuild 1029 BLAKE2B 5a0c27b029fffdfed3851928c65c6936c981eaf6b5b70322120427165eeb58078b13957b4288b4642b952854d3e8119d80914e1d36fa427bfb2a0b5a2d18f152 SHA512 a52d99dde78f30879e6d109d36d5d2d258494d5dda1548b78044731decd772ccf78c0203dc1844a4c08b96f26ac52671da4b11efdbb732a578c45cf31b68119a
-EBUILD primer3-2.3.6.ebuild 1040 BLAKE2B 93acf2275975e9af3e27f328624ea3e5931da124fc009f95f604217de212cab23b96afa5191daf2d7a47eb329dcedb0bc5b154edb7a78df617c22d97213a81e7 SHA512 f0471de087faa4e41123c94a1ef6dd32635edd5482d05724e135f8b05bcc073475206256e17f4547bbd269fbcc564f89dc0b4ff8aec33888c9095abcdc7c951d
-EBUILD primer3-2.3.7.ebuild 1072 BLAKE2B bc629de01b3d1fe7de243d8c16c6eecd89ba87074058cd0368e43ff4cffcb8b97f5b30e8e5d7386da84b93bd1e56f46f1c338b3d715e138b9d3c9294178e8da3 SHA512 0ba2a4ff56a4ecc8abd17888acd22275f8330418d250503def828f83b047bf84d6a17224e65de75199923b40e95926128a885419b65325a09c061cdeba30f05f
+EBUILD primer3-2.3.7.ebuild 1116 BLAKE2B 1aff6985a9ad3ad0ee523f18061c7f31bd26d3cc6c72f440a15c0ae2bc21f84ad360f51b021079efde09ef386f1c92f4dec7d155b970247e9ee87c376e0b36ee SHA512 56b127a7282b1c9dcc514758899d46e23ad79178f402beee270a03959eb01ae28e03720fba1c4dfbfc050e2932a15f5e2254705a048acf8ef8f7db0998327e61
 MISC metadata.xml 797 BLAKE2B 169e1065192fa4173181d9ee76a95ee83aefd398627ee65952eb14c3d3db93910c3d2239fe5ca7ce7c68f00e005bd7902a150640b85143f0f9d53fec41392318 SHA512 3d8707f6c780f3bec419c4cdf8564bf3634c4b75e4e7dffebdc29684dfbe89d9404c405e5c7b72e32fc493517e8fa36137c7a6f2b237f788fc6fb46ca43d2f7f
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 000000000000..a04ee1ac3b12
--- /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/primer3-2.3.5.ebuild b/sci-biology/primer3/primer3-2.3.5.ebuild
deleted file mode 100644
index 513c7cb5a1a3..000000000000
--- a/sci-biology/primer3/primer3-2.3.5.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Primer Design for PCR reactions"
-HOMEPAGE="http://primer3.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${PV}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-IUSE=""
-KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
-
-DEPEND="dev-lang/perl"
-RDEPEND=""
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
-
-	if [[ ${CHOST} == *-darwin* ]]; then
-		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
-	fi
-
-	tc-export CC CXX AR RANLIB
-}
-
-src_compile() {
-	emake -C src
-}
-
-src_test () {
-	emake -C test | tee "${T}"/test.log
-	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
-}
-
-src_install () {
-	dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
-	dodoc src/release_notes.txt example
-	insinto /opt/primer3_config
-	doins -r src/primer3_config/* primer3*settings.txt
-	dohtml primer3_manual.htm
-}
diff --git a/sci-biology/primer3/primer3-2.3.6.ebuild b/sci-biology/primer3/primer3-2.3.6.ebuild
deleted file mode 100644
index 21a466681109..000000000000
--- a/sci-biology/primer3/primer3-2.3.6.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Primer Design for PCR reactions"
-HOMEPAGE="http://primer3.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${PV}/${PN}-src-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-IUSE=""
-KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
-
-DEPEND="dev-lang/perl"
-RDEPEND=""
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
-
-	if [[ ${CHOST} == *-darwin* ]]; then
-		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
-	fi
-
-	tc-export CC CXX AR RANLIB
-}
-
-src_compile() {
-	emake -C src
-}
-
-src_test () {
-	emake -C test | tee "${T}"/test.log
-	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
-}
-
-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
-	dohtml primer3_manual.htm
-}
diff --git a/sci-biology/primer3/primer3-2.3.7.ebuild b/sci-biology/primer3/primer3-2.3.7.ebuild
index d0dbc7363681..4c6c9ce7bf44 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
 }