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authorDavid Seifert <soap@gentoo.org>2017-12-24 19:24:32 +0100
committerDavid Seifert <soap@gentoo.org>2017-12-24 20:46:02 +0100
commit7b52bc0205bc66c7e130b7794a76b5c455395232 (patch)
tree43f0300c42bce492178083540bf2689570ba74b1 /sci-biology
parentsys-process/procps: x86 stable wrt byg #635300 (diff)
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sci-biology/primer3: Fix building with GCC 7
Closes: https://bugs.gentoo.org/638604 Package-Manager: Portage-2.3.19, Repoman-2.3.6
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/primer3/files/primer3-2.3.7-gcc7.patch17
-rw-r--r--sci-biology/primer3/primer3-2.3.7.ebuild24
2 files changed, 32 insertions, 9 deletions
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
}