commit: 7b52bc0205bc66c7e130b7794a76b5c455395232 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Dec 24 18:24:32 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Dec 24 19:46:02 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7b52bc02
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(-) 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 }
