commit: 2e9f162bea114cf4cdf1b1f37d539592b499032c Author: Martin Mokrejš <mmokrejs <AT> gmail <DOT> com> AuthorDate: Thu Feb 2 14:35:38 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Thu Feb 2 19:18:51 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2e9f162b
sci-biology/infernal: respect EPREFIX Closes: https://github.com/gentoo/gentoo/pull/3774 .../infernal/files/infernal-1.0.2-ldflags.patch | 4 +-- .../infernal/files/infernal-1.0.2-overflows.patch | 4 +-- .../files/infernal-1.0.2-parallel-build.patch | 8 ++--- .../files/infernal-1.0.2-respect-DESTDIR.patch | 16 +++++++++ sci-biology/infernal/infernal-1.0.2-r1.ebuild | 39 ++++++++++------------ 5 files changed, 42 insertions(+), 29 deletions(-) diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch index 5bc5bd0..f688dce 100644 --- a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch +++ b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch @@ -2,8 +2,8 @@ Respect LDFLAGS http://bugs.gentoo.org/show_bug.cgi?id=338177 ---- src/Makefile.in -+++ src/Makefile.in +--- a/src/Makefile.in ++++ b/src/Makefile.in @@ -86,7 +86,7 @@ all: $(PROGS) diff --git a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch index b9791fa..67190c4 100644 --- a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch +++ b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch @@ -2,8 +2,8 @@ Fix buffer overflow http://bugs.gentoo.org/show_bug.cgi?id=338179 ---- easel/esl_getopts.c -+++ easel/esl_getopts.c +--- a/easel/esl_getopts.c ++++ b/easel/esl_getopts.c @@ -1270,7 +1270,7 @@ "Arg looks like option? Use %.24s%.24s if you really mean it.", g->opt[opti].name, *ret_optarg); diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch index 0047425..67ffa6f 100644 --- a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch +++ b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch @@ -2,8 +2,8 @@ Fix parallel build http://bugs.gentoo.org/show_bug.cgi?id=311919 ---- Makefile.in -+++ Makefile.in +--- a/Makefile.in ++++ b/Makefile.in @@ -82,9 +82,10 @@ all: core @@ -18,8 +18,8 @@ http://bugs.gentoo.org/show_bug.cgi?id=311919 #.PHONY: $(RIGFILTERS) #$(RIGFILTERS): core ---- easel/Makefile.in -+++ easel/Makefile.in +--- a/easel/Makefile.in ++++ b/easel/Makefile.in @@ -132,7 +132,7 @@ esl_wuss.o diff --git a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch new file mode 100644 index 00000000..ea465e5 --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch @@ -0,0 +1,16 @@ +Build system does not respect DESTDIR by default. + +--- a/Makefile.in ++++ b/Makefile.in +@@ -203,9 +203,9 @@ + # "make install" installs the programs in BINDIR + # + install: +- mkdir -p ${BINDIR} ++ mkdir -p $(DESTDIR)${BINDIR} + for file in $(PROGS); do\ +- cp src/$$file $(BINDIR)/;\ ++ cp src/$$file $(DESTDIR)$(BINDIR)/;\ + done + # if test -d $(RIGFILTERS); then\ + # for file in $(RFPROGS); do\ diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild index 3c0ca9a..ad87152 100644 --- a/sci-biology/infernal/infernal-1.0.2-r1.ebuild +++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild @@ -1,10 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ -EAPI=4 - -inherit eutils +EAPI=6 DESCRIPTION="Inference of RNA alignments" HOMEPAGE="http://infernal.janelia.org/"; @@ -15,33 +13,32 @@ SLOT="0" IUSE="mpi" KEYWORDS="amd64 x86" -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" +RDEPEND="mpi? ( virtual/mpi )" +DEPEND="${RDEPEND}" -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-parallel-build.patch \ - "${FILESDIR}"/${P}-overflows.patch \ - "${FILESDIR}"/${P}-perl-5.16-2.patch \ - "${FILESDIR}"/${P}-ldflags.patch -} +PATCHES=( + "${FILESDIR}"/${P}-parallel-build.patch + "${FILESDIR}"/${P}-overflows.patch + "${FILESDIR}"/${P}-perl-5.16-2.patch + "${FILESDIR}"/${P}-ldflags.patch + "${FILESDIR}"/${P}-respect-DESTDIR.patch +) src_configure() { - econf \ - --prefix="${D}/usr" \ - $(use_enable mpi) + econf $(use_enable mpi) } src_install() { + DOCS=( 00README* Userguide.pdf documentation/release-notes ) default - pushd documentation/manpages > /dev/null - for i in *; - do newman ${i} ${i/.man/.1} + pushd documentation/manpages >/dev/null || die + local i + for i in *.man; do + newman "${i}" "${i/.man/.1}" done - popd > /dev/null + pushd >/dev/null || die insinto /usr/share/${PN} doins -r benchmarks tutorial intro matrices - dodoc 00README* Userguide.pdf documentation/release-notes/* }
