[gentoo-commits] repo/gentoo:master commit in: sci-biology/infernal/files/, sci-biology/infernal/

[David Seifert]

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/*
 }