sci-biology/infernal: respect EPREFIX

Closes: https://github.com/gentoo/gentoo/pull/3774

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 5bc5bd008ff614ce83d84516e23451a4ad5bb19a..f688dce152ed4238c73453d72daeef20a4f7157f 100644 (file)
--- 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 b9791fa1ca2ea2cbbbb949bd616fb431f3f9d483..67190c4c1d42d4e836102ed7c3c9ac547a51c507 100644 (file)
--- 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 004742546f003711199c36fed2ac0a73f945bfc7..67ffa6fda7f6379777f6c1bd761dbf2a2043f371 100644 (file)
--- 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 (file)
index 0000000..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 3c0ca9aa7b12f28484fdd517deb7e35b594c3d51..ad87152391e805cb2e38e7b245047a4528407e79 100644 (file)
--- 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/*
 }