3 files changed, 15 insertions, 68 deletions
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
deleted file mode 100644
index 7b1fbba5e075..000000000000
--- a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-DESCRIPTION="Sequence analysis using profile hidden Markov models"
-LICENSE="GPL-2"
-HOMEPAGE="http://hmmer.janelia.org/"
-SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
-
-SLOT="0"
-IUSE="pvm threads"
-KEYWORDS="~alpha amd64 ia64 ~ppc ~sparc x86"
-
-DEPEND="pvm? ( sys-cluster/pvm )"
-
-src_compile() {
-	./configure \
-		--host=${CHOST} \
-		--prefix="${D}"/usr \
-		--exec_prefix="${D}"/usr \
-		--mandir="${D}"/usr/share/man \
-		--enable-lfs \
-		$(use_enable pvm) \
-		$(use_enable threads) || die
-	emake || die
-}
-
-src_install() {
-	einstall || die
-
-	cd src
-	dolib libhmmer.a
-	insinto /usr/include/hmmer
-	doins *.h
-
-	cd ../squid
-	dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate
-	dolib libsquid.a
-	insinto /usr/include/hmmer
-	doins *.h
-
-	cd ..
-	dodoc NOTES
-	newdoc 00README README
-	insinto /usr/share/doc/${PF}
-	doins Userguide.pdf
-}
-
-src_test() {
-	make check
-}
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
index 64fa50030079..9868ec14eaae 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r3.ebuild
@@ -1,45 +1,47 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
+EAPI=6
+
 DESCRIPTION="Sequence analysis using profile hidden Markov models"
 LICENSE="GPL-2"
 HOMEPAGE="http://hmmer.janelia.org/"
 SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz"
 
 SLOT="0"
-IUSE="pvm threads"
-KEYWORDS="~alpha amd64 ~ia64 ~ppc ppc64 ~sparc x86"
+IUSE="threads test"
+KEYWORDS="~alpha amd64 ia64 ~ppc ppc64 ~sparc x86"
 
-DEPEND="pvm? ( sys-cluster/pvm )"
+DEPEND=""
+RDEPEND=""
 
-src_compile() {
+src_configure() {
 	econf \
 		--host=${CHOST} \
 		--prefix="${D}"/usr \
 		--exec_prefix="${D}"/usr \
 		--mandir="${D}"/usr/share/man \
 		--enable-lfs \
-		$(use_enable pvm) \
-		$(use_enable threads) || die
-	emake || die
+		$(use_enable threads)
 }
 
 src_install() {
-	einstall || die
+	emake DESTDIR="${D}" install
 
-	cd src
+	pushd src >/dev/null || die
 	dolib libhmmer.a
 	insinto /usr/include/hmmer
 	doins *.h
+	popd >/dev/null || die
 
-	cd ../squid
+	pushd squid >/dev/null || die
 	dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate
 	dolib libsquid.a
 	insinto /usr/include/hmmer
 	doins *.h
+	popd >/dev/null || die
 
-	cd ..
 	dodoc NOTES
 	newdoc 00README README
 	insinto /usr/share/doc/${PF}
@@ -47,5 +49,5 @@ src_install() {
 }
 
 src_test() {
-	make check
+	emake check
 }
diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
index a6a17ef25823..8417d1580d40 100644
--- a/sci-biology/hmmer/metadata.xml
+++ b/sci-biology/hmmer/metadata.xml
@@ -5,8 +5,4 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
-	<use>
-		<flag name="pvm">Add support for parallel virtual machine
-    (<pkg>sys-cluster/pvm</pkg>)</flag>
-	</use>
 </pkgmetadata>