commit: d31ff028511de2e2cc29e125cae3a6862aa6e2ec
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 7 19:56:56 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Jul 7 19:56:56 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d31ff028
sci-biology/hmmer: update EAPI 6 -> 8 (3.1_beta2)
Signed-off-by: David Seifert <soap <AT> gentoo.org>
...l-path.patch => hmmer-3.1_beta2-makefile.patch} | 23 +++++++++++++++-
...-3.1_beta2.ebuild => hmmer-3.1_beta2-r1.ebuild} | 32 +++++++++++++---------
2 files changed, 41 insertions(+), 14 deletions(-)
diff --git
a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch
similarity index 85%
rename from
sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
rename to sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch
index b9ff5b92b8f9..1c08d67e7bdd 100644
--- a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
+++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch
@@ -1,4 +1,5 @@
-Install headers into 'hmmer3' subdir and not into global includedir.
+* Install headers into 'hmmer3' subdir and not into global includedir
+* Respect AR
--- a/easel/Makefile.in
+++ b/easel/Makefile.in
@@ -17,6 +18,26 @@ Install headers into 'hmmer3' subdir and not into global
includedir.
${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} install
# "make uninstall" reverses the steps of "make install"
+--- a/libdivsufsort/Makefile.in
++++ b/libdivsufsort/Makefile.in
+@@ -16,7 +16,7 @@
+ CFLAGS = @CFLAGS@ @PTHREAD_CFLAGS@ @PIC_FLAGS@
+ CPPFLAGS = @CPPFLAGS@
+ MPILIBS = @MPILIBS@
+-AR = @AR@ rc
++AR = @AR@
+ RANLIB = @RANLIB@
+ INSTALL = @INSTALL@
+
+@@ -43,7 +43,7 @@
+
+
+ libdivsufsort.a: $(OBJS)
+- ${QUIET_AR}${AR} libdivsufsort.a $(OBJS)
++ ${QUIET_AR}${AR} rc libdivsufsort.a $(OBJS)
+ @${RANLIB} libdivsufsort.a
+ @chmod 644 libdivsufsort.a
+
--- a/Makefile.in
+++ b/Makefile.in
@@ -143,6 +143,7 @@
diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
similarity index 60%
rename from sci-biology/hmmer/hmmer-3.1_beta2.ebuild
rename to sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
index b65fa0824f9b..666d21cd5532 100644
--- a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
+++ b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
@@ -1,49 +1,55 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
+
+inherit toolchain-funcs
MY_PV="${PV/_beta/b}"
DESCRIPTION="Sequence analysis using profile hidden Markov models"
HOMEPAGE="http://hmmer.org/";
SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz";
+S="${WORKDIR}/${PN}-${MY_PV}"
LICENSE="GPL-3"
SLOT="0"
-IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads"
-RESTRICT="!test? ( test )"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="cpu_flags_ppc_altivec cpu_flags_x86_sse gsl mpi test"
+RESTRICT="!test? ( test )"
RDEPEND="
mpi? ( virtual/mpi )
gsl? ( sci-libs/gsl:= )"
-DEPEND="${RDEPEND}
- test? ( dev-lang/perl )"
+DEPEND="${RDEPEND}"
+BDEPEND="test? ( dev-lang/perl )"
-S="${WORKDIR}/${PN}-${MY_PV}"
PATCHES=(
- "${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch"
- "${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch"
+ "${FILESDIR}"/${PN}-3.1_beta2-fix-perl-shebangs.patch
+ "${FILESDIR}"/${PN}-3.1_beta2-makefile.patch
)
src_configure() {
- # make build verbose, bug 429308
+ # make build verbose, bug #429308
export V=1
econf \
--disable-pic \
- $(use_enable altivec vmx) \
+ --enable-threads \
+ $(use_enable cpu_flags_ppc_altivec vmx) \
$(use_enable cpu_flags_x86_sse sse) \
$(use_enable mpi) \
- $(use_enable threads) \
$(use_with gsl)
}
+src_compile() {
+ emake AR="$(tc-getAR)"
+}
+
src_install() {
default
dodoc Userguide.pdf
- insinto /usr/share/${PN}
+ insinto /usr/share/hmmer
doins -r tutorial
}
