gentoo resync : 09.07.2022

4 files changed, 60 insertions, 28 deletions

diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
index e041a677a3af..3e02058f5767 100644
--- a/sci-biology/hmmer/Manifest
+++ b/sci-biology/hmmer/Manifest
@@ -1,9 +1,9 @@
 AUX hmmer-2.3.2-fix-build-system-destdir.patch 825 BLAKE2B 46264f43ed43a567c1f650710e1485942eb48a0b7ed3860424f00ca06cf04f9e923318c5df3d56eb312ed773bf2d42e22880b4ac6c2f81ac6c65bf2cebf44008 SHA512 f7eb3de5cbb1bf58b4ae4514e020ea059ad6a267e6f425494d8b444ac1bab056bc4709fed7f2793e68720b057ca1ac8c6dbca907125712d18dc05b77e37b1c3f
 AUX hmmer-2.3.2-fix-perl-shebangs.patch 2457 BLAKE2B 1afca014901d79416dac2c1d41e20371ef970aa3691a6b414e9a96adf8331c619753df7a42e1d9af63aab12a3fc8b8c7d2251129dd581bfb33a0d7c3e50970b2 SHA512 9597d77b3101c091bb1d005f36229cb6bedaf496a15da472495bb688fdb2750c94a38adc1236f3d90b0085caa78f61bddb350d51e0d3cc8dfa96edcdd5e2e5b9
-AUX hmmer-3.1_beta2-fix-header-install-path.patch 3202 BLAKE2B e6f8050c2edd11c890dc53bd6ba4cfaf6b537ab11ba45b88f497c0b62200029839df5f2adfa54612805ea87a5e252c9c198a52c1ba793a1c612ca99c3f8edb0b SHA512 ccaaff25a50a60526d0a16196b2b1d8cd57a7e9d016ce2b6b36ba1c0123966113b10965303dceb494810cd17a802514bba3a49d010ee6bbdc039715b84524d9a
 AUX hmmer-3.1_beta2-fix-perl-shebangs.patch 8605 BLAKE2B c0c78fed780b43df960dc24914e5dabe161243cec015deaf058d7eebf79c5e1633ded4f1305bb37b9766d74588009142fd58886e67810940e9601ef138647c21 SHA512 ce2c91c2d34d49dd5082a97ca0543bf3a176c792b4efd0cb37561114fc572b41d6cd546e16267283d33138ad54e2bb0c9c912c8fa1142e558a5452e9e72da2ff
+AUX hmmer-3.1_beta2-makefile.patch 3679 BLAKE2B e258b23bda9d0515891f1d571b94f9ef48499f25ce6cb52c3d1bcd0a28bc527f335cb25ece944afb33e4824438315cc9986243fb13e07eb128d7859e0a77f4b1 SHA512 bebd36deee48d4a043a1d84233ccbc93de8e44b5f7f57bf24a551b53a6f3dbfb3166861555755744d0abb4fce871d7c19fa8887c08115b7d8f61ca5ad38c3cc6
 DIST hmmer-2.3.2.tar.gz 1024933 BLAKE2B 34fdc7b24b28d653022c80a63b2fd8376c15c961e1550a04cb310943d165575a2721cc5e4cb516335f57414f8621b7e62c4e30ee1f107bb714e40c59ed37d418 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7
 DIST hmmer-3.1b2.tar.gz 5965253 BLAKE2B 38d1d6fb43aa814c0e3ddc551469ebd6b967f181c45df3802598f31abef10998595218167555a8862c0d2caa9118d9a7f1c22b673b6d596665f797ba903093f5 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771
-EBUILD hmmer-2.3.2-r4.ebuild 1655 BLAKE2B ffc67289bc761e07d60df1d87e11abcc311b1fccc1652d542b71e0914660f3ed03e4a6e540d76d2c38e0d5cb43c606496da34fcac48bb84ee08c2a4822f0c562 SHA512 f07e067a72e388ebaff6c4712173bd6e68004a778c36823bcc685c7727a81ca77b448d046f2dec599b9c760b0c45fc379971beef227d2f6d43917a13e75b6abb
-EBUILD hmmer-3.1_beta2.ebuild 1063 BLAKE2B a3469ebea515d16eb960fb5021ae7374b8736dbc0e0e933146f570478bf24cbfcee2eef59008126315669ab67cd70b569ddf401e07dd78b15a96e8d6b4329296 SHA512 fa75524ced910f633735ab72a1eb8d0ae0fd3ccc88dc12f98995b546fdd5084158509c8c99fe231450f5151dacc2b9477ee35090d9657401e47f8bd1dd0240b6
+EBUILD hmmer-2.3.2-r5.ebuild 1736 BLAKE2B 9ab5016f9a29c9d2dc22ed0456a064f14ea91c22d7a226aeeec02ad2c6766effb4a9933487aed37b335a113ab012829eb8aa583770e2ff01e934347445060a90 SHA512 18eb7ecb918ce4786ee1556fc641d1ca89c9255aa6009ea8b5d524752bad5046eeb50de9b0d5637b4c59cec624879d0c0f07698f5fe370aed7a25610aa377cca
+EBUILD hmmer-3.1_beta2-r1.ebuild 1140 BLAKE2B a5a0a26f2461edc08101505fa600383952501083111e828b4a0484a2c895acb63b3784247ea3a9b4fb10a13089a84f09f9721b4835cbb7b5479f0877e62c84aa SHA512 65889b5afe47d60abdd7ebb4d098510e8f25979e442df2a88d6327ab2fffc6d056fa6f96f32c0d37614473bc961c1e60fc3e194e535c5b6816b3c420816c5ea9
 MISC metadata.xml 262 BLAKE2B adaacf2ac22ce09f8b1b68f538773c1e2101156181ff302eca2ce1280ee5d45db4eb302a8eee1bbead5e55942443dd16ef924cfbfdc95a1658dc6a9f460468a2 SHA512 ac924b6b530d96645f173d40f7a2bf0e3abbf49048ebf7fadcea3dd553cd25504f0e68a103395de1fb59a2e5e11497dcead601be01cc6f0295ccbc4155f67e3f
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
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-2.3.2-r4.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
index a58b60f93288..b9f77b9dfce8 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
@@ -1,20 +1,21 @@
-# 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
 
 DESCRIPTION="Sequence analysis using profile hidden Markov models"
-LICENSE="GPL-2"
 HOMEPAGE="http://hmmer.org/"
 SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
 
+LICENSE="GPL-2"
 SLOT="2"
-IUSE="altivec test threads"
-RESTRICT="!test? ( test )"
 KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_ppc_altivec test"
+RESTRICT="!test? ( test )"
 
-DEPEND="test? ( dev-lang/perl )"
-RDEPEND=""
+BDEPEND="test? ( dev-lang/perl )"
 
 PATCHES=(
 	"${FILESDIR}/${P}-fix-perl-shebangs.patch"
@@ -28,8 +29,12 @@ src_configure() {
 
 	econf \
 		--enable-lfs \
-		$(use_enable altivec) \
-		$(use_enable threads)
+		--enable-threads \
+		$(use_enable cpu_flags_ppc_altivec altivec)
+}
+
+src_compile() {
+	emake AR="$(tc-getAR) rcs"
 }
 
 src_install() {
@@ -52,14 +57,14 @@ src_install() {
 	local i
 
 	# first rename man pages...
-	pushd "${ED%/}"/usr/share/man/man1/ >/dev/null || die
+	pushd "${ED}"/usr/share/man/man1/ >/dev/null || die
 	for i in hmm*.1; do
 		mv ${i%.1}{,2}.1 || die
 	done
 	popd >/dev/null || die
 
 	# ... then rename binaries
-	pushd "${ED%/}"/usr/bin/ >/dev/null || die
+	pushd "${ED}"/usr/bin/ >/dev/null || die
 	for i in hmm*; do
 		mv ${i}{,2} || die
 	done
diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/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
 }