gentoo auto-resync : 22:08:2024 - 12:26:19

4 files changed, 91 insertions, 6 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index b5ebc28c5f01..15208c4ebe35 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index 1626943dfb25..e2d6df08a8af 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,4 +1,6 @@
 AUX fasta-36.3.8h-ldflags.patch 2291 BLAKE2B 61c0b7d82a4c138e82148f354576fbeadf38362337ae6d2ecdb23aea5c4dbb3719f3889a0479ea2b48de8e2c3e19c5b61a7b9508507fd7f61289205b93e899ed SHA512 a34021b398e077a409bd31508b0736e7a0fda533d86b26efe998227ce628414796a0dfd88b0010154e25ef79148b1b9acac4cd94cb7aa72a59fbcbd1fbbb6726
 DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391
-EBUILD fasta-36.3.8h-r1.ebuild 1713 BLAKE2B de1276ea990e856cf562a5f970d180c3872c3ce6d3d8f73a50b398ff1408f7840872d90e690a9511cdbb14c586627c061389ad307c85b1a2662130aea66d0b33 SHA512 059b00c917565477765897b03656dfe8e67c2879ac8a78b2187edd0a5f0199f52dca45886dd8d2ac300ee0995697458fffa69e7704df951837b1c50d7ad92f9d
+DIST fasta-36.3.8i.tar.gz 1402674 BLAKE2B 5653ae18d38a8f99ac1a76235ebad7189faeaacf9a043ab81ec56036e851d45fcc47435413f81f989efc6dfbccd6e3235c9cd14a6f129719d978ffc69e5def0f SHA512 6f34bd1a5f74362fd569d9c8e7ca7c9fcb0648ea7e861c3d0b54bbdc32ba0caad4beb2aad204122178ee6bcefd579d824412a863163050c305da0a661d55c234
+EBUILD fasta-36.3.8h-r1.ebuild 1770 BLAKE2B 77f3ebcfa44b0dd96b73909ea5cfe772366985e688df007aed3205a159d5896c6be20e88ab9e294920e55452014db1f73c2fc9d0d0763c7e5bba53e89e99dc44 SHA512 d55d8345400033078b9d7e634bbf4881f2e69bb3e3c4f048f840cc44ac90af844496070836b21fd208203f98ef4cb80b0b256ccdd9a0674d83d8fef2f3398b18
+EBUILD fasta-36.3.8i.ebuild 1725 BLAKE2B 28655f72b4eccad925599f3811ba2ff86e5ea5a9d9eb90a37f1545269dea5549a47972044e41bf5e515faca12d2c42856d64439c4077419d69051bcdee168076 SHA512 0c4320a3238c93743e111864dccf73312abadd84f51a4ca8793c4d98a28e5b95185ce0f15d3c7c37ab4962e25898e8234acca1c27d4467bc9a9439ffdfd7df16
 MISC metadata.xml 344 BLAKE2B 75f42620d20abfbba91acae49acb672fe1b42fccf6227e358c1d94101c894226f51e9c2efe4014dd263b55a2940894eee9d8c96fb5ac6ff64c3c4ae6a426cc74 SHA512 13001db79cb9763ee83f1701e316287efdaef1ac5c4eab1249a1815df5ac6a34ff6b0f76e1706684058966b2201c642a2f8bda1d6d36473c0cdfbe00ca1d094a
diff --git a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
index 1cd7ca60dcde..b811765e502e 100644
--- a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
+++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -15,10 +15,7 @@ S="${WORKDIR}/${PN}36-${MY_PV}"
 LICENSE="fasta"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="debug cpu_flags_x86_sse2 test"
-RESTRICT="!test? ( test )"
-
-BDEPEND="test? ( app-shells/tcsh )"
+IUSE="debug cpu_flags_x86_sse2"
 
 src_prepare() {
 	CC_ALT=
@@ -45,6 +42,11 @@ src_prepare() {
 	export CC_ALT="${CC_ALT}"
 	export ALT="${ALT}"
 
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/862267
+	# https://github.com/wrpearson/fasta36/issues/63
+	filter-lto
+
 	eapply "${FILESDIR}"/${P}-ldflags.patch
 
 	sed \
diff --git a/sci-biology/fasta/fasta-36.3.8i.ebuild b/sci-biology/fasta/fasta-36.3.8i.ebuild
new file mode 100644
index 000000000000..6363b4b56f2d
--- /dev/null
+++ b/sci-biology/fasta/fasta-36.3.8i.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PV="${PV}_14-Nov-2020"
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}36-${MY_PV}"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="debug cpu_flags_x86_sse2"
+
+src_prepare() {
+	CC_ALT=
+	CFLAGS_ALT=
+	ALT=
+
+	use debug && append-flags -DDEBUG
+
+	if [[ "$(tc-getCC)" == *icc* ]]; then
+		CC_ALT=icc
+		ALT="${ALT}_icc"
+	else
+		CC_ALT="$(tc-getCC)"
+		use x86 && ALT="32"
+		use amd64 && ALT="64"
+	fi
+
+	if use cpu_flags_x86_sse2 ; then
+		ALT="${ALT}_sse2"
+		append-flags -msse2
+		[[ "$(tc-getCC)" == *icc* ]] || append-flags -ffast-math
+	fi
+
+	export CC_ALT="${CC_ALT}"
+	export ALT="${ALT}"
+
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/862267
+	# https://github.com/wrpearson/fasta36/issues/63
+	filter-lto
+
+	sed \
+		-e 's:-ffast-math::g' \
+		-i make/Makefile* || die
+
+	eapply_user
+}
+
+src_compile() {
+	emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS}" all
+}
+
+src_test() {
+	cd test || die
+	FASTLIBS="../conf" bash test.sh || die
+}
+
+src_install() {
+	dobin bin/*
+
+	pushd bin >/dev/null || die
+		local i
+		for i in *36; do
+			dosym ${i} /usr/bin/${i%36}
+		done
+	popd >/dev/null || die
+
+	insinto /usr/share/${PN}
+	doins -r conf/. data seq
+
+	doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
+	dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*}
+}