From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id A0BC415852A for ; Thu, 22 Aug 2024 04:17:54 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id BE9A22BC017; Thu, 22 Aug 2024 04:17:53 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 7C8A62BC017 for ; Thu, 22 Aug 2024 04:17:53 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 7BF6A340C39 for ; Thu, 22 Aug 2024 04:17:52 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id DD0A71F03 for ; Thu, 22 Aug 2024 04:17:50 +0000 (UTC) From: "Eli Schwartz" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Eli Schwartz" Message-ID: <1724300231.17f6c86d219f1f04c0cb2852ce1cd810169985a2.eschwartz@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/fasta/Manifest sci-biology/fasta/fasta-36.3.8i.ebuild X-VCS-Directories: sci-biology/fasta/ X-VCS-Committer: eschwartz X-VCS-Committer-Name: Eli Schwartz X-VCS-Revision: 17f6c86d219f1f04c0cb2852ce1cd810169985a2 X-VCS-Branch: master Date: Thu, 22 Aug 2024 04:17:50 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: aa1ada2e-7a56-4de4-86b3-3661d71aa158 X-Archives-Hash: fbdf9f020b1dd3d9f7237589d6780182 commit: 17f6c86d219f1f04c0cb2852ce1cd810169985a2 Author: Eli Schwartz gentoo org> AuthorDate: Thu Aug 22 04:14:40 2024 +0000 Commit: Eli Schwartz gentoo org> CommitDate: Thu Aug 22 04:17:11 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=17f6c86d sci-biology/fasta: add 36.3.8i A 2022 release, how modern. :D Ignore the part where the tag name contains the date "2020". It obsoletes the patch as well, which seems good. However it does NOT fix the LTO issue. Signed-off-by: Eli Schwartz gentoo.org> sci-biology/fasta/Manifest | 1 + sci-biology/fasta/fasta-36.3.8i.ebuild | 81 ++++++++++++++++++++++++++++++++++ 2 files changed, 82 insertions(+) diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest index c0bd97106d3a..8144c91b5e78 100644 --- a/sci-biology/fasta/Manifest +++ b/sci-biology/fasta/Manifest @@ -1 +1,2 @@ DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391 +DIST fasta-36.3.8i.tar.gz 1402674 BLAKE2B 5653ae18d38a8f99ac1a76235ebad7189faeaacf9a043ab81ec56036e851d45fcc47435413f81f989efc6dfbccd6e3235c9cd14a6f129719d978ffc69e5def0f SHA512 6f34bd1a5f74362fd569d9c8e7ca7c9fcb0648ea7e861c3d0b54bbdc32ba0caad4beb2aad204122178ee6bcefd579d824412a863163050c305da0a661d55c234 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*} +}