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 B0F3E158094 for ; Sat, 9 Jul 2022 09:54:08 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 85AFBE07EA; Sat, 9 Jul 2022 09:54:07 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 48620E07D4 for ; Sat, 9 Jul 2022 09:54:07 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 5581C340E78 for ; Sat, 9 Jul 2022 09:54:06 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id A7DCB4EC for ; Sat, 9 Jul 2022 09:54:04 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1657360438.01ccd8f6eb167dedd81a5ba3a3282f9e36893c4b.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/trnascan-se/, sci-biology/trnascan-se/files/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch sci-biology/trnascan-se/trnascan-se-1.31.ebuild X-VCS-Directories: sci-biology/trnascan-se/ sci-biology/trnascan-se/files/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 01ccd8f6eb167dedd81a5ba3a3282f9e36893c4b X-VCS-Branch: master Date: Sat, 9 Jul 2022 09:54:04 +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: 5a7569f0-28a7-43be-ad2e-00959dd72f45 X-Archives-Hash: 540bb30bd0eb77ba17184e39c7f71b6c commit: 01ccd8f6eb167dedd81a5ba3a3282f9e36893c4b Author: David Seifert gentoo org> AuthorDate: Sat Jul 9 09:53:58 2022 +0000 Commit: David Seifert gentoo org> CommitDate: Sat Jul 9 09:53:58 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=01ccd8f6 sci-biology/trnascan-se: drop 1.31 Signed-off-by: David Seifert gentoo.org> .../files/trnascan-se-1.31-ldflags.patch | 26 ----------- sci-biology/trnascan-se/trnascan-se-1.31.ebuild | 54 ---------------------- 2 files changed, 80 deletions(-) diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch deleted file mode 100644 index f28b1e8f6bb0..000000000000 --- a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch +++ /dev/null @@ -1,26 +0,0 @@ -diff --git a/Makefile b/Makefile -index 53e5c5b..a2d3feb 100644 ---- a/Makefile -+++ b/Makefile -@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o - all: $(PROGS) tRNAscan-SE setpaths - - covels-SE: $(OBJ) scan_main.o -- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) - - coves-SE: $(OBJ) score_main.o -- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) - - eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o -- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \ - pavesi.o $(SQUIDOBJ) $(LIBS) - - trnascan-1.4: trnascan.o -- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c -+ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c - - tRNAscan-SE: - $(PERLDIR)/$(PERLBIN) checkversion.pl diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild deleted file mode 100644 index cd8dc152d6d2..000000000000 --- a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit perl-functions toolchain-funcs - -DESCRIPTION="tRNA detection in large-scale genome sequences" -HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/" -SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" - -S="${WORKDIR}"/tRNAscan-SE-1.3.1/ - -PATCHES=( - "${FILESDIR}"/${P}-ldflags.patch -) - -src_prepare() { - default - sed \ - -e "s:BINDIR = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \ - -e "s:LIBDIR = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \ - -e "s:MANDIR = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \ - -i Makefile || die - - perl_set_version -} - -src_test() { - emake PATH="${S}:${PATH}" testrun -} - -src_install() { - dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 - - newman tRNAscan-SE.man tRNAscan-SE.man.1 - - dodoc MANUAL README Release.history - - insinto /usr/share/${PN}/ - doins *.cm gcode.* Dsignal TPCsignal - - dodoc Manual.ps - - insinto ${VENDOR_LIB} - doins -r tRNAscanSE -}