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 TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 5827D1382C5 for ; Sat, 20 Feb 2021 23:26:40 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 993E5E088F; Sat, 20 Feb 2021 23:26:39 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 83184E088F for ; Sat, 20 Feb 2021 23:26:39 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id EE482340E3C for ; Sat, 20 Feb 2021 23:26:35 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id CEE654C6 for ; Sat, 20 Feb 2021 23:26:17 +0000 (UTC) From: "Jakov Smolić" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Jakov Smolić" Message-ID: <1613858261.9abaa3304eb07a14b179b925cffd428a8ffd4681.jakov.smolic@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/grappa/files/, sci-biology/grappa/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/grappa/files/grappa-2.0-inline.patch sci-biology/grappa/grappa-2.0.ebuild X-VCS-Directories: sci-biology/grappa/files/ sci-biology/grappa/ X-VCS-Committer: jakov.smolic X-VCS-Committer-Name: Jakov Smolić X-VCS-Revision: 9abaa3304eb07a14b179b925cffd428a8ffd4681 X-VCS-Branch: master Date: Sat, 20 Feb 2021 23:26:17 +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: 55cf819a-e6e1-4f56-994c-e50d766815c0 X-Archives-Hash: a799a027df2d5ca684a9f6f1c9c69d43 commit: 9abaa3304eb07a14b179b925cffd428a8ffd4681 Author: Jakov Smolic sartura hr> AuthorDate: Sat Feb 20 20:52:34 2021 +0000 Commit: Jakov Smolić sartura hr> CommitDate: Sat Feb 20 21:57:41 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9abaa330 sci-biology/grappa: Apply gcc-10 workaround Closes: https://bugs.gentoo.org/755311 Signed-off-by: Jakov Smolic sartura.hr> sci-biology/grappa/files/grappa-2.0-inline.patch | 18 ++++++++++++++++++ sci-biology/grappa/grappa-2.0.ebuild | 9 +++++++++ 2 files changed, 27 insertions(+) diff --git a/sci-biology/grappa/files/grappa-2.0-inline.patch b/sci-biology/grappa/files/grappa-2.0-inline.patch new file mode 100644 index 000000000..a78f394e6 --- /dev/null +++ b/sci-biology/grappa/files/grappa-2.0-inline.patch @@ -0,0 +1,18 @@ +--- a/greedy_median.c ++++ b/greedy_median.c +@@ -7,7 +7,6 @@ + chosen, including the original */ + + /* i->succ1[i] is the chosen adjacency */ +-INLINE int + finish1 ( int i, int *count, int *degree, int *succ1, int *succ2, + int *pred1, int *pred2, int *tour, int *otherEnd, int num_genes ) + { +@@ -82,7 +81,6 @@ finish1 ( int i, int *count, int *degree, int *succ1, int *succ2, + + + /* i->succ2[i] is the chosen adjacency */ +-INLINE int + finish2 ( int i, int *count, int *degree, int *succ1, int *succ2, + int *pred1, int *pred2, int *tour, int *otherEnd, int num_genes ) + { diff --git a/sci-biology/grappa/grappa-2.0.ebuild b/sci-biology/grappa/grappa-2.0.ebuild index ceb0c34c9..df0392717 100644 --- a/sci-biology/grappa/grappa-2.0.ebuild +++ b/sci-biology/grappa/grappa-2.0.ebuild @@ -3,6 +3,8 @@ EAPI=7 +inherit flag-o-matic + MY_P="GRAPPA20" DESCRIPTION="Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms" @@ -15,11 +17,18 @@ KEYWORDS="~amd64 ~x86" S="${WORKDIR}/${MY_P}" +PATCHES=( "${FILESDIR}"/${P}-inline.patch ) + src_prepare() { default sed -i -e '/CFLAGS := -mcpu/ d' -e 's/\(CFLAGS := -D${OS}\)/\1 ${CFLAGS}/' "${S}/Makefile" || die } +src_configure() { + append-cflags -fcommon + default +} + src_install() { dobin grappa dosym grappa /usr/bin/invdist