[gentoo-commits] repo/gentoo:master commit in: sci-libs/libmuscle/files/, sci-libs/libmuscle/

[David Seifert]

commit:     8aca469b7b450488c3312fa2183433d9fcf42712
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Wed Mar  1 20:14:25 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Wed Mar  1 20:34:50 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8aca469b

sci-libs/libmuscle: Modernise to EAPI 6

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-libs/libmuscle/files/3.7-bufferoverflow.patch  |  8 ++---
 .../files/libmuscle-3.7-fix-build-system.patch     | 21 ++++++++++++
 sci-libs/libmuscle/libmuscle-3.7-r3.ebuild         | 40 ++++++++++++++++++++++
 3 files changed, 65 insertions(+), 4 deletions(-)

diff --git a/sci-libs/libmuscle/files/3.7-bufferoverflow.patch b/sci-libs/libmuscle/files/3.7-bufferoverflow.patch
index c34b8ccacbd..384f17acfbf 100644
--- a/sci-libs/libmuscle/files/3.7-bufferoverflow.patch
+++ b/sci-libs/libmuscle/files/3.7-bufferoverflow.patch
@@ -1,5 +1,5 @@
---- libMUSCLE/globalslinux.cpp.old	2010-03-14 19:03:14.000000000 +1300
-+++ libMUSCLE/globalslinux.cpp	2010-03-14 19:11:09.000000000 +1300
+--- a/libMUSCLE/globalslinux.cpp
++++ b/libMUSCLE/globalslinux.cpp
 @@ -159,7 +159,7 @@
  			}
  		return DEFAULT_RAM;
@@ -9,8 +9,8 @@
  	return ((double) Bytes)/1e6;
  	}
  
---- libMUSCLE/progress.cpp.old	2010-03-14 19:50:27.000000000 +1300
-+++ libMUSCLE/progress.cpp	2010-03-14 19:51:07.000000000 +1300
+--- a/libMUSCLE/progress.cpp
++++ b/libMUSCLE/progress.cpp
 @@ -48,7 +48,7 @@
  	if (MB < 0)
  		return "";

diff --git a/sci-libs/libmuscle/files/libmuscle-3.7-fix-build-system.patch b/sci-libs/libmuscle/files/libmuscle-3.7-fix-build-system.patch
new file mode 100644
index 00000000000..2b2c28c8132
--- /dev/null
+++ b/sci-libs/libmuscle/files/libmuscle-3.7-fix-build-system.patch
@@ -0,0 +1,21 @@
+* Make build system parallel buildable
+* Remove -funroll-loops and friends
+
+--- a/libMUSCLE/Makefile.am
++++ b/libMUSCLE/Makefile.am
+@@ -1,6 +1,4 @@
+-OPTIMIZATION = -O2 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations
+-AM_CXXFLAGS = $(OPTIMIZATION) -DNDEBUG=1 @OPENMP_CXXFLAGS@
+-AM_LDFLAGS = $(OPTIMIZATION)
++AM_CXXFLAGS = -DNDEBUG=1 @OPENMP_CXXFLAGS@
+ 
+ LIBMUSCLE_H = \
+ alpha.h cluster.h clust.h clustsetdf.h clustset.h clustsetmsa.h diaglist.h distcalc.h distfunc.h dpregionlist.h dpreglist.h edgelist.h enumopts.h enums.h estring.h gapscoredimer.h gonnet.h intmath.h msadist.h msa.h muscle.h objscore.h params.h profile.h pwpath.h refine.h scorehistory.h seq.h seqvect.h textfile.h timing.h tree.h types.h unixio.h threadstorage.h 
+@@ -36,6 +34,6 @@
+ 
+ 
+ muscle_SOURCES = main.cpp
+-muscle_LDADD = $(top_builddir)/libMUSCLE/libMUSCLE-3.7.la
++muscle_LDADD = libMUSCLE-3.7.la
+ 
+ 

diff --git a/sci-libs/libmuscle/libmuscle-3.7-r3.ebuild b/sci-libs/libmuscle/libmuscle-3.7-r3.ebuild
new file mode 100644
index 00000000000..d3a8107c105
--- /dev/null
+++ b/sci-libs/libmuscle/libmuscle-3.7-r3.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="Library for sci-biology/mauve"
+HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/"
+SRC_URI="mirror://gentoo/${P}-r1.tar.bz2"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc static-libs"
+
+RDEPEND="!sci-biology/muscle"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen )"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-bufferoverflow.patch
+	"${FILESDIR}"/${PN}-3.7-fix-build-system.patch
+)
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	econf $(use_enable static-libs static)
+}
+
+src_install() {
+	default
+
+	# package provides .pc file
+	find "${D}" -name '*.la' -delete || die
+}