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commit: e69a19faa0ffec52ff1aeac557daae9b115f0182 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Feb 26 12:25:06 2017 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Feb 26 12:40:33 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e69a19fa |
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|
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sci-biology/blossoc: Modernise to EAPI 6 |
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|
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Package-Manager: Portage-2.3.3, Repoman-2.3.1 |
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RepoMan-Options: --force |
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Closes: https://github.com/gentoo/gentoo/pull/4083 |
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|
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sci-biology/blossoc/blossoc-1.4.0-r1.ebuild | 37 +++ |
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.../files/blossoc-1.4.0-fix-build-system.patch | 256 +++++++++++++++++++++ |
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.../blossoc/files/blossoc-1.4.0-gcc43.patch | 4 +- |
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3 files changed, 295 insertions(+), 2 deletions(-) |
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|
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diff --git a/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild |
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new file mode 100644 |
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index 0000000000..01dbd27dd0 |
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--- /dev/null |
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+++ b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild |
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@@ -0,0 +1,37 @@ |
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+# Copyright 1999-2017 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Id$ |
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+ |
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+EAPI=6 |
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+ |
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+inherit autotools |
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+ |
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+DESCRIPTION="A linkage disequilibrium association mapping tool" |
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+HOMEPAGE="http://www.daimi.au.dk/~mailund/Blossoc/" |
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+SRC_URI="http://www.daimi.au.dk/~mailund/Blossoc/download/${P}.tar.gz" |
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+ |
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+LICENSE="GPL-3" |
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+SLOT="0" |
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+IUSE="" |
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+KEYWORDS="~amd64 ~x86" |
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+ |
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+RDEPEND=" |
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+ sci-libs/gsl:= |
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+ dev-libs/boost:= |
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+ sci-biology/snpfile" |
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+DEPEND=" |
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+ ${RDEPEND} |
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+ >=sys-devel/autoconf-archive-2016.09.16 |
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+ virtual/pkgconfig" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}"/${PN}-1.4.0-gcc43.patch |
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+ "${FILESDIR}"/${PN}-1.4.0-fix-build-system.patch |
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+) |
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+ |
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+src_prepare() { |
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+ default |
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+ mv configure.{in,ac} || die |
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+ rm m4/ax_boost.m4 || die |
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+ eautoreconf |
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+} |
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|
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diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch |
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new file mode 100644 |
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index 0000000000..21234cc3cf |
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--- /dev/null |
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+++ b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch |
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@@ -0,0 +1,256 @@ |
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+* Modernise Autoconf code |
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+* Use pkg-config for finding GSL |
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+* Use latest archvie macros to find Boost |
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+* Compile tests only when running make check |
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+ |
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+--- a/configure.in |
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++++ b/configure.in |
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+@@ -1,6 +1,6 @@ |
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+ AC_INIT(blossoc, 1.4.0, mailund@×××××××.dk) |
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+ AM_INIT_AUTOMAKE |
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+-AM_CONFIG_HEADER(config.hh) |
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++AC_CONFIG_HEADERS([config.hh]) |
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+ |
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+ AC_PROG_CXX |
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+ AC_PROG_INSTALL |
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+@@ -12,74 +12,16 @@ |
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+ fi |
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+ AC_DEFINE_UNQUOTED(PREFIX, "$thePREFIX", [Installation prefix]) |
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+ |
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+-AC_CHECK_LIB(m, sin, dnl FOUND, DO NOTHING |
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+-, dnl NOT FOUND |
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+-AC_ERROR([[ |
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+-************************************************************************ |
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+-************************************************************************ |
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+-Didn't find the math library (-lm) -- I won't even guess about what is |
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+-wrong on this machine... |
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+-************************************************************************ |
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+-************************************************************************ |
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+-]]) |
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+-) |
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+- |
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+-AX_BOOST([1.33.1],, |
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+-AC_ERROR([[ |
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+-************************************************************************ |
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+-************************************************************************ |
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+-The Boost library was not found on this system. We use this library |
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+-extensively, and cannot proceed without it. You can obtain it from |
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+-<http://www.boost.org>. |
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+-************************************************************************ |
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+-************************************************************************ |
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+-]]) |
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+-) |
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+- |
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+- |
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+-AC_CHECK_LIB(gslcblas, cblas_dsdot, dnl FOUND, DO NOTHING |
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+-, dnl NOT FOUND |
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+-AC_ERROR([[ |
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+-************************************************************************ |
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+-************************************************************************ |
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+-The GNU Scientific Library (GSL) was not found. This library is |
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+-needed for some of the numerical calculations used for scoring the |
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+-significance of local genealogies and can be obtained at |
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+-<http://www.gnu.org/software/gsl/>. |
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+-************************************************************************ |
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+-************************************************************************ |
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+-]]) |
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+-) |
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+- |
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+-AC_CHECK_LIB(gsl, gsl_cdf_chisq_Q, dnl FOUND, DO NOTHING |
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+-, dnl NOT FOUND |
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+-AC_ERROR([[ |
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+-************************************************************************ |
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+-************************************************************************ |
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+-The GNU Scientific Library (GSL) was not found. This library is |
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+-needed for some of the numerical calculations used for scoring the |
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+-significance of local genealogies and can be obtained at |
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+-<http://www.gnu.org/software/gsl/>. |
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+-************************************************************************ |
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+-************************************************************************ |
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+-]]) |
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+-) |
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+- |
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+-AC_CHECK_LIB(snpfile, main, dnl main isn't there, but this avoids namespaces |
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+-dnl FOUND |
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+-, |
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+-dnl NOT FOUND |
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+-AC_ERROR([[ |
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+-************************************************************************ |
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+-************************************************************************ |
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+-The SNPFile library was not found. This library is needed for data |
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+-representation and can be obtained at |
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+-<http://www.birc.au.dk/~mailund/SNPFile/>. |
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+-************************************************************************ |
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+-************************************************************************ |
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+-]]) |
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+-) |
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+- |
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++AC_SEARCH_LIBS([sin], [m], [], [ |
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++ AC_MSG_ERROR([unable to find the sin() function]) |
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++]) |
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++ |
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++PKG_CHECK_MODULES([GSL], [gsl]) |
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++ |
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++AX_BOOST_BASE([1.33.1]) |
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++AX_BOOST_PROGRAM_OPTIONS |
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++AX_BOOST_SERIALIZATION |
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++AX_BOOST_SIGNALS |
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+ |
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+ AC_OUTPUT([ |
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+ Makefile |
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+--- a/Makefile.am |
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++++ b/Makefile.am |
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+@@ -3,9 +3,6 @@ |
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+ AM_CXXFLAGS += -Wall |
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+ AM_CXXFLAGS += $(BOOST_CPPFLAGS) |
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+ |
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+-# for testing |
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+-AM_CXXFLAGS += -g -O0 #-lefence |
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+- |
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+ # for coverage testing |
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+ #AM_CXXFLAGS += -O3 -fexpensive-optimizations -g -fprofile-arcs -ftest-coverage |
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+ |
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+@@ -15,11 +12,11 @@ |
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+ # for production |
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+ #AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG |
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+ |
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+-noinst_PROGRAMS = |
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++check_PROGRAMS = |
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++noinst_PROGRAMS = |
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+ TESTS = |
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+ EXTRA_DIST = |
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+ |
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+-TESTS += first_test.sh |
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+ EXTRA_DIST += first_test.sh |
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+ |
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+ man_MANS = blossoc.1 snpfile_blossoc.1 blossoc_regions.1 blossoc_trees.1 |
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+@@ -37,20 +34,20 @@ |
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+ noinst_PROGRAMS += snpfile_iblossoc #ditto |
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+ noinst_PROGRAMS += fast_snpfile_iblossoc |
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+ |
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+-noinst_PROGRAMS += matrix_test |
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+-TESTS += matrix_test |
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+-noinst_PROGRAMS += incompatibility_test tree_test tree_builder_test |
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+-TESTS += incompatibility_test tree_test tree_builder_test |
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++check_PROGRAMS += matrix_test |
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++TESTS += matrix_test |
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++check_PROGRAMS += incompatibility_test tree_test tree_builder_test |
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++TESTS += incompatibility_test tree_test tree_builder_test |
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+ EXTRA_DIST += testdata/CF/cf-positions.txt |
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+ EXTRA_DIST += testdata/CF/cf-haplotypes.txt |
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+ EXTRA_DIST += testdata/interaction/positions.txt |
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+ EXTRA_DIST += testdata/interaction/haplotypes.txt |
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+-noinst_PROGRAMS += score_test io_test |
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+-TESTS += score_test io_test |
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+-noinst_PROGRAMS += incompatible_regress_test |
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+-TESTS += incompatible_regress_test |
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+-noinst_PROGRAMS += genotype_score_test |
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+-TESTS += genotype_score_test.sh |
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++check_PROGRAMS += score_test io_test |
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++TESTS += score_test io_test |
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++check_PROGRAMS += incompatible_regress_test |
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++TESTS += incompatible_regress_test |
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++check_PROGRAMS += genotype_score_test |
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++TESTS += genotype_score_test.sh |
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+ EXTRA_DIST += genotype_score_test.sh |
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+ EXTRA_DIST += genotype_score_test.expected |
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+ TESTS += interactions_regression_test.sh |
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+@@ -120,6 +117,7 @@ |
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+ |
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+ |
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+ blossoc_regions_LDADD = |
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++blossoc_regions_LDADD += -lsnpfile |
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+ blossoc_regions_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
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+ blossoc_regions_SOURCES = |
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+ blossoc_regions_SOURCES += incompatibility.hh incompatibility.cc |
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+@@ -129,6 +127,7 @@ |
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+ blossoc_regions_SOURCES += regions.cc |
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+ |
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+ blossoc_trees_LDADD = |
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++blossoc_trees_LDADD += -lsnpfile |
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+ blossoc_trees_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
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+ blossoc_trees_SOURCES = |
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+ blossoc_trees_SOURCES += matrix_utils.hh matrix_utils.cc |
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+@@ -142,6 +141,8 @@ |
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+ |
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+ |
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+ blossoc_LDADD = |
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++blossoc_LDADD += -lsnpfile |
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++blossoc_LDADD += $(GSL_LIBS) |
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+ blossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
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+ blossoc_SOURCES = |
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+ blossoc_SOURCES += tree.hh tree.cc |
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+@@ -158,6 +159,8 @@ |
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+ blossoc_SOURCES += blossoc.cc |
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+ |
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+ snpfile_blossoc_LDADD = |
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++snpfile_blossoc_LDADD += -lsnpfile |
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++snpfile_blossoc_LDADD += $(GSL_LIBS) |
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+ snpfile_blossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
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+ snpfile_blossoc_LDADD += $(BOOST_SERIALIZATION_LIB) |
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+ snpfile_blossoc_LDADD += $(BOOST_SIGNALS_LIB) |
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+@@ -176,6 +179,8 @@ |
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+ snpfile_blossoc_SOURCES += snpfile_blossoc.cc |
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+ |
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+ iblossoc_LDADD = |
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++iblossoc_LDADD += -lsnpfile |
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++iblossoc_LDADD += $(GSL_LIBS) |
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+ iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
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+ iblossoc_SOURCES = |
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+ iblossoc_SOURCES += tree.hh tree.cc |
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+@@ -191,6 +196,8 @@ |
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+ iblossoc_SOURCES += interactions.cc |
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+ |
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+ low_mem_iblossoc_LDADD = |
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++low_mem_iblossoc_LDADD += -lsnpfile |
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++low_mem_iblossoc_LDADD += $(GSL_LIBS) |
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+ low_mem_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
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+ low_mem_iblossoc_SOURCES = |
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+ low_mem_iblossoc_SOURCES += tree.hh tree.cc |
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+@@ -206,6 +213,8 @@ |
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+ low_mem_iblossoc_SOURCES += low_mem_interactions.cc |
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+ |
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+ snpfile_iblossoc_LDADD = |
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++snpfile_iblossoc_LDADD += -lsnpfile |
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++snpfile_iblossoc_LDADD += $(GSL_LIBS) |
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+ snpfile_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
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+ snpfile_iblossoc_LDADD += $(BOOST_SERIALIZATION_LIB) |
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+ snpfile_iblossoc_LDADD += $(BOOST_SIGNALS_LIB) |
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+@@ -223,6 +232,8 @@ |
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+ snpfile_iblossoc_SOURCES += snpfile_interactions.cc |
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+ |
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+ fast_snpfile_iblossoc_LDADD = |
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++fast_snpfile_iblossoc_LDADD += -lsnpfile |
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++fast_snpfile_iblossoc_LDADD += $(GSL_LIBS) |
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+ fast_snpfile_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) |
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+ fast_snpfile_iblossoc_LDADD += $(BOOST_SERIALIZATION_LIB) |
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+ fast_snpfile_iblossoc_LDADD += $(BOOST_SIGNALS_LIB) |
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+@@ -239,6 +250,28 @@ |
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+ fast_snpfile_iblossoc_SOURCES += io.hh io.cc |
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+ fast_snpfile_iblossoc_SOURCES += fast_snpfile_interactions.cc |
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+ |
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++matrix_test_LDADD = |
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++matrix_test_LDADD += -lsnpfile |
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++ |
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++incompatibility_test_LDADD = |
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++incompatibility_test_LDADD += -lsnpfile |
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++ |
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++tree_builder_test_LDADD = |
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++tree_builder_test_LDADD += -lsnpfile |
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++ |
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++score_test_LDADD = |
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++score_test_LDADD += -lsnpfile |
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++score_test_LDADD += $(GSL_LIBS) |
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++ |
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++io_test_LDADD = |
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++io_test_LDADD += -lsnpfile |
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++ |
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++incompatible_regress_test_LDADD = |
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++incompatible_regress_test_LDADD += -lsnpfile |
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++ |
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++genotype_score_test_LDADD = |
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++genotype_score_test_LDADD += -lsnpfile |
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++genotype_score_test_LDADD += $(GSL_LIBS) |
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+ |
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+ |
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+ # include GUI in source distributions... |
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|
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diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch |
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index d8e354c174..64b5fe46e3 100644 |
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--- a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch |
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+++ b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch |
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@@ -3,8 +3,8 @@ Fixes build with >=GCC-4.3 |
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http://bugs.gentoo.org/show_bug.cgi?id=292949 |
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|
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Patch written by Sebastian Luther <SebastianLuther@×××.de> |
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---- pph.cc |
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-+++ pph.cc |
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+--- a/pph.cc |
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++++ b/pph.cc |
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@@ -23,6 +23,7 @@ |
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*/ |