sci-biology/blossoc: Modernise to EAPI 6

Package-Manager: Portage-2.3.3, Repoman-2.3.1
RepoMan-Options: --force
Closes: https://github.com/gentoo/gentoo/pull/4083

3 files changed, 295 insertions, 2 deletions

diff --git a/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild
new file mode 100644
index 000000000000..01dbd27dd06c
--- /dev/null
+++ b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="A linkage disequilibrium association mapping tool"
+HOMEPAGE="http://www.daimi.au.dk/~mailund/Blossoc/"
+SRC_URI="http://www.daimi.au.dk/~mailund/Blossoc/download/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-libs/gsl:=
+	dev-libs/boost:=
+	sci-biology/snpfile"
+DEPEND="
+	${RDEPEND}
+	>=sys-devel/autoconf-archive-2016.09.16
+	virtual/pkgconfig"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.4.0-gcc43.patch
+	"${FILESDIR}"/${PN}-1.4.0-fix-build-system.patch
+)
+
+src_prepare() {
+	default
+	mv configure.{in,ac} || die
+	rm m4/ax_boost.m4 || die
+	eautoreconf
+}
diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch
new file mode 100644
index 000000000000..21234cc3cfb3
--- /dev/null
+++ b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch
@@ -0,0 +1,256 @@
+* Modernise Autoconf code
+* Use pkg-config for finding GSL
+* Use latest archvie macros to find Boost
+* Compile tests only when running make check
+
+--- a/configure.in
++++ b/configure.in
+@@ -1,6 +1,6 @@
+ AC_INIT(blossoc, 1.4.0, mailund@birc.au.dk)
+ AM_INIT_AUTOMAKE
+-AM_CONFIG_HEADER(config.hh)
++AC_CONFIG_HEADERS([config.hh])
+ 
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+@@ -12,74 +12,16 @@
+ fi
+ AC_DEFINE_UNQUOTED(PREFIX, "$thePREFIX", [Installation prefix])
+ 
+-AC_CHECK_LIB(m, sin, dnl FOUND, DO NOTHING
+-, dnl NOT FOUND
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-Didn't find the math library (-lm) -- I won't even guess about what is
+-wrong on this machine...
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
+-AX_BOOST([1.33.1],,
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-The Boost library was not found on this system.  We use this library
+-extensively, and cannot proceed without it.  You can obtain it from
+-<http://www.boost.org>.
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
+-
+-AC_CHECK_LIB(gslcblas, cblas_dsdot, dnl FOUND, DO NOTHING
+-, dnl NOT FOUND
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-The GNU Scientific Library (GSL) was not found.  This library is
+-needed for some of the numerical calculations used for scoring the
+-significance of local genealogies and can be obtained at
+-<http://www.gnu.org/software/gsl/>.
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
+-AC_CHECK_LIB(gsl, gsl_cdf_chisq_Q, dnl FOUND, DO NOTHING
+-, dnl NOT FOUND
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-The GNU Scientific Library (GSL) was not found.  This library is
+-needed for some of the numerical calculations used for scoring the
+-significance of local genealogies and can be obtained at
+-<http://www.gnu.org/software/gsl/>.
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
+-AC_CHECK_LIB(snpfile, main, dnl main isn't there, but this avoids namespaces
+-dnl FOUND
+-,
+-dnl NOT FOUND
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-The SNPFile library was not found.  This library is needed for data
+-representation and can be obtained at
+-<http://www.birc.au.dk/~mailund/SNPFile/>.
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
++AC_SEARCH_LIBS([sin], [m], [], [
++	AC_MSG_ERROR([unable to find the sin() function])
++])
++
++PKG_CHECK_MODULES([GSL], [gsl])
++
++AX_BOOST_BASE([1.33.1])
++AX_BOOST_PROGRAM_OPTIONS
++AX_BOOST_SERIALIZATION
++AX_BOOST_SIGNALS
+ 
+ AC_OUTPUT([
+ 	Makefile
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -3,9 +3,6 @@
+ AM_CXXFLAGS += -Wall
+ AM_CXXFLAGS += $(BOOST_CPPFLAGS)
+ 
+-# for testing
+-AM_CXXFLAGS += -g -O0 #-lefence
+-
+ # for coverage testing
+ #AM_CXXFLAGS += -O3 -fexpensive-optimizations -g -fprofile-arcs -ftest-coverage
+ 
+@@ -15,11 +12,11 @@
+ # for production
+ #AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG
+ 
+-noinst_PROGRAMS = 
++check_PROGRAMS =
++noinst_PROGRAMS =
+ TESTS = 
+ EXTRA_DIST =
+ 
+-TESTS += first_test.sh
+ EXTRA_DIST += first_test.sh
+ 
+ man_MANS = blossoc.1 snpfile_blossoc.1 blossoc_regions.1 blossoc_trees.1
+@@ -37,20 +34,20 @@
+ noinst_PROGRAMS     += snpfile_iblossoc #ditto
+ noinst_PROGRAMS     += fast_snpfile_iblossoc
+ 
+-noinst_PROGRAMS += matrix_test
+-TESTS +=           matrix_test
+-noinst_PROGRAMS += incompatibility_test tree_test tree_builder_test
+-TESTS +=           incompatibility_test tree_test tree_builder_test
++check_PROGRAMS += matrix_test
++TESTS +=          matrix_test
++check_PROGRAMS += incompatibility_test tree_test tree_builder_test
++TESTS +=          incompatibility_test tree_test tree_builder_test
+ EXTRA_DIST += testdata/CF/cf-positions.txt
+ EXTRA_DIST += testdata/CF/cf-haplotypes.txt
+ EXTRA_DIST += testdata/interaction/positions.txt
+ EXTRA_DIST += testdata/interaction/haplotypes.txt
+-noinst_PROGRAMS += score_test io_test 
+-TESTS +=           score_test io_test 
+-noinst_PROGRAMS += incompatible_regress_test
+-TESTS +=           incompatible_regress_test
+-noinst_PROGRAMS += genotype_score_test
+-TESTS +=           genotype_score_test.sh
++check_PROGRAMS += score_test io_test 
++TESTS +=          score_test io_test 
++check_PROGRAMS += incompatible_regress_test
++TESTS +=          incompatible_regress_test
++check_PROGRAMS += genotype_score_test
++TESTS +=          genotype_score_test.sh
+ EXTRA_DIST += genotype_score_test.sh
+ EXTRA_DIST += genotype_score_test.expected
+ TESTS +=           interactions_regression_test.sh
+@@ -120,6 +117,7 @@
+ 
+ 
+ blossoc_regions_LDADD  =
++blossoc_regions_LDADD += -lsnpfile
+ blossoc_regions_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ blossoc_regions_SOURCES  =
+ blossoc_regions_SOURCES += incompatibility.hh incompatibility.cc
+@@ -129,6 +127,7 @@
+ blossoc_regions_SOURCES += regions.cc
+ 
+ blossoc_trees_LDADD  =
++blossoc_trees_LDADD += -lsnpfile
+ blossoc_trees_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ blossoc_trees_SOURCES  =
+ blossoc_trees_SOURCES += matrix_utils.hh matrix_utils.cc 
+@@ -142,6 +141,8 @@
+ 
+ 
+ blossoc_LDADD  =
++blossoc_LDADD += -lsnpfile
++blossoc_LDADD += $(GSL_LIBS)
+ blossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ blossoc_SOURCES  =
+ blossoc_SOURCES += tree.hh tree.cc
+@@ -158,6 +159,8 @@
+ blossoc_SOURCES += blossoc.cc
+ 
+ snpfile_blossoc_LDADD  =
++snpfile_blossoc_LDADD += -lsnpfile
++snpfile_blossoc_LDADD += $(GSL_LIBS)
+ snpfile_blossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ snpfile_blossoc_LDADD += $(BOOST_SERIALIZATION_LIB)
+ snpfile_blossoc_LDADD += $(BOOST_SIGNALS_LIB)
+@@ -176,6 +179,8 @@
+ snpfile_blossoc_SOURCES += snpfile_blossoc.cc
+ 
+ iblossoc_LDADD  =
++iblossoc_LDADD += -lsnpfile
++iblossoc_LDADD += $(GSL_LIBS)
+ iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ iblossoc_SOURCES  =
+ iblossoc_SOURCES += tree.hh tree.cc
+@@ -191,6 +196,8 @@
+ iblossoc_SOURCES += interactions.cc
+ 
+ low_mem_iblossoc_LDADD  =
++low_mem_iblossoc_LDADD += -lsnpfile
++low_mem_iblossoc_LDADD += $(GSL_LIBS)
+ low_mem_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ low_mem_iblossoc_SOURCES  =
+ low_mem_iblossoc_SOURCES += tree.hh tree.cc
+@@ -206,6 +213,8 @@
+ low_mem_iblossoc_SOURCES += low_mem_interactions.cc
+ 
+ snpfile_iblossoc_LDADD  =
++snpfile_iblossoc_LDADD += -lsnpfile
++snpfile_iblossoc_LDADD += $(GSL_LIBS)
+ snpfile_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ snpfile_iblossoc_LDADD += $(BOOST_SERIALIZATION_LIB)
+ snpfile_iblossoc_LDADD += $(BOOST_SIGNALS_LIB)
+@@ -223,6 +232,8 @@
+ snpfile_iblossoc_SOURCES += snpfile_interactions.cc
+ 
+ fast_snpfile_iblossoc_LDADD  =
++fast_snpfile_iblossoc_LDADD += -lsnpfile
++fast_snpfile_iblossoc_LDADD += $(GSL_LIBS)
+ fast_snpfile_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ fast_snpfile_iblossoc_LDADD += $(BOOST_SERIALIZATION_LIB)
+ fast_snpfile_iblossoc_LDADD += $(BOOST_SIGNALS_LIB)
+@@ -239,6 +250,28 @@
+ fast_snpfile_iblossoc_SOURCES += io.hh io.cc
+ fast_snpfile_iblossoc_SOURCES += fast_snpfile_interactions.cc
+ 
++matrix_test_LDADD  =
++matrix_test_LDADD += -lsnpfile
++
++incompatibility_test_LDADD  =
++incompatibility_test_LDADD += -lsnpfile
++
++tree_builder_test_LDADD  =
++tree_builder_test_LDADD += -lsnpfile
++
++score_test_LDADD  =
++score_test_LDADD += -lsnpfile
++score_test_LDADD += $(GSL_LIBS)
++
++io_test_LDADD  =
++io_test_LDADD += -lsnpfile
++
++incompatible_regress_test_LDADD  =
++incompatible_regress_test_LDADD += -lsnpfile
++
++genotype_score_test_LDADD  =
++genotype_score_test_LDADD += -lsnpfile
++genotype_score_test_LDADD += $(GSL_LIBS)
+ 
+ 
+ # include GUI in source distributions...
diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
index d8e354c1745f..64b5fe46e30e 100644
--- a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
+++ b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
@@ -3,8 +3,8 @@ Fixes build with >=GCC-4.3
 http://bugs.gentoo.org/show_bug.cgi?id=292949
 
 Patch written by Sebastian Luther <SebastianLuther@gmx.de>
---- pph.cc
-+++ pph.cc
+--- a/pph.cc
++++ b/pph.cc
 @@ -23,6 +23,7 @@
   */