From e69a19faa0ffec52ff1aeac557daae9b115f0182 Mon Sep 17 00:00:00 2001 From: David Seifert Date: Sun, 26 Feb 2017 13:25:06 +0100 Subject: 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 --- sci-biology/blossoc/blossoc-1.4.0-r1.ebuild | 37 +++ .../files/blossoc-1.4.0-fix-build-system.patch | 256 +++++++++++++++++++++ .../blossoc/files/blossoc-1.4.0-gcc43.patch | 4 +- 3 files changed, 295 insertions(+), 2 deletions(-) create mode 100644 sci-biology/blossoc/blossoc-1.4.0-r1.ebuild create mode 100644 sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch 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 +-. +-************************************************************************ +-************************************************************************ +-]]) +-) +- +- +-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 +-. +-************************************************************************ +-************************************************************************ +-]]) +-) +- +-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 +-. +-************************************************************************ +-************************************************************************ +-]]) +-) +- +-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 +-. +-************************************************************************ +-************************************************************************ +-]]) +-) +- ++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 ---- pph.cc -+++ pph.cc +--- a/pph.cc ++++ b/pph.cc @@ -23,6 +23,7 @@ */ -- cgit v1.2.3-65-gdbad