sci-biology/{blossoc,snpfile}: Remove last-rited pkgs

Closes: https://bugs.gentoo.org/683762
Signed-off-by: David Seifert <soap@gentoo.org>

5 files changed, 0 insertions, 316 deletions

diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest
deleted file mode 100644
index 84cf1ab90b7f..000000000000
--- a/sci-biology/blossoc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST blossoc-1.4.0.tar.gz 194885 BLAKE2B 040b70d737007d691399e9ea5446b45ed119237e86f83a85521d1555fff253bc9285c5d9a91f0e4f30a38d974a43d5e439fb61aea9686c5fbff233e6491dcdce SHA512 fd47c85df5f1f97527e1abb1e56b05c02fa44c1c110abc222d895b2370324a26970446084e62adf02ce0c7dc332635d40dd1505d423571b424865425f6b2a327
diff --git a/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild
deleted file mode 100644
index 9fd1189e025a..000000000000
--- a/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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}"/${PN}-1.4.0-fix-build-system.patch
-)
-
-src_prepare() {
-	default
-	mv configure.{in,ac} || die
-	rm m4/ax_boost.m4 || die
-	eautoreconf
-}
diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch
deleted file mode 100644
index 21234cc3cfb3..000000000000
--- a/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch
+++ /dev/null
@@ -1,256 +0,0 @@
-* Modernise Autoconf code
-* Use pkg-config for finding GSL
-* Use latest archvie macros to find Boost
-* Compile tests only when running make check
-
---- a/configure.in
-+++ b/configure.in
-@@ -1,6 +1,6 @@
- AC_INIT(blossoc, 1.4.0, mailund@birc.au.dk)
- AM_INIT_AUTOMAKE
--AM_CONFIG_HEADER(config.hh)
-+AC_CONFIG_HEADERS([config.hh])
- 
- AC_PROG_CXX
- AC_PROG_INSTALL
-@@ -12,74 +12,16 @@
- fi
- AC_DEFINE_UNQUOTED(PREFIX, "$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
deleted file mode 100644
index 64b5fe46e30e..000000000000
--- a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Fixes build with >=GCC-4.3
-
-http://bugs.gentoo.org/show_bug.cgi?id=292949
-
-Patch written by Sebastian Luther <SebastianLuther@gmx.de>
---- a/pph.cc
-+++ b/pph.cc
-@@ -23,6 +23,7 @@
-  */
- 
- #include "pph.hh"
-+#include <cstdio>
- #include <cmath>
- #include <snpfile/matrix.hh>
- using namespace BiRC::SNPFile;
diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/blossoc/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>