6 files changed, 0 insertions, 454 deletions
diff --git a/sci-biology/generecon/Manifest b/sci-biology/generecon/Manifest
deleted file mode 100644
index 10f7613c1..000000000
--- a/sci-biology/generecon/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST generecon-1.2.1.tar.gz 239507 BLAKE2B b5eeaf94c8488e32b60180875c6baf6fb7b12792678f331a65166db758866ada87f97155fb35a3a011de387f93c6e08fc38951d4e7c73046f05395bc2b4770bb SHA512 59a3a7a54ce1086c8c4424aa8a2661e39c72b1896c2ac3af6147f8234ef8cfd4db9af69b709131e5ea63463fe4d8ab93109cd73cda8b59d2dc061a674af7bd4d
diff --git a/sci-biology/generecon/files/1.2.1-flags.patch b/sci-biology/generecon/files/1.2.1-flags.patch
deleted file mode 100644
index 7dd9a372e..000000000
--- a/sci-biology/generecon/files/1.2.1-flags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index 37df12b..4ff621e 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -1,10 +1,10 @@
- 
--CXXFLAGS =
-+#CXXFLAGS =
- AM_CXXFLAGS =
--CXXFLAGS += -Wall
--AM_CXXFLAGS += -Wall
-+#CXXFLAGS += -Wall
-+#AM_CXXFLAGS += -Wall
- 
--LDFLAGS = -Wl,-rpath,/usr/local/lib
-+#LDFLAGS = -Wl,-rpath,/usr/local/lib
- 
- # for testing
- #CXXFLAGS += -g -O -lefence
-@@ -14,8 +14,8 @@ LDFLAGS = -Wl,-rpath,/usr/local/lib
- #AM_CXXFLAGS += -O3 -g -pg
- 
- # for production
--CXXFLAGS    += -O3 -fexpensive-optimizations
--AM_CXXFLAGS += -O3 -fexpensive-optimizations
-+#CXXFLAGS    += -O3 -fexpensive-optimizations
-+#AM_CXXFLAGS += -O3 -fexpensive-optimizations
- 
- #CXXFLAGS    += -O3 -fexpensive-optimizations -DNDEBUG
- #AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG
diff --git a/sci-biology/generecon/files/1.2.1-gcc4.patch b/sci-biology/generecon/files/1.2.1-gcc4.patch
deleted file mode 100644
index 6b71713c3..000000000
--- a/sci-biology/generecon/files/1.2.1-gcc4.patch
+++ /dev/null
@@ -1,368 +0,0 @@
-diff --git a/affected_unaffected_genotype_cluster_test.cc b/affected_unaffected_genotype_cluster_test.cc
-index 646af06..4e5fbde 100644
---- a/affected_unaffected_genotype_cluster_test.cc
-+++ b/affected_unaffected_genotype_cluster_test.cc
-@@ -32,6 +32,7 @@
- # include "random_tree_builder.hh"
- #endif
- 
-+#include <cstring>
- 
- void test_tree(const CoalescentTree &tree,
- 	       const Haplotype &h0, const Haplotype &h1,
-diff --git a/affected_unaffected_genotype_set_test.cc b/affected_unaffected_genotype_set_test.cc
-index 07fa122..5f333f5 100644
---- a/affected_unaffected_genotype_set_test.cc
-+++ b/affected_unaffected_genotype_set_test.cc
-@@ -19,6 +19,8 @@
- # include "region.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/affected_unaffected_haplotype_cluster_test.cc b/affected_unaffected_haplotype_cluster_test.cc
-index 145e05f..b5dddaa 100644
---- a/affected_unaffected_haplotype_cluster_test.cc
-+++ b/affected_unaffected_haplotype_cluster_test.cc
-@@ -32,6 +32,7 @@
- # include "random_tree_builder.hh"
- #endif
- 
-+#include <cstring>
- 
- void test_tree(const CoalescentTree &tree,
- 	       const Haplotype &h0, const Haplotype &h1,
-diff --git a/affected_unaffected_haplotype_set_test.cc b/affected_unaffected_haplotype_set_test.cc
-index fda6173..8489c54 100644
---- a/affected_unaffected_haplotype_set_test.cc
-+++ b/affected_unaffected_haplotype_set_test.cc
-@@ -19,6 +19,8 @@
- # include "region.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/au_random_tree_builder_test.cc b/au_random_tree_builder_test.cc
-index a2d4daa..d6689e0 100644
---- a/au_random_tree_builder_test.cc
-+++ b/au_random_tree_builder_test.cc
-@@ -30,6 +30,7 @@
- # include "test_random.hh"
- #endif
- 
-+#include <cstring>
- 
- void test_tree(const CoalescentTree *tree,
- 	       const Haplotype &h0, const Haplotype &h1,
-diff --git a/change_selector_test.cc b/change_selector_test.cc
-index 5f655d1..9004bef 100644
---- a/change_selector_test.cc
-+++ b/change_selector_test.cc
-@@ -23,6 +23,8 @@
- # include "change.hh"
- #endif
- 
-+#include <cstring>
-+
- // dummy class for testing
- struct DummyChange : public Change {
-     DummyChange() : Change("Dummy change") {}
-diff --git a/coalescent_tree.cc b/coalescent_tree.cc
-index eb937e5..9e54a2b 100644
---- a/coalescent_tree.cc
-+++ b/coalescent_tree.cc
-@@ -7,6 +7,7 @@
- 
- #include "coalescent_tree.hh"
- 
-+#include <algorithm>
- 
- /** \file
-  * \brief Implementation of the coalescent tree.
-diff --git a/coalescent_tree_test.cc b/coalescent_tree_test.cc
-index 20059e9..2971ead 100644
---- a/coalescent_tree_test.cc
-+++ b/coalescent_tree_test.cc
-@@ -30,6 +30,8 @@
- # define CMATH_INCLUDED
- #endif
- 
-+#include <cstring>
-+
- namespace {
- 
-     CoalescentTree *test_tree(HaplotypePool &pool)
-diff --git a/distance_matrix_test.cc b/distance_matrix_test.cc
-index e2e8435..9d367ee 100644
---- a/distance_matrix_test.cc
-+++ b/distance_matrix_test.cc
-@@ -15,6 +15,8 @@
- # include "haplotype_pool.hh"
- #endif
- 
-+#include <cstring>
-+
- namespace {
-     int distance(const Haplotype &h1, const Haplotype &h2)
-     {
-diff --git a/distance_tree_builder_test.cc b/distance_tree_builder_test.cc
-index e252c3e..3f589f4 100644
---- a/distance_tree_builder_test.cc
-+++ b/distance_tree_builder_test.cc
-@@ -15,6 +15,8 @@
- # include "test_random.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/filter_iterator_test.cc b/filter_iterator_test.cc
-index bf5097b..e74a29f 100644
---- a/filter_iterator_test.cc
-+++ b/filter_iterator_test.cc
-@@ -21,6 +21,8 @@
- # define FUNCTIONAL_INCLUDED
- #endif
- 
-+#include <cstring>
-+
- namespace {
-   struct even : public std::unary_function<int,bool> {
-     bool operator () (int i) const { return i % 2 == 0; }
-diff --git a/genotype_pool_test.cc b/genotype_pool_test.cc
-index e62a03f..9a2badb 100644
---- a/genotype_pool_test.cc
-+++ b/genotype_pool_test.cc
-@@ -22,6 +22,8 @@
- # include "genotype.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/genotype_test.cc b/genotype_test.cc
-index 3d704e4..64b3343 100644
---- a/genotype_test.cc
-+++ b/genotype_test.cc
-@@ -22,6 +22,8 @@
- # include "haplotype.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/guile_sampler.cc b/guile_sampler.cc
-index b0d19f1..ffbec86 100644
---- a/guile_sampler.cc
-+++ b/guile_sampler.cc
-@@ -26,6 +26,7 @@
- # define CASSERT_INCLUDED
- #endif
- 
-+#include <memory>
- 
- /** \file
-  * \brief Implementation of the guile sampler wrapper.
-diff --git a/haplotype.cc b/haplotype.cc
-index a38541f..7810642 100644
---- a/haplotype.cc
-+++ b/haplotype.cc
-@@ -12,6 +12,8 @@
- # define SSTREAM_INCLUDED
- #endif
- 
-+#include <algorithm>
-+
- /** \file
-  * \brief Implementation of haplotype functionality.
-  */
-diff --git a/haplotype_pool.cc b/haplotype_pool.cc
-index ceef1b9..42c6125 100644
---- a/haplotype_pool.cc
-+++ b/haplotype_pool.cc
-@@ -7,6 +7,8 @@
- 
- #include "haplotype_pool.hh"
- 
-+#include <algorithm>
-+
- /** \file
-  * \brief Implementation of haplotype pool functionality.
-  */
-diff --git a/haplotype_pool_test.cc b/haplotype_pool_test.cc
-index a774809..4527d23 100644
---- a/haplotype_pool_test.cc
-+++ b/haplotype_pool_test.cc
-@@ -19,6 +19,8 @@
- # include "region.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/haplotype_test.cc b/haplotype_test.cc
-index 134a601..b7f5b63 100644
---- a/haplotype_test.cc
-+++ b/haplotype_test.cc
-@@ -19,6 +19,8 @@
- # include "region.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/marker_test.cc b/marker_test.cc
-index ff34d7c..317385d 100644
---- a/marker_test.cc
-+++ b/marker_test.cc
-@@ -13,6 +13,7 @@
- #include "testing.hh"
- 
- #include <cmath>
-+#include <cstring>
- 
- int main(int argc, const char *argv[])
- {
-diff --git a/markov_region_test.cc b/markov_region_test.cc
-index 58e0278..db0f9ba 100644
---- a/markov_region_test.cc
-+++ b/markov_region_test.cc
-@@ -11,7 +11,7 @@
- 
- #include "region.hh"
- #include "testing.hh"
--
-+#include <cstring>
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/qtl_haplotype_pool_test.cc b/qtl_haplotype_pool_test.cc
-index 72f763d..8c058af 100644
---- a/qtl_haplotype_pool_test.cc
-+++ b/qtl_haplotype_pool_test.cc
-@@ -19,6 +19,8 @@
- # include "region.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/random_set_test.cc b/random_set_test.cc
-index 7eae435..b7a3451 100644
---- a/random_set_test.cc
-+++ b/random_set_test.cc
-@@ -15,6 +15,8 @@
- # include "test_random.hh"
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/random_tree_builder_test.cc b/random_tree_builder_test.cc
-index e8c5957..7c95519 100644
---- a/random_tree_builder_test.cc
-+++ b/random_tree_builder_test.cc
-@@ -28,6 +28,7 @@
- # include "test_random.hh"
- #endif
- 
-+#include <cstring>
- 
- void test_tree(const CoalescentTree *tree,
- 	       const Haplotype &h0, const Haplotype &h1,
-diff --git a/region.cc b/region.cc
-index df22885..94bce6f 100644
---- a/region.cc
-+++ b/region.cc
-@@ -22,6 +22,8 @@
- # define CMATH_INCLUDED
- #endif
- 
-+#include <algorithm>
-+
- 
- /** \file
-  * \brief Implementation of region functionality.
-diff --git a/region_test.cc b/region_test.cc
-index 25f6cf0..e21084f 100644
---- a/region_test.cc
-+++ b/region_test.cc
-@@ -11,6 +11,7 @@
- 
- #include "region.hh"
- #include "testing.hh"
-+#include <cstring>
- 
- int main(int argc, const char *argv[])
- {
-diff --git a/selection_if_test.cc b/selection_if_test.cc
-index a9a6377..0fb8052 100644
---- a/selection_if_test.cc
-+++ b/selection_if_test.cc
-@@ -24,6 +24,8 @@
- # define VECTOR_INCLUDED
- #endif
- 
-+#include <cstring>
-+
- namespace {
-   struct even : public std::unary_function<int,bool> {
-     bool operator () (int i) const { return i % 2 == 0; }
-diff --git a/selection_test.cc b/selection_test.cc
-index 3bf673a..579931c 100644
---- a/selection_test.cc
-+++ b/selection_test.cc
-@@ -28,6 +28,8 @@
- # define LIST_INCLUDED
- #endif
- 
-+#include <cstring>
-+
- int main(int argc, const char *argv[])
- {
-     HANDLE_TEST_OPTIONS;
-diff --git a/testing.hh b/testing.hh
-index fbdcd87..c86dbc6 100644
---- a/testing.hh
-+++ b/testing.hh
-@@ -23,6 +23,8 @@
- # define CSTDLIB_INCLUDED
- #endif
- 
-+#include <cstring>
-+
- /// \brief Verboseness flag for running tests.
- ///
- /// If set, the test will report the failed tests, otherwise it will
-diff --git a/tree_builder.hh b/tree_builder.hh
-index 4b0ec01..c0bdc5a 100644
---- a/tree_builder.hh
-+++ b/tree_builder.hh
-@@ -34,6 +34,7 @@
- # include "meta_programming.hh"
- #endif
- 
-+#include <limits>
- 
- /**
-  * \brief Abstract class for tree builders.
diff --git a/sci-biology/generecon/files/generecon-docfiles.patch b/sci-biology/generecon/files/generecon-docfiles.patch
deleted file mode 100644
index 79d63e73f..000000000
--- a/sci-biology/generecon/files/generecon-docfiles.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Nuar generecon-1.2.1.orig/Makefile.am generecon-1.2.1/Makefile.am
---- generecon-1.2.1.orig/Makefile.am	2006-04-19 12:52:18.000000000 -0300
-+++ generecon-1.2.1/Makefile.am	2006-04-19 12:55:53.000000000 -0300
-@@ -31,7 +31,7 @@
- bin_PROGRAMS     = generecon
- 
- 
--docdir = ${prefix}/share/generecon/doc
-+docdir = ${prefix}/share/doc/#PF#
- dist_doc_DATA =
- test_inputdir = ${prefix}/share/generecon/test-input
- dist_test_input_DATA =
diff --git a/sci-biology/generecon/generecon-1.2.1-r1.ebuild b/sci-biology/generecon/generecon-1.2.1-r1.ebuild
deleted file mode 100644
index eed5ce825..000000000
--- a/sci-biology/generecon/generecon-1.2.1-r1.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="Disequilibrium gene mapping based on coalescent theory using Bayesian MC methods"
-HOMEPAGE="http://www.daimi.au.dk/~mailund/GeneRecon/"
-SRC_URI="http://www.daimi.au.dk/~mailund/GeneRecon/download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
-	dev-libs/popt
-	dev-scheme/guile:12
-	sci-libs/gsl"
-DEPEND="${DEPEND}"
-
-src_prepare() {
-	sed 's|#PF#|'${PF}'|g' "${FILESDIR}"/${PN}-docfiles.patch > ${PN}-docfiles.patch
-
-	epatch \
-		${PN}-docfiles.patch \
-		"${FILESDIR}"/${PV}-gcc4.patch \
-		"${FILESDIR}"/${PV}-flags.patch
-	eautoreconf
-}
diff --git a/sci-biology/generecon/metadata.xml b/sci-biology/generecon/metadata.xml
deleted file mode 100644
index de97c87f7..000000000
--- a/sci-biology/generecon/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>lucas.chiesa@gmail.com</email>
-		<name>Lucas Chiesa</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>