gentoo resync : 21.05.2019

23 files changed, 0 insertions, 1307 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 62558baa4eda..ac7504d61b0f 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest
deleted file mode 100644
index 17048b8c8248..000000000000
--- a/sci-biology/blossoc/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX blossoc-1.4.0-fix-build-system.patch 8380 BLAKE2B a0d682fe3d831db664d798ace2fadc30edb2feb8c2a25b04e5256b4e5ee402c38c5f5462f62aa5044c6652c735e12752ca1c74ddc27b925b1acdfeb6b2fbe9b6 SHA512 e1e97db5446916fd3ea7ca84baddde4771f6ee0081e17bd28e473a85565c1f0d1aa5e4385ee77a473f67eb5dd36eff7849dd334e31e4a4e1fb47737e3597e091
-AUX blossoc-1.4.0-gcc43.patch 303 BLAKE2B 55263656a037453fa0e1ab6237dae51f1042b08164639332cf40017d4309465c43e8a044eda0ff11025625fcd3fe85a9fae210be9da2a59cc72c56aa973d09aa SHA512 600890d9e40f56923c84e181957abfb2e75b66992b3f7b406f15a6cdb779527868e6b37c573e9b22e81964ff0600080b73ec967df60ed8d9fcfc84c2e6810093
-DIST blossoc-1.4.0.tar.gz 194885 BLAKE2B 040b70d737007d691399e9ea5446b45ed119237e86f83a85521d1555fff253bc9285c5d9a91f0e4f30a38d974a43d5e439fb61aea9686c5fbff233e6491dcdce SHA512 fd47c85df5f1f97527e1abb1e56b05c02fa44c1c110abc222d895b2370324a26970446084e62adf02ce0c7dc332635d40dd1505d423571b424865425f6b2a327
-EBUILD blossoc-1.4.0-r1.ebuild 726 BLAKE2B 07e562bb5f5a1ecf84ff337187f4fef1c97b95d7a3f613020b8010a550ac626f4cf2896fb5e4372019e4366478f897db4dbbc7d4a854424e2cc6c05a891d4a51 SHA512 f345c811c9dd49b716ec91a5cb3460a763cc125fe93a5a45a29245a08544455dd9686264e69333c54c5cc736b2b5d0cd76bc7e9b3cd279c5264a83726d81067b
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
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>
diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest
deleted file mode 100644
index 4c95c2d9efa8..000000000000
--- a/sci-biology/cufflinks/Manifest
+++ /dev/null
@@ -1,10 +0,0 @@
-AUX cufflinks-2.2.1-boost-1.65-tr1-removal.patch 344 BLAKE2B af0287f43bfd37da352fc330e3f6e06d4c6946851c6d8760302078157c8073591ccf7b508e2debf35747837216cc15e952fd7128bca500547cc180061dc2f780 SHA512 774558e93cf57ca9e9361df2271119474c8726573ff4467af4836db863d87ff0f38fe7048c9287227f18d3541891bb7b433b5fa33567616eeecda2bb5b057e9a
-AUX cufflinks-2.2.1-flags.patch 1132 BLAKE2B 675fb86a95425ed0def259b6f316e443eddb0c80a3a4f78e724f85ca3b14e58c29bb59bbc80a61ee7dcfaeb404383ffe0e58669dedc95224913c8d43939fd799 SHA512 58ea036d55d0b4835a56ea66afc2359bdb3e022f1fda3cab8402e4a2d7c6eab00fae96c739f89a25ca1e7528dad02f20c5c944a198c1eeca245e8995fbaa8f12
-AUX cufflinks-2.2.1-format-security.patch 618 BLAKE2B 1a316055af35849333c8ccbd46079a4ee1096becde474151932317bb66f81eff27b80d15306d9432f69a42fa9202a7712f9eff9921b915a92f4094ad2eadc79b SHA512 61a8cfe31988b028636f97db06d6855d9fce4ff3548da70d7e791fde85b38c09376be63714b67a0dc3e112f1d543735a51ebc437fc0b32eff98e9bf13138ff3c
-AUX cufflinks-2.2.1-gcc5-make_shared.patch 417 BLAKE2B 99fb3c7135789073089344d0f362088e5d95354b80a43e5a4fd47daa8b38d7c05b18476c491e5945b6b313925e984361915651c0b783c866273eeb4530eb35ea SHA512 81340797fe99aeb0fd118b28f729dfdcfbd3dd1a5efa2a4874a3732a167ad1c8b8d7d3408d1137db35ac5c17319d90dc1351bfd91a15af5c095de746791394d7
-AUX cufflinks-2.2.1-gcc6.patch 344 BLAKE2B 7534c9060e93f074718726e2cbf7df259ba298b447915a4162916977340d33e35a4fddbf3e1b662334b56d42ffb8e0a096c337b465b5952abe27d1248fd6d0f2 SHA512 1e8fc2e717c464e39aecf2c434857e962a809fd2a9f84bfca2b7230d5150d464262b579f1a8c13970767e929562d04994d60002834c98c204e089d2d2a8381c0
-AUX cufflinks-2.2.1-gcc7.patch 4133 BLAKE2B ac2fbf2ebadfe0e90d7163dbd839b2173a3a3a9925b25e2eba8775793545ed8e17e8075c9e562300fa0fae6fd7c35893c8bc892c3e79bd6645b2e3cf51acbdbf SHA512 cbcc2be9e1266e24801dc91ed776aa314761ac682274c103c4f4ad9c37f8ad02b63233f2a16608dd620ca67e89a21028142bdc059cbe5fd2fffdbdb3e38f0af8
-AUX cufflinks-2.2.1-samtools-legacy.patch 1105 BLAKE2B ceeb2236456f30598e0d98ce1eaa4fae908286704fb6912a19ccc008b3d41476b853cacc3fc545450dde7d883593a545110a440c044118875041f56077c963b3 SHA512 80c6eaadcfe6919d61b63efc83d3d618e939c3a1cd5e4977f936c41656a96c7c2dd71a1309d6b0422b1bf248a366643a62f011b30b37b4001efae5da04acaadf
-DIST cufflinks-2.2.1.tar.gz 766280 BLAKE2B 200ca88d15cdfca550a12a39cf69d4c41850532c76840d2a86a21654b317e28c7f35d36ba26105490e75d55c5527dd64da1ef3c14f2d467a60379c234a8e9e60 SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b
-EBUILD cufflinks-2.2.1-r2.ebuild 1303 BLAKE2B 43a7781892fd664ca50d429ee741233ec4e319a8bccda379cc18a36c8447fb65972a07480bc74dde09d964f8e34f15b5e53204d6da2b1ce9af79fbc39d566103 SHA512 45d0d18bc405809d76f26b348ae90fa0fd9453a9ca1632c052ca6354679b65c9c40460bda40b7f50745549df916704cac3b6e4ed1b833cb9114f61ab002b1640
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
deleted file mode 100644
index 3892e03e23b2..000000000000
--- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools flag-o-matic python-single-r1 toolchain-funcs
-
-DESCRIPTION="Transcript assembly and differential expression/regulation for RNA-Seq"
-HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
-SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="debug"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	sci-biology/samtools:0.1-legacy
-	>=dev-libs/boost-1.62.0:=
-	${PYTHON_DEPS}"
-DEPEND="
-	${RDEPEND}
-	dev-cpp/eigen:3
-	virtual/pkgconfig"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-samtools-legacy.patch
-	"${FILESDIR}"/${P}-flags.patch
-	"${FILESDIR}"/${P}-gcc6.patch
-	"${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch
-	"${FILESDIR}"/${P}-gcc7.patch
-	"${FILESDIR}"/${P}-format-security.patch
-	"${FILESDIR}"/${P}-gcc5-make_shared.patch
-)
-
-src_prepare() {
-	default
-	python_fix_shebang src/cuffmerge
-
-	eautoreconf
-}
-
-src_configure() {
-	# keep in sync with Boost
-	append-cxxflags -std=c++14
-	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
-
-	econf \
-		--disable-optim \
-		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \
-		--with-bam="${EPREFIX}/usr/" \
-		$(use_enable debug) \
-		PYTHON="${PYTHON}"
-}
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch
deleted file mode 100644
index 42a906e7a83a..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Boost 1.65 removed the TR1 headers.
-Bug: https://bugs.gentoo.org/show_bug.cgi?id=630654
-
---- a/src/biascorrection.h
-+++ b/src/biascorrection.h
-@@ -15,7 +15,7 @@
- #include <vector>
- #include <list>
- #include <string>
--#include <boost/tr1/unordered_map.hpp>
-+#include <boost/unordered_map.hpp>
- #include <boost/thread.hpp>
- #include "common.h"
- 
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
deleted file mode 100644
index 47784088fab9..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch
+++ /dev/null
@@ -1,28 +0,0 @@
- configure.ac | 7 ++++---
- 1 file changed, 4 insertions(+), 3 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 96ffbac..e88b8e4 100755
---- a/configure.ac
-+++ b/configure.ac
-@@ -61,7 +61,8 @@ AC_CANONICAL_HOST
- 
- # set CFLAGS and CXXFLAGS
- user_CFLAGS=${CFLAGS}
--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024"
-+generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized"
-+generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024"
- ext_CFLAGS=""
- debug_CFLAGS=""
- #echo "${host_cpu}-${host_os}"
-@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling,      [  --enable-profiling        enable profiling with
- 	  [ext_LDFLAGS="-lprofiler -ltcmalloc"], [])
- 	  
- CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
--CXXFLAGS="$CFLAGS"
--CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
-+CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}"
-+CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
- user_LDFLAGS="$LDFLAGS"
- LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"
- 
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch
deleted file mode 100644
index fa13f78d8b52..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-Date: Wed, 22 May 2013 13:27:40 +0200
-Description: When building with --format-security (Debhelper 9 hardening)
- this patch is needed to build successfully
-
---- a/src/locfit/makecmd.c
-+++ b/src/locfit/makecmd.c
-@@ -200,7 +200,7 @@ char *cmdline;
-   /* vs is used to store the command line string. */
-   sprintf(vn,"=clstr%d",clcount);
-   vs = createvar(vn,STSYSTEM,1+strlen(cmdline),VCHAR);
--  sprintf((char *)vdptr(vs),cmdline);
-+  sprintf((char *)vdptr(vs),"%s",cmdline);
- 
-   /* va is used to store pointers to the command line fields. */
-   sprintf(vn,"=cline%d",clcount);
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch
deleted file mode 100644
index 67a28df10249..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/differential.cpp
-+++ b/src/differential.cpp
-@@ -575,7 +575,7 @@
-     boost::mutex::scoped_lock lock(meta_data_lock);
- #endif
-     pair<SampleDiffMetaDataTable::iterator, bool> p;
--    p = meta_data_table.insert(make_pair(description, new SampleDifferenceMetaData()));
-+    p = meta_data_table.insert(make_pair(description, boost::make_shared<SampleDifferenceMetaData>()));
-     return p.first->second;
- }
- 
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch
deleted file mode 100644
index 6ee9bcf456d4..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- a/src/lemon/error.h
-+++ b/src/lemon/error.h
-@@ -67,9 +67,9 @@
-     }
- 
-     ExceptionMember& operator=(const ExceptionMember& copy) {
--      if (ptr.get() == 0) return;
-+      if (ptr.get() == 0) return *this;
-       try {
--	if (!copy.valid()) return;
-+	if (!copy.valid()) return *this;
-  	*ptr = copy.get();
-       } catch (...) {}
-     }
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch
deleted file mode 100644
index 48fe6e10ac96..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch
+++ /dev/null
@@ -1,121 +0,0 @@
-Author: Alex Mestiashvili <mailatgoogl@gmail.com>
-Origin: https://lists.debian.org/debian-med/2017/09/msg00021.html
-Bug-Debian: https://bugs.debian.org/871234
-Description: Fix gcc-7 build issue, thanks to Jeff Epler <jepler@unpythonic.net>
---- a/src/GHash.hh
-+++ b/src/GHash.hh
-@@ -88,7 +88,7 @@
-                                 //nextkey is SET to the corresponding key
-   GHashEntry* NextEntry() { //returns a pointer to a GHashEntry
-   	 register int pos=fCurrentEntry;
--  	 while (pos<fCapacity && hash[pos].hash<0) pos++;
-+  	 while (pos<fCapacity && (hash[pos].hash)<0) pos++;
-   	 if (pos==fCapacity) {
-   	                 fCurrentEntry=fCapacity;
-   	                 return NULL;
-@@ -186,7 +186,7 @@
-         x=HASH2(h,n);
-         GASSERT(1<=x && x<n);
-         while(k[p].hash!=-1) p=(p+x)%n;
--        GASSERT(k[p].hash<0);
-+        GASSERT((k[p].hash)<0);
-         k[p]=hash[i];
-         }
-       }
-@@ -225,7 +225,7 @@
-   GTRACE(("GHash::insert: key=\"%s\"\n",ky));
-   //GMessage("GHash::insert: key=\"%s\"\n",ky);
-   GASSERT(0<=i && i<fCapacity);
--  GASSERT(hash[i].hash<0);
-+  GASSERT((hash[i].hash)<0);
-   hash[i].hash=h;
-   hash[i].mark=mrk;
-   hash[i].key=Gstrdup(ky);
-@@ -266,7 +266,7 @@
-   GTRACE(("GHash::insert: key=\"%s\"\n",ky));
-   //GMessage("GHash::insert: key=\"%s\"\n",ky);
-   GASSERT(0<=i && i<fCapacity);
--  GASSERT(hash[i].hash<0);
-+  GASSERT((hash[i].hash)<0);
-   hash[i].hash=h;
-   hash[i].mark=mrk;
-   hash[i].key=(char *)ky;
-@@ -310,7 +310,7 @@
-   if(i==-1) i=p;
-   GTRACE(("GHash::replace: %08x: inserting: \"%s\"\n",this,ky));
-   GASSERT(0<=i && i<fCapacity);
--  GASSERT(hash[i].hash<0);
-+  GASSERT((hash[i].hash)<0);
-   hash[i].hash=h;
-   hash[i].mark=mrk;
-   hash[i].key=Gstrdup(ky);
-@@ -412,7 +412,7 @@
- 
- template <class OBJ> char* GHash<OBJ>::NextKey() {
-  register int pos=fCurrentEntry;
-- while (pos<fCapacity && hash[pos].hash<0) pos++;
-+ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
-  if (pos==fCapacity) {
-                  fCurrentEntry=fCapacity;
-                  return NULL;
-@@ -425,7 +425,7 @@
- 
- template <class OBJ> OBJ* GHash<OBJ>::NextData() {
-  register int pos=fCurrentEntry;
-- while (pos<fCapacity && hash[pos].hash<0) pos++;
-+ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
-  if (pos==fCapacity) {
-                  fCurrentEntry=fCapacity;
-                  return NULL;
-@@ -439,7 +439,7 @@
- 
- template <class OBJ> OBJ* GHash<OBJ>::NextData(char* &nextkey) {
-  register int pos=fCurrentEntry;
-- while (pos<fCapacity && hash[pos].hash<0) pos++;
-+ while (pos<fCapacity && (hash[pos].hash)<0) pos++;
-  if (pos==fCapacity) {
-                  fCurrentEntry=fCapacity;
-                  nextkey=NULL;
-@@ -457,16 +457,16 @@
- // Get first non-empty entry
- template <class OBJ> int GHash<OBJ>::First() const {
-   register int pos=0;
--  while(pos<fCapacity){ if(0<=hash[pos].hash) break; pos++; }
--  GASSERT(fCapacity<=pos || 0<=hash[pos].hash);
-+  while(pos<fCapacity){ if(0<=(hash[pos].hash)) break; pos++; }
-+  GASSERT(fCapacity<=pos || 0<=(hash[pos].hash));
-   return pos;
-   }
- 
- // Get last non-empty entry
- template <class OBJ> int GHash<OBJ>::Last() const {
-   register int pos=fCapacity-1;
--  while(0<=pos){ if(0<=hash[pos].hash) break; pos--; }
--  GASSERT(pos<0 || 0<=hash[pos].hash);
-+  while(0<=pos){ if(0<=(hash[pos].hash)) break; pos--; }
-+  GASSERT(pos<0 || 0<=(hash[pos].hash));
-   return pos;
-   }
- 
-@@ -474,8 +474,8 @@
- // Find next valid entry
- template <class OBJ> int GHash<OBJ>::Next(int pos) const {
-   GASSERT(0<=pos && pos<fCapacity);
--  while(++pos <= fCapacity-1){ if(0<=hash[pos].hash) break; }
--  GASSERT(fCapacity<=pos || 0<=hash[pos].hash);
-+  while(++pos <= fCapacity-1){ if(0<=(hash[pos].hash)) break; }
-+  GASSERT(fCapacity<=pos || 0<=(hash[pos].hash));
-   return pos;
-   }
- 
-@@ -483,8 +483,8 @@
- // Find previous valid entry
- template <class OBJ> int GHash<OBJ>::Prev(int pos) const {
-   GASSERT(0<=pos && pos<fCapacity);
--  while(--pos >= 0){ if(0<=hash[pos].hash) break; }
--  GASSERT(pos<0 || 0<=hash[pos].hash);
-+  while(--pos >= 0){ if(0<=(hash[pos].hash)) break; }
-+  GASSERT(pos<0 || 0<=(hash[pos].hash));
-   return pos;
-   }
- 
diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch
deleted file mode 100644
index 374ce519ef86..000000000000
--- a/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-Modify the buildsystem to work with the legacy version of samtools,
-which can coexist with the most recent version of samtools.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=577854
-
---- cufflinks-2.2.1/ax_bam.m4
-+++ cufflinks-2.2.1/ax_bam.m4
-@@ -102,7 +102,7 @@
- 
- 	AC_LANG_PUSH(C++)
-      	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
--	@%:@include <bam/bam.h>
-+	@%:@include <bam-0.1-legacy/bam.h>
- 	]], [[
- 	]])],[
-         AC_MSG_RESULT(yes)
-@@ -171,7 +171,7 @@
- 
- 		AC_LANG_PUSH(C++)
- 	     	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
--		@%:@include <bam/version.hpp>
-+		@%:@include <bam-0.1-legacy/version.hpp>
- 		]], [[
- 		]])],[
-         	AC_MSG_RESULT(yes)
-@@ -189,7 +189,7 @@
- 			AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).])
- 		fi
- 	else
--		BAM_LIB="-lbam"
-+		BAM_LIB="-lbam-0.1-legacy"
- 		AC_SUBST(BAM_CPPFLAGS)
- 		AC_SUBST(BAM_LDFLAGS)
- 		AC_SUBST(BAM_LIB)
---- cufflinks-2.2.1/src/hits.h
-+++ cufflinks-2.2.1/src/hits.h
-@@ -18,7 +18,7 @@
- 
- #include <boost/shared_ptr.hpp>
- 
--#include <bam/sam.h>
-+#include <bam-0.1-legacy/sam.h>
- 
- #include "common.h"
- #include "multireads.h"
diff --git a/sci-biology/cufflinks/metadata.xml b/sci-biology/cufflinks/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/cufflinks/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>
diff --git a/sci-biology/snpfile/Manifest b/sci-biology/snpfile/Manifest
deleted file mode 100644
index a6701a42a5d5..000000000000
--- a/sci-biology/snpfile/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX snpfile-2.0.1-ax-boost.patch 973 BLAKE2B ddfdefc7aae1c5e1e95498a1e3911f32455fb3918f390e0d2d741eaf67b7002b72af99e5d5bbf3cf0822b871463bb0624869c1d98fb45b2a2275b8790c0148a9 SHA512 cb517e30c06620de9d007261d238325daf48709ccd875d90c0cc99049dfd0ce80a506a3e9a97c786ac8329b1f1463a810407927cf17c1a25689b03f413417b94
-AUX snpfile-2.0.1-gcc44.patch 387 BLAKE2B 8ce01199b75387b700aaf6a3608212370aa49a0cc896cd9f2ac9c5807f03ed1c7b8663d8a6a2420bb5247ec461aafd30d6e64d3509300faeaa36b8d77259f68e SHA512 ac66850cae2bbbad9e1a989772490eb23ea3958c233e0fe32b20ffb3d7b5f547ff9d045974170c3302e8ca6bbbe5a2055acad24bb80cc6a3c527c3164e3f0e84
-AUX snpfile-2.0.1-gentoo.diff 20224 BLAKE2B 26ebe8dcccf954830621eb60f28e55f0cd4f759adb6a049b683cc5e69c084b4a3c09ee3b6b48b7d93757590686ceee8678b5bf643f65284583a894e122fcd6f8 SHA512 8628aa298b38376e439739c813ec87c80eb7c7f7874335e8f812eee05fab205ae900a00ec819021699fe835c2e9d38f880e9b391ccc4bfb46a8b91f028ed84ad
-AUX snpfile-2.0.1-gold.patch 1066 BLAKE2B 18b6353d38ffdde0f7ceb935f0162258e046e730cdf6f5a62f2d4a2918bdd3846b6306f33dda392f30bcd5c00174f1f24df3c5e94719d563a140b54922ca1cfc SHA512 81f2e5e91890e52cf40553ea70b12cdb09e5b8335303d72f6943e0058b62eb061eea4e52595c267de81af219f7b863025fb2aa7364d976101628b1f65ba27075
-DIST snpfile-2.0.1.tar.gz 171854 BLAKE2B 4f256892d3ead522c1aaef8db6fa486186233f0f6a1d3297e10104af504eace84f9396f28f00fb35242aed656e2a61fef7481a333acc69091deef746114533ab SHA512 e217e8b600d3ba7e2a8a0724d867bd9760572398f2e4e58625c1f74b0db9aa913db266da51fcfc05b90f3faf9eb6fbeb7bd988f105de013b51c24caa37c678c6
-EBUILD snpfile-2.0.1-r2.ebuild 886 BLAKE2B 03dd4c564b84e036d53af3c55a208d94975660ac53c14dcff971f25a28e8a03d3a21ed83d59bc1b0ab6f7e11b04d4e1a124c942d61fd9fc92f94deeb1620895f SHA512 7946475e80f92a1c76a4e92500cfad3f6eb4e0463014e07eb517f6a4ef0fb3ebff7143d18d22c887d970f186cc7a0847788d8b55e5b297d04820a9dfdb3475fa
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch b/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch
deleted file mode 100644
index f77b476f990d..000000000000
--- a/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-Modernise autoconf code to use modern archive macros.
-
---- a/configure.in
-+++ b/configure.in
-@@ -1,7 +1,7 @@
- AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk)
- AM_INIT_AUTOMAKE
- AC_CONFIG_MACRO_DIR([m4])
--AM_CONFIG_HEADER(config.hh)
-+AC_CONFIG_HEADERS([config.hh])
- 
- LT_INIT
- AC_PROG_CXX
-@@ -14,18 +14,9 @@
- fi
- AC_DEFINE_UNQUOTED(PREFIX, "$thePREFIX", [Installation prefix])
- 
--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>.
--************************************************************************
--************************************************************************
--]])
--)
--
-+AX_BOOST_BASE([1.33.1])
-+AX_BOOST_PROGRAM_OPTIONS
-+AX_BOOST_SIGNALS
- 
- AC_OUTPUT([
- 	Makefile
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch
deleted file mode 100644
index 2b79c2492ede..000000000000
--- a/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -ur snpfile-2.0.1.orig/input_archive.hh snpfile-2.0.1/input_archive.hh
---- snpfile-2.0.1.orig/input_archive.hh	2008-05-03 17:25:44.000000000 +0300
-+++ snpfile-2.0.1/input_archive.hh	2009-07-26 21:26:10.000000000 +0300
-@@ -26,6 +26,8 @@
- #ifndef INPUT_ARCHIVE_HH_INCLUDED
- #define INPUT_ARCHIVE_HH_INCLUDED
- 
-+#include <stdint.h>
-+
- #include <string>
- 
- #include "archive_common.hh"
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff
deleted file mode 100644
index b2a8a6b630ce..000000000000
--- a/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff
+++ /dev/null
@@ -1,533 +0,0 @@
-Fixing as-needed issues, provide shared libs
-
-https://bugs.gentoo.org/show_bug.cgi?id=294971
-
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -1,440 +1,92 @@
- ACLOCAL_AMFLAGS = -I m4
- 
--AM_CXXFLAGS =
--AM_CXXFLAGS += -Wall
--AM_CXXFLAGS += $(BOOST_CPPFLAGS)
-+AM_CXXFLAGS = -Wall $(BOOST_CPPFLAGS)
-+SUFFIXES = .cc 
-
--
--# for testing
--AM_CXXFLAGS += -g -O2 #-lefence
--
--# for profiling
--#CXXFLAGS    += -O3 -g -pg
--#AM_CXXFLAGS += -O3 -g -pg
--
--# for production
--#CXXFLAGS    += -O3 -fexpensive-optimizations -DNDEBUG
--#AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG
--
--# for coverage testing
--#CXXFLAGS    += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations
--#AM_CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations
--
--
--lib_LIBRARIES = libsnpfile.a
-+lib_LTLIBRARIES = libsnpfile.la
- 
- noinst_PROGRAMS =
--TESTS = 
--EXTRA_DIST =
--bin_PROGRAMS =
- 
- # conversion tools
--bin_PROGRAMS += text2snpfile
--bin_PROGRAMS += snpfile2text
--bin_PROGRAMS += snpfile2fastPHASE
--bin_PROGRAMS += fastPHASE2snpfile
--bin_PROGRAMS += snpfile2haploview
--bin_PROGRAMS += beagle_phase_snpfile
-+bin_PROGRAMS = text2snpfile snpfile2text snpfile2fastPHASE fastPHASE2snpfile \
-+	       snpfile2haploview beagle_phase_snpfile
- 
- # data extraction tools
--bin_PROGRAMS += snpfile_genotype_count
--bin_PROGRAMS += snpfile_phenotypes
--bin_PROGRAMS += snpfile_markers
--
--bin_PROGRAMS += snpfile_metadata_info
--bin_PROGRAMS += snpfile_set_metadata
--bin_PROGRAMS += snpfile_get_metadata
-+bin_PROGRAMS += snpfile_genotype_count snpfile_phenotypes snpfile_markers
-+
-+bin_PROGRAMS += snpfile_metadata_info snpfile_set_metadata snpfile_get_metadata
- 
- # other tools
- noinst_PROGRAMS += snpfile_split_on_column
- 
- # tests
--noinst_PROGRAMS += matrix_test
--TESTS +=           matrix_test
--noinst_PROGRAMS += file_test
--TESTS +=           file_test
--noinst_PROGRAMS += file_matrix_test
--TESTS +=           file_matrix_test
--noinst_PROGRAMS += readonly_matrix_test
--TESTS +=           readonly_matrix_test
--noinst_PROGRAMS += archives_test
--TESTS +=           archives_test
--noinst_PROGRAMS += metadata_access_test
--TESTS +=           metadata_access_test
--noinst_PROGRAMS += metadata_types_test
--TESTS +=           metadata_types_test
--noinst_PROGRAMS += iterators_test
--TESTS +=           iterators_test
--noinst_PROGRAMS += tabulate_test
--TESTS +=           tabulate_test
--noinst_PROGRAMS += metadata_filtering_test
--TESTS +=           metadata_filtering_test
-+TESTS = matrix_test file_test file_matrix_test readonly_matrix_test archives_test \
-+	metadata_access_test metadata_types_test iterators_test tabulate_test metadata_filtering_test
-+
-+noinst_PROGRAMS += $(TESTS)
- 
- #Utils for testing across different machines
--noinst_PROGRAMS += make_test_snpfile
--noinst_PROGRAMS += test_test_snpfile
-+noinst_PROGRAMS += make_test_snpfile test_test_snpfile
- 
- # other experiments...
--noinst_PROGRAMS += row_metadata_experiment
--noinst_PROGRAMS += metadata_cache_prototype
--noinst_PROGRAMS += matrix_benchmark
--noinst_PROGRAMS += matrix_benchmark_write
--noinst_PROGRAMS += matrix_benchmark_read
--
--
--
--matrix_test_LDADD =
--matrix_test_LDADD += $(BOOST_SIGNALS_LIB)
--matrix_test_SOURCES =
--matrix_test_SOURCES += test_util.hh test_util.cc
--matrix_test_SOURCES += matrix.hh matrix.cc
--matrix_test_SOURCES += array_matrix.hh array_matrix.cc
--matrix_test_SOURCES += file_matrix.hh file_matrix.cc
--matrix_test_SOURCES += input_archive.hh
--matrix_test_SOURCES += output_archive.hh
--matrix_test_SOURCES += metadata.hh metadata.cc
--matrix_test_SOURCES += snpfile.hh snpfile.cc
--matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
--matrix_test_SOURCES += matrix_test.cc
--
--
--file_test_LDADD =
--file_test_LDADD += $(BOOST_SIGNALS_LIB)
--file_test_SOURCES =
--file_test_SOURCES += test_util.hh test_util.cc
--file_test_SOURCES += metadata.hh metadata.cc
--file_test_SOURCES += snpfile.hh snpfile.cc
--file_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
--file_test_SOURCES += file_test.cc
--file_test_SOURCES += metadata_access.hh
--file_test_SOURCES += input_archive.hh
--file_test_SOURCES += output_archive.hh
--
--file_matrix_test_LDADD =
--file_matrix_test_LDADD += $(BOOST_SIGNALS_LIB)
--file_matrix_test_SOURCES =
--file_matrix_test_SOURCES += test_util.hh test_util.cc
--file_matrix_test_SOURCES += file_matrix.hh file_matrix.cc
--file_matrix_test_SOURCES += matrix.hh matrix.cc
--file_matrix_test_SOURCES += input_archive.hh
--file_matrix_test_SOURCES += output_archive.hh
--file_matrix_test_SOURCES += metadata.hh metadata.cc
--file_matrix_test_SOURCES += snpfile.hh snpfile.cc
--file_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
--file_matrix_test_SOURCES += file_matrix_test.cc
--
--
--readonly_matrix_test_LDADD =
--readonly_matrix_test_LDADD += $(BOOST_SIGNALS_LIB)
--readonly_matrix_test_SOURCES =
--readonly_matrix_test_SOURCES += test_util.hh test_util.cc
--readonly_matrix_test_SOURCES += array_matrix.hh array_matrix.cc
--readonly_matrix_test_SOURCES += file_matrix.hh file_matrix.cc
--readonly_matrix_test_SOURCES += matrix.hh matrix.cc
--readonly_matrix_test_SOURCES += input_archive.hh
--readonly_matrix_test_SOURCES += output_archive.hh
--readonly_matrix_test_SOURCES += metadata.hh metadata.cc
--readonly_matrix_test_SOURCES += snpfile.hh snpfile.cc
--readonly_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
--readonly_matrix_test_SOURCES += readonly_matrix_test.cc
--
--
--archives_test_SOURCES =
--archives_test_SOURCES += input_archive.hh
--archives_test_SOURCES += output_archive.hh
--archives_test_SOURCES += archives_test.cc
--
--
--metadata_access_test_LDADD =
--metadata_access_test_LDADD += $(BOOST_SIGNALS_LIB)
--metadata_access_test_SOURCES =
--metadata_access_test_SOURCES += test_util.hh test_util.cc
--metadata_access_test_SOURCES += metadata.hh metadata.cc
--metadata_access_test_SOURCES += snpfile.hh snpfile.cc
--metadata_access_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
--metadata_access_test_SOURCES += input_archive.hh
--metadata_access_test_SOURCES += output_archive.hh
--metadata_access_test_SOURCES += serialization_trait.hh
--metadata_access_test_SOURCES += metadata_access_test.cc
--
--
--metadata_types_test_LDADD =
--metadata_types_test_LDADD += $(BOOST_SIGNALS_LIB)
--metadata_types_test_SOURCES =
--metadata_types_test_SOURCES += test_util.hh test_util.cc
--metadata_types_test_SOURCES += metadata.hh metadata.cc
--metadata_types_test_SOURCES += snpfile.hh snpfile.cc
--metadata_types_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
--metadata_types_test_SOURCES += input_archive.hh
--metadata_types_test_SOURCES += output_archive.hh
--metadata_types_test_SOURCES += serialization_trait.hh
--metadata_types_test_SOURCES += metadata_types_test.cc
--
--
--iterators_test_SOURCES =
--iterators_test_SOURCES += iterators.hh
--iterators_test_SOURCES += array_matrix.hh array_matrix.cc
--iterators_test_SOURCES += matrix.hh matrix.cc
--iterators_test_SOURCES += iterators_test.cc
--
--
--tabulate_test_SOURCES =
--tabulate_test_SOURCES += tabulate.hh
--tabulate_test_SOURCES += array_matrix.hh array_matrix.cc
--tabulate_test_SOURCES += matrix.hh matrix.cc
--tabulate_test_SOURCES += tabulate_test.cc
--
--
--metadata_filtering_test_SOURCES =
--metadata_filtering_test_SOURCES += matrix.hh matrix.cc
--metadata_filtering_test_SOURCES += array_matrix.hh array_matrix.cc
--metadata_filtering_test_SOURCES += metadata_filtering.hh
--metadata_filtering_test_SOURCES += metadata_filtering_test.cc
--
--
--make_test_snpfile_LDADD =
--make_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB)
--make_test_snpfile_SOURCES =
--make_test_snpfile_SOURCES += metadata.hh metadata.cc
--make_test_snpfile_SOURCES += snpfile.hh snpfile.cc
--make_test_snpfile_SOURCES += matrix.hh matrix.cc
--make_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc
--make_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc
--make_test_snpfile_SOURCES += input_archive.hh
--make_test_snpfile_SOURCES += output_archive.hh
--make_test_snpfile_SOURCES += make_test_snpfile.cc
--
--
--test_test_snpfile_LDADD =
--test_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB)
--test_test_snpfile_SOURCES =
--test_test_snpfile_SOURCES += metadata.hh metadata.cc
--test_test_snpfile_SOURCES += snpfile.hh snpfile.cc
--test_test_snpfile_SOURCES += matrix.hh matrix.cc
--test_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc
--test_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc
--test_test_snpfile_SOURCES += input_archive.hh
--test_test_snpfile_SOURCES += output_archive.hh
--test_test_snpfile_SOURCES += test_test_snpfile.cc
--
--
--row_metadata_experiment_LDADD = 
--row_metadata_experiment_LDADD += $(BOOST_SIGNALS_LIB)
--row_metadata_experiment_SOURCES =
--row_metadata_experiment_SOURCES += matrix.hh matrix.cc
--row_metadata_experiment_SOURCES += array_matrix.hh array_matrix.cc
--row_metadata_experiment_SOURCES += file_matrix.hh file_matrix.cc
--row_metadata_experiment_SOURCES += input_archive.hh
--row_metadata_experiment_SOURCES += output_archive.hh
--row_metadata_experiment_SOURCES += metadata.hh metadata.cc
--row_metadata_experiment_SOURCES += snpfile.hh snpfile.cc
--row_metadata_experiment_SOURCES += byte_order_handler.hh byte_order_handler.cc
--row_metadata_experiment_SOURCES += test_util.hh test_util.cc
--row_metadata_experiment_SOURCES += row_metadata_experiment.cc
--
--
--metadata_cache_prototype_SOURCES  =
--metadata_cache_prototype_SOURCES += metadata_cache_prototype.cc
--metadata_cache_prototype_LDFLAGS  =
--metadata_cache_prototype_LDFLAGS += -L.
--metadata_cache_prototype_LDADD  = 
--metadata_cache_prototype_LDADD += $(BOOST_SIGNALS_LIB)
--metadata_cache_prototype_LDADD += -lsnpfile
--
--
--matrix_benchmark_LDADD  = 
--matrix_benchmark_LDADD += $(BOOST_SIGNALS_LIB)
--matrix_benchmark_SOURCES  =
--matrix_benchmark_SOURCES += test_util.hh test_util.cc
--matrix_benchmark_SOURCES += file_matrix.hh file_matrix.cc
--matrix_benchmark_SOURCES += array_matrix.hh array_matrix.cc
--matrix_benchmark_SOURCES += matrix.hh matrix.cc
--matrix_benchmark_SOURCES += input_archive.hh
--matrix_benchmark_SOURCES += output_archive.hh
--matrix_benchmark_SOURCES += metadata.hh metadata.cc
--matrix_benchmark_SOURCES += snpfile.hh snpfile.cc
--matrix_benchmark_SOURCES += byte_order_handler.hh byte_order_handler.cc
--matrix_benchmark_SOURCES += timing.hh timing.cc
--matrix_benchmark_SOURCES += matrix_benchmark.cc
--
--
--matrix_benchmark_write_LDADD  = 
--matrix_benchmark_write_LDADD += $(BOOST_SIGNALS_LIB)
--matrix_benchmark_write_SOURCES  =
--matrix_benchmark_write_SOURCES += file_matrix.hh file_matrix.cc
--matrix_benchmark_write_SOURCES += matrix.hh matrix.cc
--matrix_benchmark_write_SOURCES += input_archive.hh
--matrix_benchmark_write_SOURCES += output_archive.hh
--matrix_benchmark_write_SOURCES += metadata.hh metadata.cc
--matrix_benchmark_write_SOURCES += snpfile.hh snpfile.cc
--matrix_benchmark_write_SOURCES += byte_order_handler.hh byte_order_handler.cc
--matrix_benchmark_write_SOURCES += timing.hh timing.cc
--matrix_benchmark_write_SOURCES += matrix_benchmark_write.cc
--
--
--matrix_benchmark_read_LDADD  = 
--matrix_benchmark_read_LDADD += $(BOOST_SIGNALS_LIB)
--matrix_benchmark_read_SOURCES  =
--matrix_benchmark_read_SOURCES += file_matrix.hh file_matrix.cc
--matrix_benchmark_read_SOURCES += matrix.hh matrix.cc
--matrix_benchmark_read_SOURCES += input_archive.hh
--matrix_benchmark_read_SOURCES += output_archive.hh
--matrix_benchmark_read_SOURCES += metadata.hh metadata.cc
--matrix_benchmark_read_SOURCES += snpfile.hh snpfile.cc
--matrix_benchmark_read_SOURCES += byte_order_handler.hh byte_order_handler.cc
--matrix_benchmark_read_SOURCES += timing.hh timing.cc
--matrix_benchmark_read_SOURCES += matrix_benchmark_read.cc
-+noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \
-+	matrix_benchmark_write matrix_benchmark_read
-+
-+LDADD = $(top_builddir)/libsnpfile.la
-+
-+matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc
-+
-+file_test_SOURCES = test_util.hh test_util.cc file_test.cc metadata_access.hh input_archive.hh \
-+	output_archive.hh
-+
-+file_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
-+	file_matrix_test.cc
-+
-+readonly_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
-+	readonly_matrix_test.cc
- 
-+archives_test_SOURCES = input_archive.hh output_archive.hh archives_test.cc
-+
-+metadata_access_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
-+	serialization_trait.hh metadata_access_test.cc
-+
-+metadata_types_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
-+	serialization_trait.hh metadata_types_test.cc
-+
-+iterators_test_SOURCES = iterators.hh iterators_test.cc
-+
-+tabulate_test_SOURCES = tabulate.hh tabulate_test.cc
-+
-+metadata_filtering_test_SOURCES = metadata_filtering.hh metadata_filtering_test.cc
-+
-+make_test_snpfile_SOURCES = input_archive.hh output_archive.hh make_test_snpfile.cc
-+
-+test_test_snpfile_SOURCES = input_archive.hh output_archive.hh test_test_snpfile.cc
-+
-+row_metadata_experiment_SOURCES = input_archive.hh output_archive.hh test_util.hh test_util.cc \
-+	row_metadata_experiment.cc
-+
-+matrix_benchmark_SOURCES  = test_util.hh test_util.cc input_archive.hh \
-+	output_archive.hh timing.hh timing.cc matrix_benchmark.cc
-+
-+matrix_benchmark_write_SOURCES  = input_archive.hh output_archive.hh \
-+	timing.hh timing.cc matrix_benchmark_write.cc
-+
-+matrix_benchmark_read_SOURCES  = input_archive.hh output_archive.hh \
-+	timing.hh timing.cc matrix_benchmark_read.cc
-+
-+snpfile_genotype_count_SOURCES = genotype_count.cc
- 
- snpfileincludedir = $(includedir)/snpfile
--snpfileinclude_HEADERS  =
--snpfileinclude_HEADERS += common.hh
--snpfileinclude_HEADERS += matrix.hh
--snpfileinclude_HEADERS += file_matrix.hh
--snpfileinclude_HEADERS += array_matrix.hh
--snpfileinclude_HEADERS += byte_order_handler.hh
--snpfileinclude_HEADERS += metadata.hh
--snpfileinclude_HEADERS += metadata_access.hh
--snpfileinclude_HEADERS += archive_common.hh
--snpfileinclude_HEADERS += archives.hh
--snpfileinclude_HEADERS += input_archive.hh
--snpfileinclude_HEADERS += output_archive.hh
--snpfileinclude_HEADERS += snpfile.hh
--snpfileinclude_HEADERS += serialization_trait.hh
--snpfileinclude_HEADERS += type_trait.hh
--snpfileinclude_HEADERS += iterators.hh
--snpfileinclude_HEADERS += tabulate.hh
--
--libsnpfile_a_SOURCES  =
--libsnpfile_a_SOURCES += common.hh
--libsnpfile_a_SOURCES += matrix.hh matrix.cc
--libsnpfile_a_SOURCES += file_matrix.hh file_matrix.cc
--libsnpfile_a_SOURCES += array_matrix.cc array_matrix.hh
--libsnpfile_a_SOURCES += byte_order_handler.cc byte_order_handler.hh
--libsnpfile_a_SOURCES += metadata.hh metadata.cc metadata_access.hh
--libsnpfile_a_SOURCES += archive_common.hh
--libsnpfile_a_SOURCES += archives.hh
--libsnpfile_a_SOURCES += input_archive.hh
--libsnpfile_a_SOURCES += output_archive.hh
--libsnpfile_a_SOURCES += snpfile.hh snpfile.cc
--libsnpfile_a_SOURCES += serialization_trait.hh
--libsnpfile_a_SOURCES += type_trait.hh
--
--text2snpfile_SOURCES =
--text2snpfile_SOURCES += text2snpfile.cc
--text2snpfile_LDFLAGS  =
--text2snpfile_LDFLAGS += -L.
--text2snpfile_LDADD  =
--text2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
--text2snpfile_LDADD += $(BOOST_SIGNALS_LIB)
--text2snpfile_LDADD += -lsnpfile
--
--snpfile2text_SOURCES =
--snpfile2text_SOURCES += snpfile2text.cc
--snpfile2text_LDFLAGS  =
--snpfile2text_LDFLAGS += -L.
--snpfile2text_LDADD  =
--snpfile2text_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
--snpfile2text_LDADD += $(BOOST_SIGNALS_LIB)
--snpfile2text_LDADD += -lsnpfile
--
--
--snpfile2fastPHASE_SOURCES =
--snpfile2fastPHASE_SOURCES += snpfile2fastPHASE.cc
--snpfile2fastPHASE_LDFLAGS  =
--snpfile2fastPHASE_LDFLAGS += -L.
--snpfile2fastPHASE_LDADD  =
--snpfile2fastPHASE_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
--snpfile2fastPHASE_LDADD += $(BOOST_SIGNALS_LIB)
--snpfile2fastPHASE_LDADD += -lsnpfile
--
--fastPHASE2snpfile_SOURCES =				   
--fastPHASE2snpfile_SOURCES += fastPHASE2snpfile.cc	   
--fastPHASE2snpfile_LDFLAGS  =				   
--fastPHASE2snpfile_LDFLAGS += -L.			   
--fastPHASE2snpfile_LDADD  =				   
--fastPHASE2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)	   
--fastPHASE2snpfile_LDADD += $(BOOST_SIGNALS_LIB)		   
--fastPHASE2snpfile_LDADD += -lsnpfile                       
--
--
--snpfile2haploview_SOURCES =
--snpfile2haploview_SOURCES += snpfile2haploview.cc
--snpfile2haploview_LDFLAGS  =
--snpfile2haploview_LDFLAGS += -L.
--snpfile2haploview_LDADD  =
--snpfile2haploview_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
--snpfile2haploview_LDADD += $(BOOST_SIGNALS_LIB)
--snpfile2haploview_LDADD += -lsnpfile
--
--
--beagle_phase_snpfile_SOURCES =				 
--beagle_phase_snpfile_SOURCES += beagle_phase_snpfile.cc	 
--beagle_phase_snpfile_LDFLAGS  =				 
--beagle_phase_snpfile_LDFLAGS += -L.			 
--beagle_phase_snpfile_LDADD  =				 
--beagle_phase_snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)	 
--beagle_phase_snpfile_LDADD += $(BOOST_SIGNALS_LIB)		 
--beagle_phase_snpfile_LDADD += -lsnpfile                     
--
--snpfile_genotype_count_SOURCES =
--snpfile_genotype_count_SOURCES += genotype_count.cc
--snpfile_genotype_count_LDFLAGS  =
--snpfile_genotype_count_LDFLAGS += -L.
--snpfile_genotype_count_LDADD  =
--snpfile_genotype_count_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
--snpfile_genotype_count_LDADD += $(BOOST_SIGNALS_LIB)
--snpfile_genotype_count_LDADD += -lsnpfile
--
--snpfile_phenotypes_SOURCES =
--snpfile_phenotypes_SOURCES += snpfile_phenotypes.cc
--snpfile_phenotypes_LDFLAGS  =
--snpfile_phenotypes_LDFLAGS += -L.
--snpfile_phenotypes_LDADD  =
--snpfile_phenotypes_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
--snpfile_phenotypes_LDADD += $(BOOST_SIGNALS_LIB)
--snpfile_phenotypes_LDADD += -lsnpfile
--
--snpfile_markers_SOURCES =
--snpfile_markers_SOURCES += snpfile_markers.cc
--snpfile_markers_LDFLAGS  =
--snpfile_markers_LDFLAGS += -L.
--snpfile_markers_LDADD  =
--snpfile_markers_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
--snpfile_markers_LDADD += $(BOOST_SIGNALS_LIB)
--snpfile_markers_LDADD += -lsnpfile
--
--snpfile_metadata_info_SOURCES =
--snpfile_metadata_info_SOURCES += snpfile_metadata_info.cc
--snpfile_metadata_info_LDFLAGS  =
--snpfile_metadata_info_LDFLAGS += -L.
--snpfile_metadata_info_LDADD  =
--snpfile_metadata_info_LDADD += $(BOOST_SIGNALS_LIB)
--snpfile_metadata_info_LDADD += -lsnpfile
--
--snpfile_set_metadata_SOURCES =
--snpfile_set_metadata_SOURCES += snpfile_set_metadata.cc
--snpfile_set_metadata_LDFLAGS  =
--snpfile_set_metadata_LDFLAGS += -L.
--snpfile_set_metadata_LDADD  =
--snpfile_set_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
--snpfile_set_metadata_LDADD += $(BOOST_SIGNALS_LIB)
--snpfile_set_metadata_LDADD += -lsnpfile
--
--snpfile_get_metadata_SOURCES =
--snpfile_get_metadata_SOURCES += snpfile_get_metadata.cc
--snpfile_get_metadata_LDFLAGS  =
--snpfile_get_metadata_LDFLAGS += -L.
--snpfile_get_metadata_LDADD  =
--snpfile_get_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
--snpfile_get_metadata_LDADD += $(BOOST_SIGNALS_LIB)
--snpfile_get_metadata_LDADD += -lsnpfile
--
--snpfile_split_on_column_SOURCES =
--snpfile_split_on_column_SOURCES += snpfile_split_on_column.cc
--snpfile_split_on_column_LDFLAGS =
--snpfile_split_on_column_LDFLAGS += -L.
--snpfile_split_on_column_LDADD  =
--snpfile_split_on_column_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
--snpfile_split_on_column_LDADD += $(BOOST_SIGNALS_LIB)
--snpfile_split_on_column_LDADD += -lsnpfile
-+snpfileinclude_HEADERS = common.hh matrix.hh file_matrix.hh array_matrix.hh \
-+	byte_order_handler.hh metadata.hh metadata_access.hh archive_common.hh \
-+	archives.hh input_archive.hh output_archive.hh snpfile.hh serialization_trait.hh \
-+	type_trait.hh iterators.hh tabulate.hh
-+
-+libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix.cc \
-+	array_matrix.cc array_matrix.hh byte_order_handler.cc byte_order_handler.hh \
-+	metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \
-+	input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \
-+	type_trait.hh
-+libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB)
-+
---- a/configure.in
-+++ b/configure.in
-@@ -1,10 +1,11 @@
- AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk)
- AM_INIT_AUTOMAKE
-+AC_CONFIG_MACRO_DIR([m4])
- AM_CONFIG_HEADER(config.hh)
- 
-+LT_INIT
- AC_PROG_CXX
- AC_PROG_INSTALL
--AC_PROG_RANLIB
- 
- if test "x$prefix" != xNONE; then
-    thePREFIX=$prefix
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch
deleted file mode 100644
index 2211aa36c0ca..000000000000
--- a/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch
+++ /dev/null
@@ -1,23 +0,0 @@
- Makefile.am |    4 ++--
- 1 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/Makefile.am b/Makefile.am
-index 06fd733..5805c48 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -32,7 +32,7 @@ noinst_PROGRAMS += make_test_snpfile test_test_snpfile
- noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \
- 	matrix_benchmark_write matrix_benchmark_read
- 
--LDADD = $(top_builddir)/libsnpfile.la
-+LDADD = $(top_builddir)/libsnpfile.la $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++
- 
- matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc
- 
-@@ -88,5 +88,5 @@ libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix
- 	metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \
- 	input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \
- 	type_trait.hh
--libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB)
-+libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++
- 
diff --git a/sci-biology/snpfile/metadata.xml b/sci-biology/snpfile/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/snpfile/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild b/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild
deleted file mode 100644
index bbeb3111901f..000000000000
--- a/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools
-
-DESCRIPTION="A library and API for manipulating large SNP datasets"
-HOMEPAGE="http://www.birc.au.dk/~mailund/SNPFile/"
-SRC_URI="http://www.birc.au.dk/~mailund/SNPFile/download/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="static-libs"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-libs/boost:="
-DEPEND="
-	${RDEPEND}
-	>=sys-devel/autoconf-archive-2016.09.16"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc44.patch
-	"${FILESDIR}"/${P}-gentoo.diff
-	"${FILESDIR}"/${P}-gold.patch
-	"${FILESDIR}"/${P}-ax-boost.patch
-)
-
-src_prepare() {
-	default
-	mv configure.{in,ac} || die
-	rm m4/ax_boost.m4 || die
-	eautoreconf
-}
-
-src_configure() {
-	econf $(use_enable static-libs static)
-}
-
-src_install() {
-	default
-
-	if ! use static-libs; then
-		find "${D}" -name '*.la' -delete || die
-	fi
-}