gentoo resync : 21.05.2019

7 files changed, 0 insertions, 664 deletions

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
-}