proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

7 files changed, 636 insertions, 0 deletions

diff --git a/sci-biology/snpfile/Manifest b/sci-biology/snpfile/Manifest
new file mode 100644
index 000000000000..370468a92b39
--- /dev/null
+++ b/sci-biology/snpfile/Manifest
@@ -0,0 +1 @@
+DIST snpfile-2.0.1.tar.gz 171854 SHA256 71569e0dcd426447d1a5d215fb47615074a4c8d935cf70ef63c5f47a411b0b76
diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch
new file mode 100644
index 000000000000..2b79c2492ede
--- /dev/null
+++ b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch
@@ -0,0 +1,12 @@
+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
new file mode 100644
index 000000000000..e6a8d60ec69c
--- /dev/null
+++ b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff
@@ -0,0 +1,533 @@
+Fixing as-needed issues, provide shared libs
+
+https://bugs.gentoo.org/show_bug.cgi?id=294971
+
+--- Makefile.am
++++ 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) $(BOOST_SIGNALS_LIB)
++
+--- configure.in
++++ configure.in
+@@ -1,10 +1,11 @@
+ AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk)
+ AM_INIT_AUTOMAKE
++AC_CONFIG_MACRO_DIR([m4])
+ AM_CONFIG_HEADER(config.hh)
+ 
++LT_INIT
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+-AC_PROG_RANLIB
+ 
+ if test "x$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
new file mode 100644
index 000000000000..2211aa36c0ca
--- /dev/null
+++ b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch
@@ -0,0 +1,23 @@
+ 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
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/snpfile/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/snpfile/snpfile-2.0.1-r1.ebuild b/sci-biology/snpfile/snpfile-2.0.1-r1.ebuild
new file mode 100644
index 000000000000..b06f628fa020
--- /dev/null
+++ b/sci-biology/snpfile/snpfile-2.0.1-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit autotools eutils multilib
+
+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/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="static-libs"
+KEYWORDS="amd64 x86"
+
+DEPEND="dev-libs/boost"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-gcc44.patch \
+		"${FILESDIR}"/${P}-gentoo.diff \
+		"${FILESDIR}"/${P}-gold.patch
+	eautoreconf
+}
+
+src_configure() {
+	econf $(use_enable static-libs static)
+}
+
+src_install() {
+	default
+	use static-libs || rm "${D}"/usr/$(get_libdir)/lib${PN}.la
+}
diff --git a/sci-biology/snpfile/snpfile-2.0.1.ebuild b/sci-biology/snpfile/snpfile-2.0.1.ebuild
new file mode 100644
index 000000000000..6f57debb2930
--- /dev/null
+++ b/sci-biology/snpfile/snpfile-2.0.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=2
+inherit eutils
+
+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/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+RDEPEND="dev-libs/boost"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-gcc44.patch
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "emake install failed"
+}