commit: 68e3a80a1418cd79a1a32a00cd193a3cffe70974
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun May 19 21:50:02 2019 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun May 19 21:50:02 2019 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=68e3a80a
sci-biology/{blossoc,snpfile}: Remove last-rited pkgs
Closes: https://bugs.gentoo.org/683762
Signed-off-by: David Seifert <soap <AT> gentoo.org>
profiles/package.mask | 7 -
sci-biology/blossoc/Manifest | 1 -
sci-biology/blossoc/blossoc-1.4.0-r1.ebuild | 36 --
.../files/blossoc-1.4.0-fix-build-system.patch | 256 ----------
.../blossoc/files/blossoc-1.4.0-gcc43.patch | 15 -
sci-biology/blossoc/metadata.xml | 8 -
sci-biology/snpfile/Manifest | 1 -
.../snpfile/files/snpfile-2.0.1-ax-boost.patch | 35 --
.../snpfile/files/snpfile-2.0.1-gcc44.patch | 12 -
.../snpfile/files/snpfile-2.0.1-gentoo.diff | 533 ---------------------
sci-biology/snpfile/files/snpfile-2.0.1-gold.patch | 23 -
sci-biology/snpfile/metadata.xml | 8 -
sci-biology/snpfile/snpfile-2.0.1-r2.ebuild | 46 --
13 files changed, 981 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index b44080fc58e..450f394b454 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -421,13 +421,6 @@ app-emulation/e-uae
# Depends on >=virtual/{jdk,jre}-11 which is masked
=www-servers/tomcat-9.0.19
-# David Seifert <s...@gentoo.org> (19 Apr 2019)
-# Fails to build with >=dev-libs/boost-1.70 due to Boost.Signals1
-# removal. No development, no maintenance, no homepage.
-# Removal in 30 days. Bug #683762.
-sci-biology/blossoc
-sci-biology/snpfile
-
# Georgy Yakovlev <gyakov...@gentoo.org> (18 Apr 2019)
# This version is provided for testing of the upcoming 0.8.0 release.
# It is not recommended for use, it contains known bugs.
diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest
deleted file mode 100644
index 84cf1ab90b7..00000000000
--- a/sci-biology/blossoc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST blossoc-1.4.0.tar.gz 194885 BLAKE2B
040b70d737007d691399e9ea5446b45ed119237e86f83a85521d1555fff253bc9285c5d9a91f0e4f30a38d974a43d5e439fb61aea9686c5fbff233e6491dcdce
SHA512
fd47c85df5f1f97527e1abb1e56b05c02fa44c1c110abc222d895b2370324a26970446084e62adf02ce0c7dc332635d40dd1505d423571b424865425f6b2a327
diff --git a/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild
b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild
deleted file mode 100644
index 9fd1189e025..00000000000
--- 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}"/${PN}-1.4.0-fix-build-system.patch
-)
-
-src_prepare() {
- default
- mv configure.{in,ac} || die
- rm m4/ax_boost.m4 || die
- eautoreconf
-}
diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch
b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch
deleted file mode 100644
index 21234cc3cfb..00000000000
--- a/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch
+++ /dev/null
@@ -1,256 +0,0 @@
-* Modernise Autoconf code
-* Use pkg-config for finding GSL
-* Use latest archvie macros to find Boost
-* Compile tests only when running make check
-
---- a/configure.in
-+++ b/configure.in
-@@ -1,6 +1,6 @@
- AC_INIT(blossoc, 1.4.0, mail...@birc.au.dk)
- AM_INIT_AUTOMAKE
--AM_CONFIG_HEADER(config.hh)
-+AC_CONFIG_HEADERS([config.hh])
-
- AC_PROG_CXX
- AC_PROG_INSTALL
-@@ -12,74 +12,16 @@
- fi
- AC_DEFINE_UNQUOTED(PREFIX, "$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 64b5fe46e30..00000000000
--- 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 <sebastianlut...@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 959160fe46b..00000000000
--- 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-biol...@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 c72ea82041b..00000000000
--- a/sci-biology/snpfile/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST snpfile-2.0.1.tar.gz 171854 BLAKE2B
4f256892d3ead522c1aaef8db6fa486186233f0f6a1d3297e10104af504eace84f9396f28f00fb35242aed656e2a61fef7481a333acc69091deef746114533ab
SHA512
e217e8b600d3ba7e2a8a0724d867bd9760572398f2e4e58625c1f74b0db9aa913db266da51fcfc05b90f3faf9eb6fbeb7bd988f105de013b51c24caa37c678c6
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 f77b476f990..00000000000
--- 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, mail...@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 2b79c2492ed..00000000000
--- 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 b2a8a6b630c..00000000000
--- 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) $(BOOST_SIGNALS_LIB)
-+
---- a/configure.in
-+++ b/configure.in
-@@ -1,10 +1,11 @@
- AC_INIT(snpfile, 2.0.1, mail...@birc.au.dk)
- AM_INIT_AUTOMAKE
-+AC_CONFIG_MACRO_DIR([m4])
- AM_CONFIG_HEADER(config.hh)
-
-+LT_INIT
- AC_PROG_CXX
- AC_PROG_INSTALL
--AC_PROG_RANLIB
-
- if test "x$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 2211aa36c0c..00000000000
--- 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) $(BOOST_SIGNALS_LIB)
-lstdc++
-
diff --git a/sci-biology/snpfile/metadata.xml b/sci-biology/snpfile/metadata.xml
deleted file mode 100644
index 959160fe46b..00000000000
--- a/sci-biology/snpfile/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biol...@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild
b/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild
deleted file mode 100644
index bbeb3111901..00000000000
--- a/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools
-
-DESCRIPTION="A library and API for manipulating large SNP datasets"
-HOMEPAGE="http://www.birc.au.dk/~mailund/SNPFile/";
-SRC_URI="http://www.birc.au.dk/~mailund/SNPFile/download/${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
-}
