diff options
Diffstat (limited to 'sci-biology')
23 files changed, 0 insertions, 1307 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex 62558baa4eda..ac7504d61b0f 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest deleted file mode 100644 index 17048b8c8248..000000000000 --- a/sci-biology/blossoc/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -AUX blossoc-1.4.0-fix-build-system.patch 8380 BLAKE2B a0d682fe3d831db664d798ace2fadc30edb2feb8c2a25b04e5256b4e5ee402c38c5f5462f62aa5044c6652c735e12752ca1c74ddc27b925b1acdfeb6b2fbe9b6 SHA512 e1e97db5446916fd3ea7ca84baddde4771f6ee0081e17bd28e473a85565c1f0d1aa5e4385ee77a473f67eb5dd36eff7849dd334e31e4a4e1fb47737e3597e091 -AUX blossoc-1.4.0-gcc43.patch 303 BLAKE2B 55263656a037453fa0e1ab6237dae51f1042b08164639332cf40017d4309465c43e8a044eda0ff11025625fcd3fe85a9fae210be9da2a59cc72c56aa973d09aa SHA512 600890d9e40f56923c84e181957abfb2e75b66992b3f7b406f15a6cdb779527868e6b37c573e9b22e81964ff0600080b73ec967df60ed8d9fcfc84c2e6810093 -DIST blossoc-1.4.0.tar.gz 194885 BLAKE2B 040b70d737007d691399e9ea5446b45ed119237e86f83a85521d1555fff253bc9285c5d9a91f0e4f30a38d974a43d5e439fb61aea9686c5fbff233e6491dcdce SHA512 fd47c85df5f1f97527e1abb1e56b05c02fa44c1c110abc222d895b2370324a26970446084e62adf02ce0c7dc332635d40dd1505d423571b424865425f6b2a327 -EBUILD blossoc-1.4.0-r1.ebuild 726 BLAKE2B 07e562bb5f5a1ecf84ff337187f4fef1c97b95d7a3f613020b8010a550ac626f4cf2896fb5e4372019e4366478f897db4dbbc7d4a854424e2cc6c05a891d4a51 SHA512 f345c811c9dd49b716ec91a5cb3460a763cc125fe93a5a45a29245a08544455dd9686264e69333c54c5cc736b2b5d0cd76bc7e9b3cd279c5264a83726d81067b -MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild deleted file mode 100644 index 9fd1189e025a..000000000000 --- a/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools - -DESCRIPTION="A linkage disequilibrium association mapping tool" -HOMEPAGE="http://www.daimi.au.dk/~mailund/Blossoc/" -SRC_URI="http://www.daimi.au.dk/~mailund/Blossoc/download/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-libs/gsl:= - dev-libs/boost:= - sci-biology/snpfile" -DEPEND=" - ${RDEPEND} - >=sys-devel/autoconf-archive-2016.09.16 - virtual/pkgconfig" - -PATCHES=( - "${FILESDIR}"/${PN}-1.4.0-gcc43.patch - "${FILESDIR}"/${PN}-1.4.0-fix-build-system.patch -) - -src_prepare() { - default - mv configure.{in,ac} || die - rm m4/ax_boost.m4 || die - eautoreconf -} diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch deleted file mode 100644 index 21234cc3cfb3..000000000000 --- a/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch +++ /dev/null @@ -1,256 +0,0 @@ -* Modernise Autoconf code -* Use pkg-config for finding GSL -* Use latest archvie macros to find Boost -* Compile tests only when running make check - ---- a/configure.in -+++ b/configure.in -@@ -1,6 +1,6 @@ - AC_INIT(blossoc, 1.4.0, mailund@birc.au.dk) - AM_INIT_AUTOMAKE --AM_CONFIG_HEADER(config.hh) -+AC_CONFIG_HEADERS([config.hh]) - - AC_PROG_CXX - AC_PROG_INSTALL -@@ -12,74 +12,16 @@ - fi - AC_DEFINE_UNQUOTED(PREFIX, "$thePREFIX", [Installation prefix]) - --AC_CHECK_LIB(m, sin, dnl FOUND, DO NOTHING --, dnl NOT FOUND --AC_ERROR([[ --************************************************************************ --************************************************************************ --Didn't find the math library (-lm) -- I won't even guess about what is --wrong on this machine... --************************************************************************ --************************************************************************ --]]) --) -- --AX_BOOST([1.33.1],, --AC_ERROR([[ --************************************************************************ --************************************************************************ --The Boost library was not found on this system. We use this library --extensively, and cannot proceed without it. You can obtain it from --<http://www.boost.org>. --************************************************************************ --************************************************************************ --]]) --) -- -- --AC_CHECK_LIB(gslcblas, cblas_dsdot, dnl FOUND, DO NOTHING --, dnl NOT FOUND --AC_ERROR([[ --************************************************************************ --************************************************************************ --The GNU Scientific Library (GSL) was not found. This library is --needed for some of the numerical calculations used for scoring the --significance of local genealogies and can be obtained at --<http://www.gnu.org/software/gsl/>. --************************************************************************ --************************************************************************ --]]) --) -- --AC_CHECK_LIB(gsl, gsl_cdf_chisq_Q, dnl FOUND, DO NOTHING --, dnl NOT FOUND --AC_ERROR([[ --************************************************************************ --************************************************************************ --The GNU Scientific Library (GSL) was not found. This library is --needed for some of the numerical calculations used for scoring the --significance of local genealogies and can be obtained at --<http://www.gnu.org/software/gsl/>. --************************************************************************ --************************************************************************ --]]) --) -- --AC_CHECK_LIB(snpfile, main, dnl main isn't there, but this avoids namespaces --dnl FOUND --, --dnl NOT FOUND --AC_ERROR([[ --************************************************************************ --************************************************************************ --The SNPFile library was not found. This library is needed for data --representation and can be obtained at --<http://www.birc.au.dk/~mailund/SNPFile/>. --************************************************************************ --************************************************************************ --]]) --) -- -+AC_SEARCH_LIBS([sin], [m], [], [ -+ AC_MSG_ERROR([unable to find the sin() function]) -+]) -+ -+PKG_CHECK_MODULES([GSL], [gsl]) -+ -+AX_BOOST_BASE([1.33.1]) -+AX_BOOST_PROGRAM_OPTIONS -+AX_BOOST_SERIALIZATION -+AX_BOOST_SIGNALS - - AC_OUTPUT([ - Makefile ---- a/Makefile.am -+++ b/Makefile.am -@@ -3,9 +3,6 @@ - AM_CXXFLAGS += -Wall - AM_CXXFLAGS += $(BOOST_CPPFLAGS) - --# for testing --AM_CXXFLAGS += -g -O0 #-lefence -- - # for coverage testing - #AM_CXXFLAGS += -O3 -fexpensive-optimizations -g -fprofile-arcs -ftest-coverage - -@@ -15,11 +12,11 @@ - # for production - #AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG - --noinst_PROGRAMS = -+check_PROGRAMS = -+noinst_PROGRAMS = - TESTS = - EXTRA_DIST = - --TESTS += first_test.sh - EXTRA_DIST += first_test.sh - - man_MANS = blossoc.1 snpfile_blossoc.1 blossoc_regions.1 blossoc_trees.1 -@@ -37,20 +34,20 @@ - noinst_PROGRAMS += snpfile_iblossoc #ditto - noinst_PROGRAMS += fast_snpfile_iblossoc - --noinst_PROGRAMS += matrix_test --TESTS += matrix_test --noinst_PROGRAMS += incompatibility_test tree_test tree_builder_test --TESTS += incompatibility_test tree_test tree_builder_test -+check_PROGRAMS += matrix_test -+TESTS += matrix_test -+check_PROGRAMS += incompatibility_test tree_test tree_builder_test -+TESTS += incompatibility_test tree_test tree_builder_test - EXTRA_DIST += testdata/CF/cf-positions.txt - EXTRA_DIST += testdata/CF/cf-haplotypes.txt - EXTRA_DIST += testdata/interaction/positions.txt - EXTRA_DIST += testdata/interaction/haplotypes.txt --noinst_PROGRAMS += score_test io_test --TESTS += score_test io_test --noinst_PROGRAMS += incompatible_regress_test --TESTS += incompatible_regress_test --noinst_PROGRAMS += genotype_score_test --TESTS += genotype_score_test.sh -+check_PROGRAMS += score_test io_test -+TESTS += score_test io_test -+check_PROGRAMS += incompatible_regress_test -+TESTS += incompatible_regress_test -+check_PROGRAMS += genotype_score_test -+TESTS += genotype_score_test.sh - EXTRA_DIST += genotype_score_test.sh - EXTRA_DIST += genotype_score_test.expected - TESTS += interactions_regression_test.sh -@@ -120,6 +117,7 @@ - - - blossoc_regions_LDADD = -+blossoc_regions_LDADD += -lsnpfile - blossoc_regions_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) - blossoc_regions_SOURCES = - blossoc_regions_SOURCES += incompatibility.hh incompatibility.cc -@@ -129,6 +127,7 @@ - blossoc_regions_SOURCES += regions.cc - - blossoc_trees_LDADD = -+blossoc_trees_LDADD += -lsnpfile - blossoc_trees_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) - blossoc_trees_SOURCES = - blossoc_trees_SOURCES += matrix_utils.hh matrix_utils.cc -@@ -142,6 +141,8 @@ - - - blossoc_LDADD = -+blossoc_LDADD += -lsnpfile -+blossoc_LDADD += $(GSL_LIBS) - blossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) - blossoc_SOURCES = - blossoc_SOURCES += tree.hh tree.cc -@@ -158,6 +159,8 @@ - blossoc_SOURCES += blossoc.cc - - snpfile_blossoc_LDADD = -+snpfile_blossoc_LDADD += -lsnpfile -+snpfile_blossoc_LDADD += $(GSL_LIBS) - snpfile_blossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) - snpfile_blossoc_LDADD += $(BOOST_SERIALIZATION_LIB) - snpfile_blossoc_LDADD += $(BOOST_SIGNALS_LIB) -@@ -176,6 +179,8 @@ - snpfile_blossoc_SOURCES += snpfile_blossoc.cc - - iblossoc_LDADD = -+iblossoc_LDADD += -lsnpfile -+iblossoc_LDADD += $(GSL_LIBS) - iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) - iblossoc_SOURCES = - iblossoc_SOURCES += tree.hh tree.cc -@@ -191,6 +196,8 @@ - iblossoc_SOURCES += interactions.cc - - low_mem_iblossoc_LDADD = -+low_mem_iblossoc_LDADD += -lsnpfile -+low_mem_iblossoc_LDADD += $(GSL_LIBS) - low_mem_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) - low_mem_iblossoc_SOURCES = - low_mem_iblossoc_SOURCES += tree.hh tree.cc -@@ -206,6 +213,8 @@ - low_mem_iblossoc_SOURCES += low_mem_interactions.cc - - snpfile_iblossoc_LDADD = -+snpfile_iblossoc_LDADD += -lsnpfile -+snpfile_iblossoc_LDADD += $(GSL_LIBS) - snpfile_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) - snpfile_iblossoc_LDADD += $(BOOST_SERIALIZATION_LIB) - snpfile_iblossoc_LDADD += $(BOOST_SIGNALS_LIB) -@@ -223,6 +232,8 @@ - snpfile_iblossoc_SOURCES += snpfile_interactions.cc - - fast_snpfile_iblossoc_LDADD = -+fast_snpfile_iblossoc_LDADD += -lsnpfile -+fast_snpfile_iblossoc_LDADD += $(GSL_LIBS) - fast_snpfile_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) - fast_snpfile_iblossoc_LDADD += $(BOOST_SERIALIZATION_LIB) - fast_snpfile_iblossoc_LDADD += $(BOOST_SIGNALS_LIB) -@@ -239,6 +250,28 @@ - fast_snpfile_iblossoc_SOURCES += io.hh io.cc - fast_snpfile_iblossoc_SOURCES += fast_snpfile_interactions.cc - -+matrix_test_LDADD = -+matrix_test_LDADD += -lsnpfile -+ -+incompatibility_test_LDADD = -+incompatibility_test_LDADD += -lsnpfile -+ -+tree_builder_test_LDADD = -+tree_builder_test_LDADD += -lsnpfile -+ -+score_test_LDADD = -+score_test_LDADD += -lsnpfile -+score_test_LDADD += $(GSL_LIBS) -+ -+io_test_LDADD = -+io_test_LDADD += -lsnpfile -+ -+incompatible_regress_test_LDADD = -+incompatible_regress_test_LDADD += -lsnpfile -+ -+genotype_score_test_LDADD = -+genotype_score_test_LDADD += -lsnpfile -+genotype_score_test_LDADD += $(GSL_LIBS) - - - # include GUI in source distributions... diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch deleted file mode 100644 index 64b5fe46e30e..000000000000 --- a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch +++ /dev/null @@ -1,15 +0,0 @@ -Fixes build with >=GCC-4.3 - -http://bugs.gentoo.org/show_bug.cgi?id=292949 - -Patch written by Sebastian Luther <SebastianLuther@gmx.de> ---- a/pph.cc -+++ b/pph.cc -@@ -23,6 +23,7 @@ - */ - - #include "pph.hh" -+#include <cstdio> - #include <cmath> - #include <snpfile/matrix.hh> - using namespace BiRC::SNPFile; diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/blossoc/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest deleted file mode 100644 index 4c95c2d9efa8..000000000000 --- a/sci-biology/cufflinks/Manifest +++ /dev/null @@ -1,10 +0,0 @@ -AUX cufflinks-2.2.1-boost-1.65-tr1-removal.patch 344 BLAKE2B af0287f43bfd37da352fc330e3f6e06d4c6946851c6d8760302078157c8073591ccf7b508e2debf35747837216cc15e952fd7128bca500547cc180061dc2f780 SHA512 774558e93cf57ca9e9361df2271119474c8726573ff4467af4836db863d87ff0f38fe7048c9287227f18d3541891bb7b433b5fa33567616eeecda2bb5b057e9a -AUX cufflinks-2.2.1-flags.patch 1132 BLAKE2B 675fb86a95425ed0def259b6f316e443eddb0c80a3a4f78e724f85ca3b14e58c29bb59bbc80a61ee7dcfaeb404383ffe0e58669dedc95224913c8d43939fd799 SHA512 58ea036d55d0b4835a56ea66afc2359bdb3e022f1fda3cab8402e4a2d7c6eab00fae96c739f89a25ca1e7528dad02f20c5c944a198c1eeca245e8995fbaa8f12 -AUX cufflinks-2.2.1-format-security.patch 618 BLAKE2B 1a316055af35849333c8ccbd46079a4ee1096becde474151932317bb66f81eff27b80d15306d9432f69a42fa9202a7712f9eff9921b915a92f4094ad2eadc79b SHA512 61a8cfe31988b028636f97db06d6855d9fce4ff3548da70d7e791fde85b38c09376be63714b67a0dc3e112f1d543735a51ebc437fc0b32eff98e9bf13138ff3c -AUX cufflinks-2.2.1-gcc5-make_shared.patch 417 BLAKE2B 99fb3c7135789073089344d0f362088e5d95354b80a43e5a4fd47daa8b38d7c05b18476c491e5945b6b313925e984361915651c0b783c866273eeb4530eb35ea SHA512 81340797fe99aeb0fd118b28f729dfdcfbd3dd1a5efa2a4874a3732a167ad1c8b8d7d3408d1137db35ac5c17319d90dc1351bfd91a15af5c095de746791394d7 -AUX cufflinks-2.2.1-gcc6.patch 344 BLAKE2B 7534c9060e93f074718726e2cbf7df259ba298b447915a4162916977340d33e35a4fddbf3e1b662334b56d42ffb8e0a096c337b465b5952abe27d1248fd6d0f2 SHA512 1e8fc2e717c464e39aecf2c434857e962a809fd2a9f84bfca2b7230d5150d464262b579f1a8c13970767e929562d04994d60002834c98c204e089d2d2a8381c0 -AUX cufflinks-2.2.1-gcc7.patch 4133 BLAKE2B ac2fbf2ebadfe0e90d7163dbd839b2173a3a3a9925b25e2eba8775793545ed8e17e8075c9e562300fa0fae6fd7c35893c8bc892c3e79bd6645b2e3cf51acbdbf SHA512 cbcc2be9e1266e24801dc91ed776aa314761ac682274c103c4f4ad9c37f8ad02b63233f2a16608dd620ca67e89a21028142bdc059cbe5fd2fffdbdb3e38f0af8 -AUX cufflinks-2.2.1-samtools-legacy.patch 1105 BLAKE2B ceeb2236456f30598e0d98ce1eaa4fae908286704fb6912a19ccc008b3d41476b853cacc3fc545450dde7d883593a545110a440c044118875041f56077c963b3 SHA512 80c6eaadcfe6919d61b63efc83d3d618e939c3a1cd5e4977f936c41656a96c7c2dd71a1309d6b0422b1bf248a366643a62f011b30b37b4001efae5da04acaadf -DIST cufflinks-2.2.1.tar.gz 766280 BLAKE2B 200ca88d15cdfca550a12a39cf69d4c41850532c76840d2a86a21654b317e28c7f35d36ba26105490e75d55c5527dd64da1ef3c14f2d467a60379c234a8e9e60 SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b -EBUILD cufflinks-2.2.1-r2.ebuild 1303 BLAKE2B 43a7781892fd664ca50d429ee741233ec4e319a8bccda379cc18a36c8447fb65972a07480bc74dde09d964f8e34f15b5e53204d6da2b1ce9af79fbc39d566103 SHA512 45d0d18bc405809d76f26b348ae90fa0fd9453a9ca1632c052ca6354679b65c9c40460bda40b7f50745549df916704cac3b6e4ed1b833cb9114f61ab002b1640 -MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild deleted file mode 100644 index 3892e03e23b2..000000000000 --- a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools flag-o-matic python-single-r1 toolchain-funcs - -DESCRIPTION="Transcript assembly and differential expression/regulation for RNA-Seq" -HOMEPAGE="http://cufflinks.cbcb.umd.edu/" -SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - sci-biology/samtools:0.1-legacy - >=dev-libs/boost-1.62.0:= - ${PYTHON_DEPS}" -DEPEND=" - ${RDEPEND} - dev-cpp/eigen:3 - virtual/pkgconfig" - -PATCHES=( - "${FILESDIR}"/${P}-samtools-legacy.patch - "${FILESDIR}"/${P}-flags.patch - "${FILESDIR}"/${P}-gcc6.patch - "${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch - "${FILESDIR}"/${P}-gcc7.patch - "${FILESDIR}"/${P}-format-security.patch - "${FILESDIR}"/${P}-gcc5-make_shared.patch -) - -src_prepare() { - default - python_fix_shebang src/cuffmerge - - eautoreconf -} - -src_configure() { - # keep in sync with Boost - append-cxxflags -std=c++14 - append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) - - econf \ - --disable-optim \ - --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \ - --with-bam="${EPREFIX}/usr/" \ - $(use_enable debug) \ - PYTHON="${PYTHON}" -} diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch deleted file mode 100644 index 42a906e7a83a..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-boost-1.65-tr1-removal.patch +++ /dev/null @@ -1,14 +0,0 @@ -Boost 1.65 removed the TR1 headers. -Bug: https://bugs.gentoo.org/show_bug.cgi?id=630654 - ---- a/src/biascorrection.h -+++ b/src/biascorrection.h -@@ -15,7 +15,7 @@ - #include <vector> - #include <list> - #include <string> --#include <boost/tr1/unordered_map.hpp> -+#include <boost/unordered_map.hpp> - #include <boost/thread.hpp> - #include "common.h" - diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch deleted file mode 100644 index 47784088fab9..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch +++ /dev/null @@ -1,28 +0,0 @@ - configure.ac | 7 ++++--- - 1 file changed, 4 insertions(+), 3 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 96ffbac..e88b8e4 100755 ---- a/configure.ac -+++ b/configure.ac -@@ -61,7 +61,8 @@ AC_CANONICAL_HOST - - # set CFLAGS and CXXFLAGS - user_CFLAGS=${CFLAGS} --generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024" -+generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized" -+generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024" - ext_CFLAGS="" - debug_CFLAGS="" - #echo "${host_cpu}-${host_os}" -@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with - [ext_LDFLAGS="-lprofiler -ltcmalloc"], []) - - CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" --CXXFLAGS="$CFLAGS" --CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" -+CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}" -+CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" - user_LDFLAGS="$LDFLAGS" - LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" - diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch deleted file mode 100644 index fa13f78d8b52..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ -Author: Andreas Tille <tille@debian.org> -Date: Wed, 22 May 2013 13:27:40 +0200 -Description: When building with --format-security (Debhelper 9 hardening) - this patch is needed to build successfully - ---- a/src/locfit/makecmd.c -+++ b/src/locfit/makecmd.c -@@ -200,7 +200,7 @@ char *cmdline; - /* vs is used to store the command line string. */ - sprintf(vn,"=clstr%d",clcount); - vs = createvar(vn,STSYSTEM,1+strlen(cmdline),VCHAR); -- sprintf((char *)vdptr(vs),cmdline); -+ sprintf((char *)vdptr(vs),"%s",cmdline); - - /* va is used to store pointers to the command line fields. */ - sprintf(vn,"=cline%d",clcount); diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch deleted file mode 100644 index 67a28df10249..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc5-make_shared.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/src/differential.cpp -+++ b/src/differential.cpp -@@ -575,7 +575,7 @@ - boost::mutex::scoped_lock lock(meta_data_lock); - #endif - pair<SampleDiffMetaDataTable::iterator, bool> p; -- p = meta_data_table.insert(make_pair(description, new SampleDifferenceMetaData())); -+ p = meta_data_table.insert(make_pair(description, boost::make_shared<SampleDifferenceMetaData>())); - return p.first->second; - } - diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch deleted file mode 100644 index 6ee9bcf456d4..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc6.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- a/src/lemon/error.h -+++ b/src/lemon/error.h -@@ -67,9 +67,9 @@ - } - - ExceptionMember& operator=(const ExceptionMember& copy) { -- if (ptr.get() == 0) return; -+ if (ptr.get() == 0) return *this; - try { -- if (!copy.valid()) return; -+ if (!copy.valid()) return *this; - *ptr = copy.get(); - } catch (...) {} - } diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch deleted file mode 100644 index 48fe6e10ac96..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch +++ /dev/null @@ -1,121 +0,0 @@ -Author: Alex Mestiashvili <mailatgoogl@gmail.com> -Origin: https://lists.debian.org/debian-med/2017/09/msg00021.html -Bug-Debian: https://bugs.debian.org/871234 -Description: Fix gcc-7 build issue, thanks to Jeff Epler <jepler@unpythonic.net> ---- a/src/GHash.hh -+++ b/src/GHash.hh -@@ -88,7 +88,7 @@ - //nextkey is SET to the corresponding key - GHashEntry* NextEntry() { //returns a pointer to a GHashEntry - register int pos=fCurrentEntry; -- while (pos<fCapacity && hash[pos].hash<0) pos++; -+ while (pos<fCapacity && (hash[pos].hash)<0) pos++; - if (pos==fCapacity) { - fCurrentEntry=fCapacity; - return NULL; -@@ -186,7 +186,7 @@ - x=HASH2(h,n); - GASSERT(1<=x && x<n); - while(k[p].hash!=-1) p=(p+x)%n; -- GASSERT(k[p].hash<0); -+ GASSERT((k[p].hash)<0); - k[p]=hash[i]; - } - } -@@ -225,7 +225,7 @@ - GTRACE(("GHash::insert: key=\"%s\"\n",ky)); - //GMessage("GHash::insert: key=\"%s\"\n",ky); - GASSERT(0<=i && i<fCapacity); -- GASSERT(hash[i].hash<0); -+ GASSERT((hash[i].hash)<0); - hash[i].hash=h; - hash[i].mark=mrk; - hash[i].key=Gstrdup(ky); -@@ -266,7 +266,7 @@ - GTRACE(("GHash::insert: key=\"%s\"\n",ky)); - //GMessage("GHash::insert: key=\"%s\"\n",ky); - GASSERT(0<=i && i<fCapacity); -- GASSERT(hash[i].hash<0); -+ GASSERT((hash[i].hash)<0); - hash[i].hash=h; - hash[i].mark=mrk; - hash[i].key=(char *)ky; -@@ -310,7 +310,7 @@ - if(i==-1) i=p; - GTRACE(("GHash::replace: %08x: inserting: \"%s\"\n",this,ky)); - GASSERT(0<=i && i<fCapacity); -- GASSERT(hash[i].hash<0); -+ GASSERT((hash[i].hash)<0); - hash[i].hash=h; - hash[i].mark=mrk; - hash[i].key=Gstrdup(ky); -@@ -412,7 +412,7 @@ - - template <class OBJ> char* GHash<OBJ>::NextKey() { - register int pos=fCurrentEntry; -- while (pos<fCapacity && hash[pos].hash<0) pos++; -+ while (pos<fCapacity && (hash[pos].hash)<0) pos++; - if (pos==fCapacity) { - fCurrentEntry=fCapacity; - return NULL; -@@ -425,7 +425,7 @@ - - template <class OBJ> OBJ* GHash<OBJ>::NextData() { - register int pos=fCurrentEntry; -- while (pos<fCapacity && hash[pos].hash<0) pos++; -+ while (pos<fCapacity && (hash[pos].hash)<0) pos++; - if (pos==fCapacity) { - fCurrentEntry=fCapacity; - return NULL; -@@ -439,7 +439,7 @@ - - template <class OBJ> OBJ* GHash<OBJ>::NextData(char* &nextkey) { - register int pos=fCurrentEntry; -- while (pos<fCapacity && hash[pos].hash<0) pos++; -+ while (pos<fCapacity && (hash[pos].hash)<0) pos++; - if (pos==fCapacity) { - fCurrentEntry=fCapacity; - nextkey=NULL; -@@ -457,16 +457,16 @@ - // Get first non-empty entry - template <class OBJ> int GHash<OBJ>::First() const { - register int pos=0; -- while(pos<fCapacity){ if(0<=hash[pos].hash) break; pos++; } -- GASSERT(fCapacity<=pos || 0<=hash[pos].hash); -+ while(pos<fCapacity){ if(0<=(hash[pos].hash)) break; pos++; } -+ GASSERT(fCapacity<=pos || 0<=(hash[pos].hash)); - return pos; - } - - // Get last non-empty entry - template <class OBJ> int GHash<OBJ>::Last() const { - register int pos=fCapacity-1; -- while(0<=pos){ if(0<=hash[pos].hash) break; pos--; } -- GASSERT(pos<0 || 0<=hash[pos].hash); -+ while(0<=pos){ if(0<=(hash[pos].hash)) break; pos--; } -+ GASSERT(pos<0 || 0<=(hash[pos].hash)); - return pos; - } - -@@ -474,8 +474,8 @@ - // Find next valid entry - template <class OBJ> int GHash<OBJ>::Next(int pos) const { - GASSERT(0<=pos && pos<fCapacity); -- while(++pos <= fCapacity-1){ if(0<=hash[pos].hash) break; } -- GASSERT(fCapacity<=pos || 0<=hash[pos].hash); -+ while(++pos <= fCapacity-1){ if(0<=(hash[pos].hash)) break; } -+ GASSERT(fCapacity<=pos || 0<=(hash[pos].hash)); - return pos; - } - -@@ -483,8 +483,8 @@ - // Find previous valid entry - template <class OBJ> int GHash<OBJ>::Prev(int pos) const { - GASSERT(0<=pos && pos<fCapacity); -- while(--pos >= 0){ if(0<=hash[pos].hash) break; } -- GASSERT(pos<0 || 0<=hash[pos].hash); -+ while(--pos >= 0){ if(0<=(hash[pos].hash)) break; } -+ GASSERT(pos<0 || 0<=(hash[pos].hash)); - return pos; - } - diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch deleted file mode 100644 index 374ce519ef86..000000000000 --- a/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch +++ /dev/null @@ -1,44 +0,0 @@ -Modify the buildsystem to work with the legacy version of samtools, -which can coexist with the most recent version of samtools. -See also: https://bugs.gentoo.org/show_bug.cgi?id=577854 - ---- cufflinks-2.2.1/ax_bam.m4 -+++ cufflinks-2.2.1/ax_bam.m4 -@@ -102,7 +102,7 @@ - - AC_LANG_PUSH(C++) - AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ -- @%:@include <bam/bam.h> -+ @%:@include <bam-0.1-legacy/bam.h> - ]], [[ - ]])],[ - AC_MSG_RESULT(yes) -@@ -171,7 +171,7 @@ - - AC_LANG_PUSH(C++) - AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ -- @%:@include <bam/version.hpp> -+ @%:@include <bam-0.1-legacy/version.hpp> - ]], [[ - ]])],[ - AC_MSG_RESULT(yes) -@@ -189,7 +189,7 @@ - AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).]) - fi - else -- BAM_LIB="-lbam" -+ BAM_LIB="-lbam-0.1-legacy" - AC_SUBST(BAM_CPPFLAGS) - AC_SUBST(BAM_LDFLAGS) - AC_SUBST(BAM_LIB) ---- cufflinks-2.2.1/src/hits.h -+++ cufflinks-2.2.1/src/hits.h -@@ -18,7 +18,7 @@ - - #include <boost/shared_ptr.hpp> - --#include <bam/sam.h> -+#include <bam-0.1-legacy/sam.h> - - #include "common.h" - #include "multireads.h" diff --git a/sci-biology/cufflinks/metadata.xml b/sci-biology/cufflinks/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/cufflinks/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/snpfile/Manifest b/sci-biology/snpfile/Manifest deleted file mode 100644 index a6701a42a5d5..000000000000 --- a/sci-biology/snpfile/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -AUX snpfile-2.0.1-ax-boost.patch 973 BLAKE2B ddfdefc7aae1c5e1e95498a1e3911f32455fb3918f390e0d2d741eaf67b7002b72af99e5d5bbf3cf0822b871463bb0624869c1d98fb45b2a2275b8790c0148a9 SHA512 cb517e30c06620de9d007261d238325daf48709ccd875d90c0cc99049dfd0ce80a506a3e9a97c786ac8329b1f1463a810407927cf17c1a25689b03f413417b94 -AUX snpfile-2.0.1-gcc44.patch 387 BLAKE2B 8ce01199b75387b700aaf6a3608212370aa49a0cc896cd9f2ac9c5807f03ed1c7b8663d8a6a2420bb5247ec461aafd30d6e64d3509300faeaa36b8d77259f68e SHA512 ac66850cae2bbbad9e1a989772490eb23ea3958c233e0fe32b20ffb3d7b5f547ff9d045974170c3302e8ca6bbbe5a2055acad24bb80cc6a3c527c3164e3f0e84 -AUX snpfile-2.0.1-gentoo.diff 20224 BLAKE2B 26ebe8dcccf954830621eb60f28e55f0cd4f759adb6a049b683cc5e69c084b4a3c09ee3b6b48b7d93757590686ceee8678b5bf643f65284583a894e122fcd6f8 SHA512 8628aa298b38376e439739c813ec87c80eb7c7f7874335e8f812eee05fab205ae900a00ec819021699fe835c2e9d38f880e9b391ccc4bfb46a8b91f028ed84ad -AUX snpfile-2.0.1-gold.patch 1066 BLAKE2B 18b6353d38ffdde0f7ceb935f0162258e046e730cdf6f5a62f2d4a2918bdd3846b6306f33dda392f30bcd5c00174f1f24df3c5e94719d563a140b54922ca1cfc SHA512 81f2e5e91890e52cf40553ea70b12cdb09e5b8335303d72f6943e0058b62eb061eea4e52595c267de81af219f7b863025fb2aa7364d976101628b1f65ba27075 -DIST snpfile-2.0.1.tar.gz 171854 BLAKE2B 4f256892d3ead522c1aaef8db6fa486186233f0f6a1d3297e10104af504eace84f9396f28f00fb35242aed656e2a61fef7481a333acc69091deef746114533ab SHA512 e217e8b600d3ba7e2a8a0724d867bd9760572398f2e4e58625c1f74b0db9aa913db266da51fcfc05b90f3faf9eb6fbeb7bd988f105de013b51c24caa37c678c6 -EBUILD snpfile-2.0.1-r2.ebuild 886 BLAKE2B 03dd4c564b84e036d53af3c55a208d94975660ac53c14dcff971f25a28e8a03d3a21ed83d59bc1b0ab6f7e11b04d4e1a124c942d61fd9fc92f94deeb1620895f SHA512 7946475e80f92a1c76a4e92500cfad3f6eb4e0463014e07eb517f6a4ef0fb3ebff7143d18d22c887d970f186cc7a0847788d8b55e5b297d04820a9dfdb3475fa -MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch b/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch deleted file mode 100644 index f77b476f990d..000000000000 --- a/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch +++ /dev/null @@ -1,35 +0,0 @@ -Modernise autoconf code to use modern archive macros. - ---- a/configure.in -+++ b/configure.in -@@ -1,7 +1,7 @@ - AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk) - AM_INIT_AUTOMAKE - AC_CONFIG_MACRO_DIR([m4]) --AM_CONFIG_HEADER(config.hh) -+AC_CONFIG_HEADERS([config.hh]) - - LT_INIT - AC_PROG_CXX -@@ -14,18 +14,9 @@ - fi - AC_DEFINE_UNQUOTED(PREFIX, "$thePREFIX", [Installation prefix]) - --AX_BOOST([1.33.1],, --AC_ERROR([[ --************************************************************************ --************************************************************************ --The Boost library was not found on this system. We use this library --extensively, and cannot proceed without it. You can obtain it from --<http://www.boost.org>. --************************************************************************ --************************************************************************ --]]) --) -- -+AX_BOOST_BASE([1.33.1]) -+AX_BOOST_PROGRAM_OPTIONS -+AX_BOOST_SIGNALS - - AC_OUTPUT([ - Makefile diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch deleted file mode 100644 index 2b79c2492ede..000000000000 --- a/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ur snpfile-2.0.1.orig/input_archive.hh snpfile-2.0.1/input_archive.hh ---- snpfile-2.0.1.orig/input_archive.hh 2008-05-03 17:25:44.000000000 +0300 -+++ snpfile-2.0.1/input_archive.hh 2009-07-26 21:26:10.000000000 +0300 -@@ -26,6 +26,8 @@ - #ifndef INPUT_ARCHIVE_HH_INCLUDED - #define INPUT_ARCHIVE_HH_INCLUDED - -+#include <stdint.h> -+ - #include <string> - - #include "archive_common.hh" diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff deleted file mode 100644 index b2a8a6b630ce..000000000000 --- a/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff +++ /dev/null @@ -1,533 +0,0 @@ -Fixing as-needed issues, provide shared libs - -https://bugs.gentoo.org/show_bug.cgi?id=294971 - ---- a/Makefile.am -+++ b/Makefile.am -@@ -1,440 +1,92 @@ - ACLOCAL_AMFLAGS = -I m4 - --AM_CXXFLAGS = --AM_CXXFLAGS += -Wall --AM_CXXFLAGS += $(BOOST_CPPFLAGS) -+AM_CXXFLAGS = -Wall $(BOOST_CPPFLAGS) -+SUFFIXES = .cc - -- --# for testing --AM_CXXFLAGS += -g -O2 #-lefence -- --# for profiling --#CXXFLAGS += -O3 -g -pg --#AM_CXXFLAGS += -O3 -g -pg -- --# for production --#CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG --#AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG -- --# for coverage testing --#CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations --#AM_CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations -- -- --lib_LIBRARIES = libsnpfile.a -+lib_LTLIBRARIES = libsnpfile.la - - noinst_PROGRAMS = --TESTS = --EXTRA_DIST = --bin_PROGRAMS = - - # conversion tools --bin_PROGRAMS += text2snpfile --bin_PROGRAMS += snpfile2text --bin_PROGRAMS += snpfile2fastPHASE --bin_PROGRAMS += fastPHASE2snpfile --bin_PROGRAMS += snpfile2haploview --bin_PROGRAMS += beagle_phase_snpfile -+bin_PROGRAMS = text2snpfile snpfile2text snpfile2fastPHASE fastPHASE2snpfile \ -+ snpfile2haploview beagle_phase_snpfile - - # data extraction tools --bin_PROGRAMS += snpfile_genotype_count --bin_PROGRAMS += snpfile_phenotypes --bin_PROGRAMS += snpfile_markers -- --bin_PROGRAMS += snpfile_metadata_info --bin_PROGRAMS += snpfile_set_metadata --bin_PROGRAMS += snpfile_get_metadata -+bin_PROGRAMS += snpfile_genotype_count snpfile_phenotypes snpfile_markers -+ -+bin_PROGRAMS += snpfile_metadata_info snpfile_set_metadata snpfile_get_metadata - - # other tools - noinst_PROGRAMS += snpfile_split_on_column - - # tests --noinst_PROGRAMS += matrix_test --TESTS += matrix_test --noinst_PROGRAMS += file_test --TESTS += file_test --noinst_PROGRAMS += file_matrix_test --TESTS += file_matrix_test --noinst_PROGRAMS += readonly_matrix_test --TESTS += readonly_matrix_test --noinst_PROGRAMS += archives_test --TESTS += archives_test --noinst_PROGRAMS += metadata_access_test --TESTS += metadata_access_test --noinst_PROGRAMS += metadata_types_test --TESTS += metadata_types_test --noinst_PROGRAMS += iterators_test --TESTS += iterators_test --noinst_PROGRAMS += tabulate_test --TESTS += tabulate_test --noinst_PROGRAMS += metadata_filtering_test --TESTS += metadata_filtering_test -+TESTS = matrix_test file_test file_matrix_test readonly_matrix_test archives_test \ -+ metadata_access_test metadata_types_test iterators_test tabulate_test metadata_filtering_test -+ -+noinst_PROGRAMS += $(TESTS) - - #Utils for testing across different machines --noinst_PROGRAMS += make_test_snpfile --noinst_PROGRAMS += test_test_snpfile -+noinst_PROGRAMS += make_test_snpfile test_test_snpfile - - # other experiments... --noinst_PROGRAMS += row_metadata_experiment --noinst_PROGRAMS += metadata_cache_prototype --noinst_PROGRAMS += matrix_benchmark --noinst_PROGRAMS += matrix_benchmark_write --noinst_PROGRAMS += matrix_benchmark_read -- -- -- --matrix_test_LDADD = --matrix_test_LDADD += $(BOOST_SIGNALS_LIB) --matrix_test_SOURCES = --matrix_test_SOURCES += test_util.hh test_util.cc --matrix_test_SOURCES += matrix.hh matrix.cc --matrix_test_SOURCES += array_matrix.hh array_matrix.cc --matrix_test_SOURCES += file_matrix.hh file_matrix.cc --matrix_test_SOURCES += input_archive.hh --matrix_test_SOURCES += output_archive.hh --matrix_test_SOURCES += metadata.hh metadata.cc --matrix_test_SOURCES += snpfile.hh snpfile.cc --matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc --matrix_test_SOURCES += matrix_test.cc -- -- --file_test_LDADD = --file_test_LDADD += $(BOOST_SIGNALS_LIB) --file_test_SOURCES = --file_test_SOURCES += test_util.hh test_util.cc --file_test_SOURCES += metadata.hh metadata.cc --file_test_SOURCES += snpfile.hh snpfile.cc --file_test_SOURCES += byte_order_handler.hh byte_order_handler.cc --file_test_SOURCES += file_test.cc --file_test_SOURCES += metadata_access.hh --file_test_SOURCES += input_archive.hh --file_test_SOURCES += output_archive.hh -- --file_matrix_test_LDADD = --file_matrix_test_LDADD += $(BOOST_SIGNALS_LIB) --file_matrix_test_SOURCES = --file_matrix_test_SOURCES += test_util.hh test_util.cc --file_matrix_test_SOURCES += file_matrix.hh file_matrix.cc --file_matrix_test_SOURCES += matrix.hh matrix.cc --file_matrix_test_SOURCES += input_archive.hh --file_matrix_test_SOURCES += output_archive.hh --file_matrix_test_SOURCES += metadata.hh metadata.cc --file_matrix_test_SOURCES += snpfile.hh snpfile.cc --file_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc --file_matrix_test_SOURCES += file_matrix_test.cc -- -- --readonly_matrix_test_LDADD = --readonly_matrix_test_LDADD += $(BOOST_SIGNALS_LIB) --readonly_matrix_test_SOURCES = --readonly_matrix_test_SOURCES += test_util.hh test_util.cc --readonly_matrix_test_SOURCES += array_matrix.hh array_matrix.cc --readonly_matrix_test_SOURCES += file_matrix.hh file_matrix.cc --readonly_matrix_test_SOURCES += matrix.hh matrix.cc --readonly_matrix_test_SOURCES += input_archive.hh --readonly_matrix_test_SOURCES += output_archive.hh --readonly_matrix_test_SOURCES += metadata.hh metadata.cc --readonly_matrix_test_SOURCES += snpfile.hh snpfile.cc --readonly_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc --readonly_matrix_test_SOURCES += readonly_matrix_test.cc -- -- --archives_test_SOURCES = --archives_test_SOURCES += input_archive.hh --archives_test_SOURCES += output_archive.hh --archives_test_SOURCES += archives_test.cc -- -- --metadata_access_test_LDADD = --metadata_access_test_LDADD += $(BOOST_SIGNALS_LIB) --metadata_access_test_SOURCES = --metadata_access_test_SOURCES += test_util.hh test_util.cc --metadata_access_test_SOURCES += metadata.hh metadata.cc --metadata_access_test_SOURCES += snpfile.hh snpfile.cc --metadata_access_test_SOURCES += byte_order_handler.hh byte_order_handler.cc --metadata_access_test_SOURCES += input_archive.hh --metadata_access_test_SOURCES += output_archive.hh --metadata_access_test_SOURCES += serialization_trait.hh --metadata_access_test_SOURCES += metadata_access_test.cc -- -- --metadata_types_test_LDADD = --metadata_types_test_LDADD += $(BOOST_SIGNALS_LIB) --metadata_types_test_SOURCES = --metadata_types_test_SOURCES += test_util.hh test_util.cc --metadata_types_test_SOURCES += metadata.hh metadata.cc --metadata_types_test_SOURCES += snpfile.hh snpfile.cc --metadata_types_test_SOURCES += byte_order_handler.hh byte_order_handler.cc --metadata_types_test_SOURCES += input_archive.hh --metadata_types_test_SOURCES += output_archive.hh --metadata_types_test_SOURCES += serialization_trait.hh --metadata_types_test_SOURCES += metadata_types_test.cc -- -- --iterators_test_SOURCES = --iterators_test_SOURCES += iterators.hh --iterators_test_SOURCES += array_matrix.hh array_matrix.cc --iterators_test_SOURCES += matrix.hh matrix.cc --iterators_test_SOURCES += iterators_test.cc -- -- --tabulate_test_SOURCES = --tabulate_test_SOURCES += tabulate.hh --tabulate_test_SOURCES += array_matrix.hh array_matrix.cc --tabulate_test_SOURCES += matrix.hh matrix.cc --tabulate_test_SOURCES += tabulate_test.cc -- -- --metadata_filtering_test_SOURCES = --metadata_filtering_test_SOURCES += matrix.hh matrix.cc --metadata_filtering_test_SOURCES += array_matrix.hh array_matrix.cc --metadata_filtering_test_SOURCES += metadata_filtering.hh --metadata_filtering_test_SOURCES += metadata_filtering_test.cc -- -- --make_test_snpfile_LDADD = --make_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB) --make_test_snpfile_SOURCES = --make_test_snpfile_SOURCES += metadata.hh metadata.cc --make_test_snpfile_SOURCES += snpfile.hh snpfile.cc --make_test_snpfile_SOURCES += matrix.hh matrix.cc --make_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc --make_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc --make_test_snpfile_SOURCES += input_archive.hh --make_test_snpfile_SOURCES += output_archive.hh --make_test_snpfile_SOURCES += make_test_snpfile.cc -- -- --test_test_snpfile_LDADD = --test_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB) --test_test_snpfile_SOURCES = --test_test_snpfile_SOURCES += metadata.hh metadata.cc --test_test_snpfile_SOURCES += snpfile.hh snpfile.cc --test_test_snpfile_SOURCES += matrix.hh matrix.cc --test_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc --test_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc --test_test_snpfile_SOURCES += input_archive.hh --test_test_snpfile_SOURCES += output_archive.hh --test_test_snpfile_SOURCES += test_test_snpfile.cc -- -- --row_metadata_experiment_LDADD = --row_metadata_experiment_LDADD += $(BOOST_SIGNALS_LIB) --row_metadata_experiment_SOURCES = --row_metadata_experiment_SOURCES += matrix.hh matrix.cc --row_metadata_experiment_SOURCES += array_matrix.hh array_matrix.cc --row_metadata_experiment_SOURCES += file_matrix.hh file_matrix.cc --row_metadata_experiment_SOURCES += input_archive.hh --row_metadata_experiment_SOURCES += output_archive.hh --row_metadata_experiment_SOURCES += metadata.hh metadata.cc --row_metadata_experiment_SOURCES += snpfile.hh snpfile.cc --row_metadata_experiment_SOURCES += byte_order_handler.hh byte_order_handler.cc --row_metadata_experiment_SOURCES += test_util.hh test_util.cc --row_metadata_experiment_SOURCES += row_metadata_experiment.cc -- -- --metadata_cache_prototype_SOURCES = --metadata_cache_prototype_SOURCES += metadata_cache_prototype.cc --metadata_cache_prototype_LDFLAGS = --metadata_cache_prototype_LDFLAGS += -L. --metadata_cache_prototype_LDADD = --metadata_cache_prototype_LDADD += $(BOOST_SIGNALS_LIB) --metadata_cache_prototype_LDADD += -lsnpfile -- -- --matrix_benchmark_LDADD = --matrix_benchmark_LDADD += $(BOOST_SIGNALS_LIB) --matrix_benchmark_SOURCES = --matrix_benchmark_SOURCES += test_util.hh test_util.cc --matrix_benchmark_SOURCES += file_matrix.hh file_matrix.cc --matrix_benchmark_SOURCES += array_matrix.hh array_matrix.cc --matrix_benchmark_SOURCES += matrix.hh matrix.cc --matrix_benchmark_SOURCES += input_archive.hh --matrix_benchmark_SOURCES += output_archive.hh --matrix_benchmark_SOURCES += metadata.hh metadata.cc --matrix_benchmark_SOURCES += snpfile.hh snpfile.cc --matrix_benchmark_SOURCES += byte_order_handler.hh byte_order_handler.cc --matrix_benchmark_SOURCES += timing.hh timing.cc --matrix_benchmark_SOURCES += matrix_benchmark.cc -- -- --matrix_benchmark_write_LDADD = --matrix_benchmark_write_LDADD += $(BOOST_SIGNALS_LIB) --matrix_benchmark_write_SOURCES = --matrix_benchmark_write_SOURCES += file_matrix.hh file_matrix.cc --matrix_benchmark_write_SOURCES += matrix.hh matrix.cc --matrix_benchmark_write_SOURCES += input_archive.hh --matrix_benchmark_write_SOURCES += output_archive.hh --matrix_benchmark_write_SOURCES += metadata.hh metadata.cc --matrix_benchmark_write_SOURCES += snpfile.hh snpfile.cc --matrix_benchmark_write_SOURCES += byte_order_handler.hh byte_order_handler.cc --matrix_benchmark_write_SOURCES += timing.hh timing.cc --matrix_benchmark_write_SOURCES += matrix_benchmark_write.cc -- -- --matrix_benchmark_read_LDADD = --matrix_benchmark_read_LDADD += $(BOOST_SIGNALS_LIB) --matrix_benchmark_read_SOURCES = --matrix_benchmark_read_SOURCES += file_matrix.hh file_matrix.cc --matrix_benchmark_read_SOURCES += matrix.hh matrix.cc --matrix_benchmark_read_SOURCES += input_archive.hh --matrix_benchmark_read_SOURCES += output_archive.hh --matrix_benchmark_read_SOURCES += metadata.hh metadata.cc --matrix_benchmark_read_SOURCES += snpfile.hh snpfile.cc --matrix_benchmark_read_SOURCES += byte_order_handler.hh byte_order_handler.cc --matrix_benchmark_read_SOURCES += timing.hh timing.cc --matrix_benchmark_read_SOURCES += matrix_benchmark_read.cc -+noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \ -+ matrix_benchmark_write matrix_benchmark_read -+ -+LDADD = $(top_builddir)/libsnpfile.la -+ -+matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc -+ -+file_test_SOURCES = test_util.hh test_util.cc file_test.cc metadata_access.hh input_archive.hh \ -+ output_archive.hh -+ -+file_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ -+ file_matrix_test.cc -+ -+readonly_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ -+ readonly_matrix_test.cc - -+archives_test_SOURCES = input_archive.hh output_archive.hh archives_test.cc -+ -+metadata_access_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ -+ serialization_trait.hh metadata_access_test.cc -+ -+metadata_types_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ -+ serialization_trait.hh metadata_types_test.cc -+ -+iterators_test_SOURCES = iterators.hh iterators_test.cc -+ -+tabulate_test_SOURCES = tabulate.hh tabulate_test.cc -+ -+metadata_filtering_test_SOURCES = metadata_filtering.hh metadata_filtering_test.cc -+ -+make_test_snpfile_SOURCES = input_archive.hh output_archive.hh make_test_snpfile.cc -+ -+test_test_snpfile_SOURCES = input_archive.hh output_archive.hh test_test_snpfile.cc -+ -+row_metadata_experiment_SOURCES = input_archive.hh output_archive.hh test_util.hh test_util.cc \ -+ row_metadata_experiment.cc -+ -+matrix_benchmark_SOURCES = test_util.hh test_util.cc input_archive.hh \ -+ output_archive.hh timing.hh timing.cc matrix_benchmark.cc -+ -+matrix_benchmark_write_SOURCES = input_archive.hh output_archive.hh \ -+ timing.hh timing.cc matrix_benchmark_write.cc -+ -+matrix_benchmark_read_SOURCES = input_archive.hh output_archive.hh \ -+ timing.hh timing.cc matrix_benchmark_read.cc -+ -+snpfile_genotype_count_SOURCES = genotype_count.cc - - snpfileincludedir = $(includedir)/snpfile --snpfileinclude_HEADERS = --snpfileinclude_HEADERS += common.hh --snpfileinclude_HEADERS += matrix.hh --snpfileinclude_HEADERS += file_matrix.hh --snpfileinclude_HEADERS += array_matrix.hh --snpfileinclude_HEADERS += byte_order_handler.hh --snpfileinclude_HEADERS += metadata.hh --snpfileinclude_HEADERS += metadata_access.hh --snpfileinclude_HEADERS += archive_common.hh --snpfileinclude_HEADERS += archives.hh --snpfileinclude_HEADERS += input_archive.hh --snpfileinclude_HEADERS += output_archive.hh --snpfileinclude_HEADERS += snpfile.hh --snpfileinclude_HEADERS += serialization_trait.hh --snpfileinclude_HEADERS += type_trait.hh --snpfileinclude_HEADERS += iterators.hh --snpfileinclude_HEADERS += tabulate.hh -- --libsnpfile_a_SOURCES = --libsnpfile_a_SOURCES += common.hh --libsnpfile_a_SOURCES += matrix.hh matrix.cc --libsnpfile_a_SOURCES += file_matrix.hh file_matrix.cc --libsnpfile_a_SOURCES += array_matrix.cc array_matrix.hh --libsnpfile_a_SOURCES += byte_order_handler.cc byte_order_handler.hh --libsnpfile_a_SOURCES += metadata.hh metadata.cc metadata_access.hh --libsnpfile_a_SOURCES += archive_common.hh --libsnpfile_a_SOURCES += archives.hh --libsnpfile_a_SOURCES += input_archive.hh --libsnpfile_a_SOURCES += output_archive.hh --libsnpfile_a_SOURCES += snpfile.hh snpfile.cc --libsnpfile_a_SOURCES += serialization_trait.hh --libsnpfile_a_SOURCES += type_trait.hh -- --text2snpfile_SOURCES = --text2snpfile_SOURCES += text2snpfile.cc --text2snpfile_LDFLAGS = --text2snpfile_LDFLAGS += -L. --text2snpfile_LDADD = --text2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --text2snpfile_LDADD += $(BOOST_SIGNALS_LIB) --text2snpfile_LDADD += -lsnpfile -- --snpfile2text_SOURCES = --snpfile2text_SOURCES += snpfile2text.cc --snpfile2text_LDFLAGS = --snpfile2text_LDFLAGS += -L. --snpfile2text_LDADD = --snpfile2text_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --snpfile2text_LDADD += $(BOOST_SIGNALS_LIB) --snpfile2text_LDADD += -lsnpfile -- -- --snpfile2fastPHASE_SOURCES = --snpfile2fastPHASE_SOURCES += snpfile2fastPHASE.cc --snpfile2fastPHASE_LDFLAGS = --snpfile2fastPHASE_LDFLAGS += -L. --snpfile2fastPHASE_LDADD = --snpfile2fastPHASE_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --snpfile2fastPHASE_LDADD += $(BOOST_SIGNALS_LIB) --snpfile2fastPHASE_LDADD += -lsnpfile -- --fastPHASE2snpfile_SOURCES = --fastPHASE2snpfile_SOURCES += fastPHASE2snpfile.cc --fastPHASE2snpfile_LDFLAGS = --fastPHASE2snpfile_LDFLAGS += -L. --fastPHASE2snpfile_LDADD = --fastPHASE2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --fastPHASE2snpfile_LDADD += $(BOOST_SIGNALS_LIB) --fastPHASE2snpfile_LDADD += -lsnpfile -- -- --snpfile2haploview_SOURCES = --snpfile2haploview_SOURCES += snpfile2haploview.cc --snpfile2haploview_LDFLAGS = --snpfile2haploview_LDFLAGS += -L. --snpfile2haploview_LDADD = --snpfile2haploview_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --snpfile2haploview_LDADD += $(BOOST_SIGNALS_LIB) --snpfile2haploview_LDADD += -lsnpfile -- -- --beagle_phase_snpfile_SOURCES = --beagle_phase_snpfile_SOURCES += beagle_phase_snpfile.cc --beagle_phase_snpfile_LDFLAGS = --beagle_phase_snpfile_LDFLAGS += -L. --beagle_phase_snpfile_LDADD = --beagle_phase_snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --beagle_phase_snpfile_LDADD += $(BOOST_SIGNALS_LIB) --beagle_phase_snpfile_LDADD += -lsnpfile -- --snpfile_genotype_count_SOURCES = --snpfile_genotype_count_SOURCES += genotype_count.cc --snpfile_genotype_count_LDFLAGS = --snpfile_genotype_count_LDFLAGS += -L. --snpfile_genotype_count_LDADD = --snpfile_genotype_count_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --snpfile_genotype_count_LDADD += $(BOOST_SIGNALS_LIB) --snpfile_genotype_count_LDADD += -lsnpfile -- --snpfile_phenotypes_SOURCES = --snpfile_phenotypes_SOURCES += snpfile_phenotypes.cc --snpfile_phenotypes_LDFLAGS = --snpfile_phenotypes_LDFLAGS += -L. --snpfile_phenotypes_LDADD = --snpfile_phenotypes_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --snpfile_phenotypes_LDADD += $(BOOST_SIGNALS_LIB) --snpfile_phenotypes_LDADD += -lsnpfile -- --snpfile_markers_SOURCES = --snpfile_markers_SOURCES += snpfile_markers.cc --snpfile_markers_LDFLAGS = --snpfile_markers_LDFLAGS += -L. --snpfile_markers_LDADD = --snpfile_markers_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --snpfile_markers_LDADD += $(BOOST_SIGNALS_LIB) --snpfile_markers_LDADD += -lsnpfile -- --snpfile_metadata_info_SOURCES = --snpfile_metadata_info_SOURCES += snpfile_metadata_info.cc --snpfile_metadata_info_LDFLAGS = --snpfile_metadata_info_LDFLAGS += -L. --snpfile_metadata_info_LDADD = --snpfile_metadata_info_LDADD += $(BOOST_SIGNALS_LIB) --snpfile_metadata_info_LDADD += -lsnpfile -- --snpfile_set_metadata_SOURCES = --snpfile_set_metadata_SOURCES += snpfile_set_metadata.cc --snpfile_set_metadata_LDFLAGS = --snpfile_set_metadata_LDFLAGS += -L. --snpfile_set_metadata_LDADD = --snpfile_set_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --snpfile_set_metadata_LDADD += $(BOOST_SIGNALS_LIB) --snpfile_set_metadata_LDADD += -lsnpfile -- --snpfile_get_metadata_SOURCES = --snpfile_get_metadata_SOURCES += snpfile_get_metadata.cc --snpfile_get_metadata_LDFLAGS = --snpfile_get_metadata_LDFLAGS += -L. --snpfile_get_metadata_LDADD = --snpfile_get_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --snpfile_get_metadata_LDADD += $(BOOST_SIGNALS_LIB) --snpfile_get_metadata_LDADD += -lsnpfile -- --snpfile_split_on_column_SOURCES = --snpfile_split_on_column_SOURCES += snpfile_split_on_column.cc --snpfile_split_on_column_LDFLAGS = --snpfile_split_on_column_LDFLAGS += -L. --snpfile_split_on_column_LDADD = --snpfile_split_on_column_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) --snpfile_split_on_column_LDADD += $(BOOST_SIGNALS_LIB) --snpfile_split_on_column_LDADD += -lsnpfile -+snpfileinclude_HEADERS = common.hh matrix.hh file_matrix.hh array_matrix.hh \ -+ byte_order_handler.hh metadata.hh metadata_access.hh archive_common.hh \ -+ archives.hh input_archive.hh output_archive.hh snpfile.hh serialization_trait.hh \ -+ type_trait.hh iterators.hh tabulate.hh -+ -+libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix.cc \ -+ array_matrix.cc array_matrix.hh byte_order_handler.cc byte_order_handler.hh \ -+ metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \ -+ input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \ -+ type_trait.hh -+libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -+ ---- a/configure.in -+++ b/configure.in -@@ -1,10 +1,11 @@ - AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk) - AM_INIT_AUTOMAKE -+AC_CONFIG_MACRO_DIR([m4]) - AM_CONFIG_HEADER(config.hh) - -+LT_INIT - AC_PROG_CXX - AC_PROG_INSTALL --AC_PROG_RANLIB - - if test "x$prefix" != xNONE; then - thePREFIX=$prefix diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch deleted file mode 100644 index 2211aa36c0ca..000000000000 --- a/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch +++ /dev/null @@ -1,23 +0,0 @@ - Makefile.am | 4 ++-- - 1 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/Makefile.am b/Makefile.am -index 06fd733..5805c48 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -32,7 +32,7 @@ noinst_PROGRAMS += make_test_snpfile test_test_snpfile - noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \ - matrix_benchmark_write matrix_benchmark_read - --LDADD = $(top_builddir)/libsnpfile.la -+LDADD = $(top_builddir)/libsnpfile.la $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++ - - matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc - -@@ -88,5 +88,5 @@ libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix - metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \ - input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \ - type_trait.hh --libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -+libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++ - diff --git a/sci-biology/snpfile/metadata.xml b/sci-biology/snpfile/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/snpfile/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild b/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild deleted file mode 100644 index bbeb3111901f..000000000000 --- a/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools - -DESCRIPTION="A library and API for manipulating large SNP datasets" -HOMEPAGE="http://www.birc.au.dk/~mailund/SNPFile/" -SRC_URI="http://www.birc.au.dk/~mailund/SNPFile/download/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="static-libs" -KEYWORDS="~amd64 ~x86" - -RDEPEND="dev-libs/boost:=" -DEPEND=" - ${RDEPEND} - >=sys-devel/autoconf-archive-2016.09.16" - -PATCHES=( - "${FILESDIR}"/${P}-gcc44.patch - "${FILESDIR}"/${P}-gentoo.diff - "${FILESDIR}"/${P}-gold.patch - "${FILESDIR}"/${P}-ax-boost.patch -) - -src_prepare() { - default - mv configure.{in,ac} || die - rm m4/ax_boost.m4 || die - eautoreconf -} - -src_configure() { - econf $(use_enable static-libs static) -} - -src_install() { - default - - if ! use static-libs; then - find "${D}" -name '*.la' -delete || die - fi -} |