diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/generecon/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/generecon/Manifest | 18 | ||||
| -rw-r--r-- | sci-biology/generecon/files/1.2.1-flags.patch | 30 | ||||
| -rw-r--r-- | sci-biology/generecon/files/1.2.1-gcc4.patch | 368 | ||||
| -rw-r--r-- | sci-biology/generecon/generecon-1.2.1-r1.ebuild | 39 |
5 files changed, 436 insertions, 25 deletions
diff --git a/sci-biology/generecon/ChangeLog b/sci-biology/generecon/ChangeLog index ff5a98428..32ccb1557 100644 --- a/sci-biology/generecon/ChangeLog +++ b/sci-biology/generecon/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/generecon -# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/1.2.1-flags.patch, + generecon-1.2.1-r1.ebuild, +files/1.2.1-gcc4.patch: + Fixing compilation with gcc4, repecting CXXFLAGS/LDFLAGS, reMANIFEST + *generecon-1.2.1 (19 Apr 2006) 19 Apr 2006; Lucas Chiesa <lucas.chiesa@gmail.com>: diff --git a/sci-biology/generecon/Manifest b/sci-biology/generecon/Manifest index 9157588f1..4c92bf0e7 100644 --- a/sci-biology/generecon/Manifest +++ b/sci-biology/generecon/Manifest @@ -1,5 +1,17 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX 1.2.1-flags.patch 774 RMD160 b3f2be43d23e2bdda26008d7f46e755e26ac542b SHA1 e23b6ff6b3114208e32d0e2d9d13f9c02188eeb5 SHA256 238016e07be6ef109bbfda1038509bf43d32e6c471d0f6ca70b267c642c6be1a +AUX 1.2.1-gcc4.patch 8880 RMD160 a96111d82cd32d6fd678dd0606d0e6c560ba1280 SHA1 00b6268bb41980cae987609ff7ce21f55dd460a7 SHA256 b5e1ef9feccb2f9fd2eee0ab4d25e4de790be04a8958cb35446f8a443ab5fbbf AUX generecon-docfiles.patch 435 RMD160 ce732399b02f42a0089ea82ea240098dfb8207c5 SHA1 4f6ed16b9ce8f118b99a47d9e36ffa304e42e8bb SHA256 37fbf94d6716a489e6a59f119cf617b9ff024e612dc96323d2297f9c09360175 -DIST generecon-1.2.1.tar.gz 238270 RMD160 f625ec81db88556a33e76f63c5c242b70e951f0f SHA1 a1562a21eab88d6ac1b2d2c046b87414ff703d4b SHA256 b35496ab6baf0bda45dc7a934385441cc92bfac39cb0a261a541ad8b258ba446 -EBUILD generecon-1.2.1-r1.ebuild 1017 RMD160 74ae5fc49e83237421fdcd81270a393e3657107b SHA1 d8ee9592d814f78d4751bb7a32e69bbd2c545815 SHA256 7ba69a4147c5feac1f03a63e5db6c7fa6d0dec342681f45b10b437874588b396 -MISC ChangeLog 363 RMD160 19d0d4926d34d52c906e11fef60b3d7d713c0b4f SHA1 d3248b7ba9d5b2aa8af1c6c77802199041720c0e SHA256 9a3bb08c6357408656ecf892cbe5e25eb62f53211e8276237b383d7548755242 +DIST generecon-1.2.1.tar.gz 239507 RMD160 1d756645a091b5d7cb3eefac253e65389f416f42 SHA1 e49afec006df58f27c0f083008b0ad51789ae469 SHA256 2a6230891ca4d42408a98afdd820da56c26c225625fed03d5a9b4c0b6c1cbb48 +EBUILD generecon-1.2.1-r1.ebuild 814 RMD160 28aedf862dc48a1bdac4c22078ec69e055a7755b SHA1 1ad7fbbd524c0c6f5bd35af23b4d8bfa015fa9c0 SHA256 6fd20aeac97709793b66ab496e7799f0d0dc33c456737fcbb98af57d2da8b191 +MISC ChangeLog 562 RMD160 427d75ddf6c3450ec22787d6389e033eba1b3b02 SHA1 f39a13121fbd0e2a27f5d4ecc35d2c7fa82c62ae SHA256 a3b1f93faeef8d55fe98e0aca3f2f3983607be9ba010c07babd8d56a7244c38a MISC metadata.xml 261 RMD160 d7630eceb5ae049fa36c58ed3c9f6fe7780c15bf SHA1 6ded05d9eaded2a6b810b7f80dd2dc3270bbff8e SHA256 8bbae243cac9cf6fc1d24a0582390bd1184df161f4d7f87300874e6a7860b15c +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.15 (GNU/Linux) + +iEYEARECAAYFAkwaX4YACgkQgAnW8HDreRaRywCaA+ChDL3jht2tJ+X7zDgxGaRI +CUAAn3YLr8QTlzHtHEyCkNM17kqeThZg +=zJth +-----END PGP SIGNATURE----- diff --git a/sci-biology/generecon/files/1.2.1-flags.patch b/sci-biology/generecon/files/1.2.1-flags.patch new file mode 100644 index 000000000..7dd9a372e --- /dev/null +++ b/sci-biology/generecon/files/1.2.1-flags.patch @@ -0,0 +1,30 @@ +diff --git a/Makefile.am b/Makefile.am +index 37df12b..4ff621e 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,10 +1,10 @@ + +-CXXFLAGS = ++#CXXFLAGS = + AM_CXXFLAGS = +-CXXFLAGS += -Wall +-AM_CXXFLAGS += -Wall ++#CXXFLAGS += -Wall ++#AM_CXXFLAGS += -Wall + +-LDFLAGS = -Wl,-rpath,/usr/local/lib ++#LDFLAGS = -Wl,-rpath,/usr/local/lib + + # for testing + #CXXFLAGS += -g -O -lefence +@@ -14,8 +14,8 @@ LDFLAGS = -Wl,-rpath,/usr/local/lib + #AM_CXXFLAGS += -O3 -g -pg + + # for production +-CXXFLAGS += -O3 -fexpensive-optimizations +-AM_CXXFLAGS += -O3 -fexpensive-optimizations ++#CXXFLAGS += -O3 -fexpensive-optimizations ++#AM_CXXFLAGS += -O3 -fexpensive-optimizations + + #CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG + #AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG diff --git a/sci-biology/generecon/files/1.2.1-gcc4.patch b/sci-biology/generecon/files/1.2.1-gcc4.patch new file mode 100644 index 000000000..6b71713c3 --- /dev/null +++ b/sci-biology/generecon/files/1.2.1-gcc4.patch @@ -0,0 +1,368 @@ +diff --git a/affected_unaffected_genotype_cluster_test.cc b/affected_unaffected_genotype_cluster_test.cc +index 646af06..4e5fbde 100644 +--- a/affected_unaffected_genotype_cluster_test.cc ++++ b/affected_unaffected_genotype_cluster_test.cc +@@ -32,6 +32,7 @@ + # include "random_tree_builder.hh" + #endif + ++#include <cstring> + + void test_tree(const CoalescentTree &tree, + const Haplotype &h0, const Haplotype &h1, +diff --git a/affected_unaffected_genotype_set_test.cc b/affected_unaffected_genotype_set_test.cc +index 07fa122..5f333f5 100644 +--- a/affected_unaffected_genotype_set_test.cc ++++ b/affected_unaffected_genotype_set_test.cc +@@ -19,6 +19,8 @@ + # include "region.hh" + #endif + ++#include <cstring> ++ + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/affected_unaffected_haplotype_cluster_test.cc b/affected_unaffected_haplotype_cluster_test.cc +index 145e05f..b5dddaa 100644 +--- a/affected_unaffected_haplotype_cluster_test.cc ++++ b/affected_unaffected_haplotype_cluster_test.cc +@@ -32,6 +32,7 @@ + # include "random_tree_builder.hh" + #endif + ++#include <cstring> + + void test_tree(const CoalescentTree &tree, + const Haplotype &h0, const Haplotype &h1, +diff --git a/affected_unaffected_haplotype_set_test.cc b/affected_unaffected_haplotype_set_test.cc +index fda6173..8489c54 100644 +--- a/affected_unaffected_haplotype_set_test.cc ++++ b/affected_unaffected_haplotype_set_test.cc +@@ -19,6 +19,8 @@ + # include "region.hh" + #endif + ++#include <cstring> ++ + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/au_random_tree_builder_test.cc b/au_random_tree_builder_test.cc +index a2d4daa..d6689e0 100644 +--- a/au_random_tree_builder_test.cc ++++ b/au_random_tree_builder_test.cc +@@ -30,6 +30,7 @@ + # include "test_random.hh" + #endif + ++#include <cstring> + + void test_tree(const CoalescentTree *tree, + const Haplotype &h0, const Haplotype &h1, +diff --git a/change_selector_test.cc b/change_selector_test.cc +index 5f655d1..9004bef 100644 +--- a/change_selector_test.cc ++++ b/change_selector_test.cc +@@ -23,6 +23,8 @@ + # include "change.hh" + #endif + ++#include <cstring> ++ + // dummy class for testing + struct DummyChange : public Change { + DummyChange() : Change("Dummy change") {} +diff --git a/coalescent_tree.cc b/coalescent_tree.cc +index eb937e5..9e54a2b 100644 +--- a/coalescent_tree.cc ++++ b/coalescent_tree.cc +@@ -7,6 +7,7 @@ + + #include "coalescent_tree.hh" + ++#include <algorithm> + + /** \file + * \brief Implementation of the coalescent tree. +diff --git a/coalescent_tree_test.cc b/coalescent_tree_test.cc +index 20059e9..2971ead 100644 +--- a/coalescent_tree_test.cc ++++ b/coalescent_tree_test.cc +@@ -30,6 +30,8 @@ + # define CMATH_INCLUDED + #endif + ++#include <cstring> ++ + namespace { + + CoalescentTree *test_tree(HaplotypePool &pool) +diff --git a/distance_matrix_test.cc b/distance_matrix_test.cc +index e2e8435..9d367ee 100644 +--- a/distance_matrix_test.cc ++++ b/distance_matrix_test.cc +@@ -15,6 +15,8 @@ + # include "haplotype_pool.hh" + #endif + ++#include <cstring> ++ + namespace { + int distance(const Haplotype &h1, const Haplotype &h2) + { +diff --git a/distance_tree_builder_test.cc b/distance_tree_builder_test.cc +index e252c3e..3f589f4 100644 +--- a/distance_tree_builder_test.cc ++++ b/distance_tree_builder_test.cc +@@ -15,6 +15,8 @@ + # include "test_random.hh" + #endif + ++#include <cstring> ++ + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/filter_iterator_test.cc b/filter_iterator_test.cc +index bf5097b..e74a29f 100644 +--- a/filter_iterator_test.cc ++++ b/filter_iterator_test.cc +@@ -21,6 +21,8 @@ + # define FUNCTIONAL_INCLUDED + #endif + ++#include <cstring> ++ + namespace { + struct even : public std::unary_function<int,bool> { + bool operator () (int i) const { return i % 2 == 0; } +diff --git a/genotype_pool_test.cc b/genotype_pool_test.cc +index e62a03f..9a2badb 100644 +--- a/genotype_pool_test.cc ++++ b/genotype_pool_test.cc +@@ -22,6 +22,8 @@ + # include "genotype.hh" + #endif + ++#include <cstring> ++ + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/genotype_test.cc b/genotype_test.cc +index 3d704e4..64b3343 100644 +--- a/genotype_test.cc ++++ b/genotype_test.cc +@@ -22,6 +22,8 @@ + # include "haplotype.hh" + #endif + ++#include <cstring> ++ + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/guile_sampler.cc b/guile_sampler.cc +index b0d19f1..ffbec86 100644 +--- a/guile_sampler.cc ++++ b/guile_sampler.cc +@@ -26,6 +26,7 @@ + # define CASSERT_INCLUDED + #endif + ++#include <memory> + + /** \file + * \brief Implementation of the guile sampler wrapper. +diff --git a/haplotype.cc b/haplotype.cc +index a38541f..7810642 100644 +--- a/haplotype.cc ++++ b/haplotype.cc +@@ -12,6 +12,8 @@ + # define SSTREAM_INCLUDED + #endif + ++#include <algorithm> ++ + /** \file + * \brief Implementation of haplotype functionality. + */ +diff --git a/haplotype_pool.cc b/haplotype_pool.cc +index ceef1b9..42c6125 100644 +--- a/haplotype_pool.cc ++++ b/haplotype_pool.cc +@@ -7,6 +7,8 @@ + + #include "haplotype_pool.hh" + ++#include <algorithm> ++ + /** \file + * \brief Implementation of haplotype pool functionality. + */ +diff --git a/haplotype_pool_test.cc b/haplotype_pool_test.cc +index a774809..4527d23 100644 +--- a/haplotype_pool_test.cc ++++ b/haplotype_pool_test.cc +@@ -19,6 +19,8 @@ + # include "region.hh" + #endif + ++#include <cstring> ++ + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/haplotype_test.cc b/haplotype_test.cc +index 134a601..b7f5b63 100644 +--- a/haplotype_test.cc ++++ b/haplotype_test.cc +@@ -19,6 +19,8 @@ + # include "region.hh" + #endif + ++#include <cstring> ++ + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/marker_test.cc b/marker_test.cc +index ff34d7c..317385d 100644 +--- a/marker_test.cc ++++ b/marker_test.cc +@@ -13,6 +13,7 @@ + #include "testing.hh" + + #include <cmath> ++#include <cstring> + + int main(int argc, const char *argv[]) + { +diff --git a/markov_region_test.cc b/markov_region_test.cc +index 58e0278..db0f9ba 100644 +--- a/markov_region_test.cc ++++ b/markov_region_test.cc +@@ -11,7 +11,7 @@ + + #include "region.hh" + #include "testing.hh" +- ++#include <cstring> + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/qtl_haplotype_pool_test.cc b/qtl_haplotype_pool_test.cc +index 72f763d..8c058af 100644 +--- a/qtl_haplotype_pool_test.cc ++++ b/qtl_haplotype_pool_test.cc +@@ -19,6 +19,8 @@ + # include "region.hh" + #endif + ++#include <cstring> ++ + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/random_set_test.cc b/random_set_test.cc +index 7eae435..b7a3451 100644 +--- a/random_set_test.cc ++++ b/random_set_test.cc +@@ -15,6 +15,8 @@ + # include "test_random.hh" + #endif + ++#include <cstring> ++ + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/random_tree_builder_test.cc b/random_tree_builder_test.cc +index e8c5957..7c95519 100644 +--- a/random_tree_builder_test.cc ++++ b/random_tree_builder_test.cc +@@ -28,6 +28,7 @@ + # include "test_random.hh" + #endif + ++#include <cstring> + + void test_tree(const CoalescentTree *tree, + const Haplotype &h0, const Haplotype &h1, +diff --git a/region.cc b/region.cc +index df22885..94bce6f 100644 +--- a/region.cc ++++ b/region.cc +@@ -22,6 +22,8 @@ + # define CMATH_INCLUDED + #endif + ++#include <algorithm> ++ + + /** \file + * \brief Implementation of region functionality. +diff --git a/region_test.cc b/region_test.cc +index 25f6cf0..e21084f 100644 +--- a/region_test.cc ++++ b/region_test.cc +@@ -11,6 +11,7 @@ + + #include "region.hh" + #include "testing.hh" ++#include <cstring> + + int main(int argc, const char *argv[]) + { +diff --git a/selection_if_test.cc b/selection_if_test.cc +index a9a6377..0fb8052 100644 +--- a/selection_if_test.cc ++++ b/selection_if_test.cc +@@ -24,6 +24,8 @@ + # define VECTOR_INCLUDED + #endif + ++#include <cstring> ++ + namespace { + struct even : public std::unary_function<int,bool> { + bool operator () (int i) const { return i % 2 == 0; } +diff --git a/selection_test.cc b/selection_test.cc +index 3bf673a..579931c 100644 +--- a/selection_test.cc ++++ b/selection_test.cc +@@ -28,6 +28,8 @@ + # define LIST_INCLUDED + #endif + ++#include <cstring> ++ + int main(int argc, const char *argv[]) + { + HANDLE_TEST_OPTIONS; +diff --git a/testing.hh b/testing.hh +index fbdcd87..c86dbc6 100644 +--- a/testing.hh ++++ b/testing.hh +@@ -23,6 +23,8 @@ + # define CSTDLIB_INCLUDED + #endif + ++#include <cstring> ++ + /// \brief Verboseness flag for running tests. + /// + /// If set, the test will report the failed tests, otherwise it will +diff --git a/tree_builder.hh b/tree_builder.hh +index 4b0ec01..c0bdc5a 100644 +--- a/tree_builder.hh ++++ b/tree_builder.hh +@@ -34,6 +34,7 @@ + # include "meta_programming.hh" + #endif + ++#include <limits> + + /** + * \brief Abstract class for tree builders. diff --git a/sci-biology/generecon/generecon-1.2.1-r1.ebuild b/sci-biology/generecon/generecon-1.2.1-r1.ebuild index 7adfb5cf5..41e2607e5 100644 --- a/sci-biology/generecon/generecon-1.2.1-r1.ebuild +++ b/sci-biology/generecon/generecon-1.2.1-r1.ebuild @@ -1,37 +1,34 @@ -# Copyright 1999-2007 Gentoo Foundation +# Copyright 1999-2010 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit eutils +EAPI="3" -DESCRIPTION="Generecon performs linkage disequilibrium gene mapping based on coalescent theory using Bayesian Markov Chain Monte Carlo methods." +inherit autotools eutils + +DESCRIPTION="Disequilibrium gene mapping based on coalescent theory using Bayesian Markov Chain MC methods" HOMEPAGE="http://www.daimi.au.dk/~mailund/GeneRecon/" SRC_URI="http://www.daimi.au.dk/~mailund/GeneRecon/download/${P}.tar.gz" -SLOT="0" -# License of the package. This must match the name of file(s) in -# /usr/portage/licenses/. For complex license combination see the developer -# docs on gentoo.org for details. +SLOT="0" LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86" +IUSE="" -KEYWORDS="x86" +RDEPEND=" + dev-scheme/guile + sci-libs/gsl" +DEPEND="${DEPEND}" -DEPEND="dev-scheme/guile - sci-libs/gsl" - -src_unpack() { - unpack ${A} - sed 's|#PF#|'${PF}'|g' ${FILESDIR}/${PN}-docfiles.patch > ${PN}-docfiles.patch +src_prepare() { + sed 's|#PF#|'${PF}'|g' "${FILESDIR}"/${PN}-docfiles.patch > ${PN}-docfiles.patch epatch ${PN}-docfiles.patch - - cd ${S} - pwd - einfo "Regenerating autotools files..." - aclocal || die "aclocal failed" - automake || die "automake failed" + epatch "${FILESDIR}"/${PV}-gcc4.patch + epatch "${FILESDIR}"/${PV}-flags.patch + eautoreconf } src_install() { - make DESTDIR=${D} install || die "make install failed" + emake DESTDIR="${D}" install || die "make install failed" } |