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authorJustin Lecher <jlec@gentoo.org>2010-06-17 19:46:46 +0200
committerJustin Lecher <jlec@gentoo.org>2010-06-19 15:34:13 +0200
commitbd5afd76e35a6cad321d23cffb3964cd6f996c07 (patch)
tree762022a123552c518c798ee5aa51ccfdcea5a790 /sci-biology/generecon
parentRename 1.4.1 as 1.4.1-r1 so users can easily get stable version from main tree. (diff)
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Fixing compilation with gcc4, repecting CXXFLAGS/LDFLAGS, reMANIFEST
(Portage version: 2.2_rc67/git/Linux x86_64) (Signed Manifest commit)
Diffstat (limited to 'sci-biology/generecon')
-rw-r--r--sci-biology/generecon/ChangeLog6
-rw-r--r--sci-biology/generecon/Manifest18
-rw-r--r--sci-biology/generecon/files/1.2.1-flags.patch30
-rw-r--r--sci-biology/generecon/files/1.2.1-gcc4.patch368
-rw-r--r--sci-biology/generecon/generecon-1.2.1-r1.ebuild39
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"
}