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authorJustin Lecher <jlec@gentoo.org>2011-01-12 17:21:42 +0100
committerJustin Lecher <jlec@gentoo.org>2011-01-12 17:21:42 +0100
commitbb9486ef452c39c8390d8913c3121014136c48aa (patch)
treea6e56b6e2e67cc86c30f36a6c1313315fa68449a /sci-chemistry/coot
parentmore cleaning (diff)
downloadsci-bb9486ef452c39c8390d8913c3121014136c48aa.tar.gz
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Correctly manage openmp and otehr linking
(Portage version: 2.2.0_alpha14/git/Linux x86_64, signed Manifest commit with key 70EB7916)
Diffstat (limited to 'sci-chemistry/coot')
-rw-r--r--sci-chemistry/coot/ChangeLog7
-rw-r--r--sci-chemistry/coot/Manifest17
-rw-r--r--sci-chemistry/coot/coot-9999.ebuild9
-rw-r--r--sci-chemistry/coot/files/9999-clipper.patch9
-rw-r--r--sci-chemistry/coot/files/9999-goocanvas.patch26
-rw-r--r--sci-chemistry/coot/files/9999-gsl.patch14
-rw-r--r--sci-chemistry/coot/files/9999-lidia.patch16
-rw-r--r--sci-chemistry/coot/files/9999-openmp.patch17
8 files changed, 84 insertions, 31 deletions
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 86c863207..a35a218d8 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,7 +1,12 @@
# ChangeLog for sci-chemistry/coot
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 12 Jan 2011; Justin Lecher <jlec@gentoo.org> +files/9999-clipper.patch,
+ +files/9999-gsl.patch, +files/9999-lidia.patch, files/9999-goocanvas.patch,
+ files/9999-openmp.patch, coot-9999.ebuild:
+ Correctly manage openmp and otehr linking
+
17 Dec 2010; Justin Lecher <jlec@gentoo.org> files/9999-openmp.patch,
coot-9999.ebuild:
Correct handling of OpenMp support
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index aaee3157f..da699d528 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1,21 +1,24 @@
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
-AUX 9999-goocanvas.patch 1050 RMD160 3d87866b3ef15b42c8f92b839e338f357d8bb9e3 SHA1 3525db644d8c6fb6a99de5a61d33646284c9e5bd SHA256 02cad7059c877b9fc99f50dfa91eaacb83132dbc8c2530e0f46bb989d71be24b
+AUX 9999-clipper.patch 314 RMD160 23780b108f2cabb1ba54de038b2e1716e4e4566e SHA1 a0832f4375c790ea6fd6888e9abb842a974c3909 SHA256 989fe91aa3760e2c0d34983943a9744a0ec9eb740737baeaa46c2bf8ea5c7169
+AUX 9999-goocanvas.patch 702 RMD160 9b26975eb658f15dfd806e47be9c11bcb7f850db SHA1 37bb70847ced34b754fe7cf5fea878b93bb6ed12 SHA256 162b21a3afb2d523df315ec021faf7a6497eb3b4fe00f90f601527fe1c22621a
+AUX 9999-gsl.patch 478 RMD160 c3df04b30699b8a534dc69cde67c805bb5ac1fdb SHA1 b32b9404c85df75e8149c8ec8f6dc48d0b4c64fa SHA256 fc6b256c655d7390f5270f266cbf22d34d6e27e1726d09f1747fd3d14ab393a4
AUX 9999-include.patch 345 RMD160 6e42ce2afa7141f9cdcda0ca3ea5a11ef4f0f15f SHA1 3df3955307115ed8527f55fb49452905991c36cc SHA256 07b61fb298da857c5c37abb492cf192c65f9b538a3fc2d316aca7f4269e25a75
-AUX 9999-openmp.patch 397 RMD160 4cbfc6af2589718aa514efc59bb19f7f98a71640 SHA1 ed7157da29251054ffe89aea16eb2378676e0a9e SHA256 6dd87625db48e630450da8352f5ba7a52002129ed0576dc4ac1373dd1a387b28
+AUX 9999-lidia.patch 531 RMD160 45c5929020a735121e54b4a1240c8f3fb0d97ec5 SHA1 ca0b119af0e39dfc19b606cb629c26f55ca3bf01 SHA256 c7b49c6a0689c467e9298a230f1a8c8f8c669ef04b51632e581f9a63f43c0a34
+AUX 9999-openmp.patch 850 RMD160 5d128c3451a496f95ca33d7cd5447a0c85d55c13 SHA1 ee8a8823a70cf4c194daf7879c6b3ff011c99e3d SHA256 97da619ba47f16ff14a5b9496cb3e377f65c533dfe861c5cb4c7f19d293cae5c
AUX 9999-rappermc.patch 477 RMD160 5d67f80be6e4bc303d7999cfa645ea36dbfc834a SHA1 4c2ff98125b6a4664f77e8b5f39f6a9a1ac72622 SHA256 83dd4ddda627baec52a0754117741d97e7b2c61e42813a314b258db93903d7c0
AUX fix-namespace-error.patch 1081 RMD160 ebecd51b87c39dc2c37e565f18fc88b7aa837d05 SHA1 f732df5f4795e728bdf217aac9c9f53952e2890c SHA256 fd271dd22eec5725fcbd20c68b57008eed0f435d1e0ac212fbfd389a0a970beb
AUX glib.m4 8444 RMD160 f3f4b2987796f16d17758f2af3459279351d6f2c SHA1 201eb58c2b3f3c5395dacd3913a4fb9d950d3276 SHA256 ada4a0a46bd00eda39afe77f675b721f60cd20c0080170848f4d7e92b4ba4dc8
AUX gtk.m4 8516 RMD160 3860fe211902d5b9290f0a70e7d75ebec6b0ec67 SHA1 98b93b820423a52ebd80e3f1822a8f2bd4b3f15d SHA256 4eb6e0bb2c6863139d1fb4ca2d1d0f0ef07e3a85fdbb5ba98d03373f610f0c37
DIST greg-data.tar.gz 8041681 RMD160 dc03bc233bed69fd6288a92a48b9a7e0bbf56129 SHA1 6e27bd0053758cf829a3ff8bd07b94c9e1ffb777 SHA256 46b9bb2dc9f5dfff463a5fe95e8e583e2a44760ae96fc0b8b5b4bd455e35862d
-EBUILD coot-9999.ebuild 3847 RMD160 303fa6064a7331d4ff39b98d38c8d2956ca644e3 SHA1 1a1049721f14bacb79623c20429c7978864fdb61 SHA256 eaf27586890b8742b382fde62c7885f0962e0340868b62b46999f6510bd1e220
-MISC ChangeLog 8662 RMD160 87b879c02dfdf9762c4f2643e8cbed4c9a66ae7d SHA1 28706061aa7523a275ee04937e948bacbe7a830b SHA256 e9803318f35df5070f4b8c4aa462c3f7f86034776553485c8849b0d18afd5fea
+EBUILD coot-9999.ebuild 3922 RMD160 e5564411a7ba8b1c7e4faa7196fbec30d445f422 SHA1 f3c7ba68ef09c153d879eb878b888ace388a2db7 SHA256 19afdccca2cf790096f603d1762008db6a2eb5706356f3586381cc1b59ed28a1
+MISC ChangeLog 8904 RMD160 1bdabd655300eabdfe8fe659bdafd293102b6589 SHA1 ed4d5344785315ff34d73b46e28f4e6c00e6e7ad SHA256 a929a677452e1a113cd9c15ca908e8adfec24405c76b02a05b281f094d729994
MISC metadata.xml 306 RMD160 303613d4bb58ea149f418efc0d41f550ecbb94ca SHA1 1caeb2549f7f6a1dd44f2200784be8f2a7f294ab SHA256 f0ead885a2ede3186db2797473c72249fb525de661c279ca2ce7b8b152399bf6
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v2.0.16 (GNU/Linux)
-iEYEARECAAYFAk0LrGAACgkQgAnW8HDreRbhBgCeOeggv1+cchBDIiDg4KWzELXw
-k7gAoIcmQu/upoW+ATFMssKGUKo7cRTZ
-=/JwB
+iEYEARECAAYFAk0t1RYACgkQgAnW8HDreRYr+wCeIJ/WnP97Cc9AbTAZjFcqkesN
+JbUAn2wabNnZhM4Xro5IHI0YrtMHDwIO
+=Gv6L
-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index ab7bc0ee7..19d5c7df7 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -22,7 +22,7 @@ SRC_URI="test? ( http://www.biop.ox.ac.uk/coot/devel/greg-data.tar.gz )"
SLOT="0"
LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="test"
SCIDEPS="
@@ -61,6 +61,7 @@ RDEPEND="
net-dns/libidn"
DEPEND="${RDEPEND}
dev-lang/swig
+ sys-devel/bc
test? ( dev-scheme/greg )"
S="${WORKDIR}"
@@ -70,7 +71,8 @@ pkg_setup() {
}
PATCHES=(
- "${FILESDIR}"/${PV}-openmp.patch
+ "${FILESDIR}"/${PV}-goocanvas.patch
+ "${FILESDIR}"/${PV}-clipper.patch
"${FILESDIR}"/${PV}-include.patch
)
@@ -94,7 +96,6 @@ src_prepare() {
return ${ESVN_WC_REVISION:-0};
}
}
-
EOF
eautoreconf
diff --git a/sci-chemistry/coot/files/9999-clipper.patch b/sci-chemistry/coot/files/9999-clipper.patch
new file mode 100644
index 000000000..e3f028f98
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-clipper.patch
@@ -0,0 +1,9 @@
+Index: lidia-core/Makefile.am
+===================================================================
+--- lidia-core/Makefile.am (revision 3299)
++++ lidia-core/Makefile.am (working copy)
+@@ -23,3 +23,4 @@
+
+ libcoot_lidia_core_la_SOURCES = lbg-molfile.cc lig-build.cc
+
++libcoot_lidia_core_la_LIBADD = $(CLIPPER_LIBS)
diff --git a/sci-chemistry/coot/files/9999-goocanvas.patch b/sci-chemistry/coot/files/9999-goocanvas.patch
index 0a8d3f3ed..ce0d4a00a 100644
--- a/sci-chemistry/coot/files/9999-goocanvas.patch
+++ b/sci-chemistry/coot/files/9999-goocanvas.patch
@@ -1,30 +1,20 @@
-Index: trunk/macros/goo-canvas.m4
+Index: macros/goo-canvas.m4
===================================================================
---- trunk/macros/goo-canvas.m4 (revision 3249)
-+++ trunk/macros/goo-canvas.m4 (working copy)
-@@ -28,15 +28,15 @@
- # GCC c++ does not.
- #
- GOOCANVAS_LDOPTS="$goocanvas_prefix/lib/libgoocanvas.la"
-+
-+ # PKG_CHECK_MODULES has a AC_MSG itself
-+ AC_MSG_CHECKING([for Goocanvas])
-+
- else
-- # the compiler looks in the "standard" places for GOOCANVAS.
-- GOOCANVAS_CFLAGS="-I/usr/include/goocanvas-1.0"
-- GOOCANVAS_LDOPTS="libgoocanvas.la"
-+ PKG_CHECK_MODULES(GOOCANVAS, goocanvas)
+--- macros/goo-canvas.m4 (revision 3307)
++++ macros/goo-canvas.m4 (working copy)
+@@ -56,9 +56,9 @@
+ fi
fi
-AC_MSG_CHECKING([for Goocanvas])
--
++PKG_CHECK_MODULES(GOOCANVAS, goocanvas)
+
-LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
+LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
#
# AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
-@@ -54,7 +54,7 @@
+@@ -76,7 +76,7 @@
if test x$have_goocanvas = xyes; then
GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
diff --git a/sci-chemistry/coot/files/9999-gsl.patch b/sci-chemistry/coot/files/9999-gsl.patch
new file mode 100644
index 000000000..af7a405f8
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-gsl.patch
@@ -0,0 +1,14 @@
+Index: coot-utils/Makefile.am
+===================================================================
+--- coot-utils/Makefile.am (revision 3299)
++++ coot-utils/Makefile.am (working copy)
+@@ -90,7 +90,8 @@
+ $(top_builddir)/mini-mol/libcoot-mini-mol.la \
+ libcoot-map-utils.la \
+ libcoot-coord-utils.la \
+- $(top_builddir)/utils/libcoot-utils.la
++ $(top_builddir)/utils/libcoot-utils.la \
++ $(GSL_LIBS)
+
+
+ noinst_PROGRAMS = test-h-bonds testshelxreader testcootutils
diff --git a/sci-chemistry/coot/files/9999-lidia.patch b/sci-chemistry/coot/files/9999-lidia.patch
new file mode 100644
index 000000000..2ac3fccb9
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-lidia.patch
@@ -0,0 +1,16 @@
+Index: lbg/Makefile.am
+===================================================================
+--- lbg/Makefile.am (revision 3299)
++++ lbg/Makefile.am (working copy)
+@@ -24,6 +24,11 @@
+ lbg-search.cc some-coot-utils.cc residue-circles.cc rdkit-interface.cc \
+ flev-annotations.cc
+
++libcoot_lidia_la_LIBADD = \
++ $(top_builddir)/coot-utils/libcoot-coord-utils.la \
++ $(top_builddir)/lidia-core/libcoot-lidia-core.la \
++ $(GSL_LIBS) $(GTK_LIBS) $(GOOCANVAS_LIBS)
++
+ lidia_SOURCES = lidia-main.cc
+
+ # some-coot-utils.hh needed?
diff --git a/sci-chemistry/coot/files/9999-openmp.patch b/sci-chemistry/coot/files/9999-openmp.patch
index 3cc9501a8..a239c1fe5 100644
--- a/sci-chemistry/coot/files/9999-openmp.patch
+++ b/sci-chemistry/coot/files/9999-openmp.patch
@@ -7,7 +7,22 @@ Index: surface/Makefile.am
INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(FFTW_CXXFLAGS)
-AM_CPPFLAGS = $(OPENMP_CFLAGS)
-+AM_CPPFLAGS = $(OPENMP_CXXFLAGS)
++AM_CXXFLAGS = $(OPENMP_CFLAGS)
lib_LTLIBRARIES = libccp4mg-surface.la
+Index: src/Makefile.am
+===================================================================
+--- src/Makefile.am (revision 3299)
++++ src/Makefile.am (working copy)
+@@ -417,8 +417,8 @@
+ # coot_real_LDFLAGS = -static -lstdc++
+ coot_real_LDFLAGS =
+
+-coot_real_LDADD = $(OPENMP_CFLAGS) \
+- $(COOT_EXTRA_LIBS) \
++coot_real_LDADD = \
++ $(COOT_EXTRA_LIBS) \
+ $(GUILE_GTK_LIBS) \
+ $(GUILE_LDFLAGS) \
+ $(CLIPPER_LIBS) \