Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

6 files changed, 18 insertions, 176 deletions

diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index abbe4bcf3..4251eafc3 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 0.5.2-as-needed.patch 19562 RMD160 7c242801251cbd11a8143df793a832a860c5aacb SHA1 a7d6552e5a3bbdf4e28ac995a31b3c3059241dab SHA256 9f5be12beb7691eb1e187923b95edc5890e385fecb2ef2ecb5eb9991858bebc1
 AUX 0.5.2-gcc-4.3.patch 260 RMD160 e6d72c24d7dc02e84c67198f3e82aa4215df9b77 SHA1 1dd99a49d35181808a9e30a1f41ab63b6077dda0 SHA256 2d215b8009449e2f234eeb6c1e08da1f2e7804fedcf5e1d69997a6d8355d37da
 AUX 0.5.2-gcc-4.4.patch 257 RMD160 d1ec251cda36ac201a8baa84d7dad542e72e0c7b SHA1 069af29c1de34e6af94ff463ca04e3fb3c19c209 SHA256 761db5b8cb4cc11050b833df1f87b9ea5d9ca8b3637d7e7b1f5b4f6b7d795177
@@ -8,7 +11,7 @@ AUX 9999-as-needed.patch 18539 RMD160 2596dac3eb33e1704f84a11613fdc52c42fe8765 S
 AUX 9999-as-needed2.patch 18539 RMD160 2596dac3eb33e1704f84a11613fdc52c42fe8765 SHA1 b6d932312e38d7822866df6449226d90ea1c38c3 SHA256 1646003be0db635ff9b9ef7726adb06f4da8de8a4dbe77baa5074ec8a2faa68a
 AUX 9999-check-include.patch 833 RMD160 7b877f8973b06119779518b433b607665930a382 SHA1 c8a0c80d3a3f5e85592c9925b35c6d5462fc36ad SHA256 98a6c8ef47953501e360b1bdd568ac99d5a53749738d940939e9f6a47cf85cd1
 AUX 9999-gcc4.4.patch 299 RMD160 75374bd38981d4383d926a3b6529ef955a18e893 SHA1 e05d1caeb3dd13d101d417e7f2613402b6712005 SHA256 02c18e695086d70152b923af5d0aecd334bc18f1b6b955d3133c2ae7b6f218af
-AUX 9999-rappermc.patch 552 RMD160 66feba0ce4e6539ef67ab69e5b6d1bed448e18db SHA1 1806984097fde639a282a27c3de60945daeb1e6d SHA256 01ada3aac5413acfa9328e6235dc6d3e7fa7dc08455c560e97d498e5adea9523
+AUX 9999-rappermc.patch 477 RMD160 5d67f80be6e4bc303d7999cfa645ea36dbfc834a SHA1 4c2ff98125b6a4664f77e8b5f39f6a9a1ac72622 SHA256 83dd4ddda627baec52a0754117741d97e7b2c61e42813a314b258db93903d7c0
 AUX 9999-test-rama.patch 497 RMD160 6db4732c088d6435dfa1eab0b036f5d37cf13df4 SHA1 dea0505ccdfae27c5632c1c57ce889024a8681bc SHA256 13eed941e596f5a8f1a7a266f8f7c44a359ab35d7df1dad6cae1d91461a7f3bf
 AUX fix-namespace-error.patch 1081 RMD160 ebecd51b87c39dc2c37e565f18fc88b7aa837d05 SHA1 f732df5f4795e728bdf217aac9c9f53952e2890c SHA256 fd271dd22eec5725fcbd20c68b57008eed0f435d1e0ac212fbfd389a0a970beb
 AUX glib.m4 8444 RMD160 f3f4b2987796f16d17758f2af3459279351d6f2c SHA1 201eb58c2b3f3c5395dacd3913a4fb9d950d3276 SHA256 ada4a0a46bd00eda39afe77f675b721f60cd20c0080170848f4d7e92b4ba4dc8
@@ -24,3 +27,10 @@ EBUILD coot-0.6_pre1-r2312.ebuild 4318 RMD160 8164ef691b3ef718bdd0aad743789624d7
 EBUILD coot-9999.ebuild 3955 RMD160 7d7a828e19fb04af1019b11367317a9249e47c34 SHA1 8df6be6a3509860fc8a765e0a43b14848eed0808 SHA256 0238b3dd286545721eee66ff8cac1830e459a2c75f692e8c6f51be9b2cf1fe16
 MISC ChangeLog 6323 RMD160 0e60847ef994e7cbbf2028f270cac668e8d7913f SHA1 af8f517f6ef640eeb5391eccbd573f1363232043 SHA256 069c46e345e102923526a11604ed534bc0698e0d33cf8487d7077a0c5fea0238
 MISC metadata.xml 316 RMD160 845cc100ac244efa5f02595717b5da635f87d2f1 SHA1 c870d2c52c44dee3bab8623e5b6095266f400813 SHA256 64f6dbcd3bb41b26fd7897089cd60ddb93f1ea7d75f9531bca94f28b07e21b2f
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.11 (GNU/Linux)
+
+iEYEARECAAYFAkrYQoYACgkQgAnW8HDreRZfFwCffTScjFWIDPyRNGgfC+UJE12s
+Jr4AnRi8HPYkRFNiIgFrIQssGY/qBE16
+=/llm
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/coot/coot-9999.ebuild.save b/sci-chemistry/coot/coot-9999.ebuild.save
deleted file mode 100644
index e69de29bb..000000000
--- a/sci-chemistry/coot/coot-9999.ebuild.save
+++ /dev/null
diff --git a/sci-chemistry/coot/coot-9999.ebuild.save.1 b/sci-chemistry/coot/coot-9999.ebuild.save.1
deleted file mode 100644
index 9ba1f1eca..000000000
--- a/sci-chemistry/coot/coot-9999.ebuild.save.1
+++ /dev/null
@@ -1,172 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit autotools base versionator subversion
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-ESVN_REPO_URI="http://coot.googlecode.com/svn/trunk"
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
-SRC_URI="test? ( http://www.biop.ox.ac.uk/coot/devel/greg-data.tar.gz )"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-SCIDEPS="
-	>=sci-libs/ccp4-libs-6.1
-	>=sci-libs/clipper-20090520
-	>=sci-libs/coot-data-2
-	>=sci-libs/gsl-1.3
-	sci-chemistry/reduce
-	sci-chemistry/refmac
-	sci-chemistry/probe"
-
-XDEPS="
-	gnome-base/libgnomecanvas
-	gnome-base/librsvg
-	virtual/glut
-	>=x11-libs/gtk+-2.2
-	x11-libs/gtkglext"
-
-SCHEMEDEPS="
-	dev-scheme/net-http
-	dev-scheme/goosh
-	dev-scheme/guile-gui
-	>=dev-scheme/guile-lib-0.1.6
-	dev-scheme/guile-www
-	=x11-libs/guile-gtk-2.1"
-
-RDEPEND="
-	${SCIDEPS}
-	${XDEPS}
-	${SCHEMEDEPS}
-	dev-python/pygtk
-	>=dev-libs/gmp-4.2.2-r2
-	>=net-misc/curl-7.19.6"
-DEPEND="${RDEPEND}
-	dev-lang/swig
-	test? ( dev-scheme/greg )"
-
-S="${WORKDIR}"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-rappermc.patch
-	"${FILESDIR}"/link-against-guile-gtk-properly.patch
-	"${FILESDIR}"/fix-namespace-error.patch
-	)
-
-src_unpack() {
-	subversion_src_unpack
-	use test && unpack ${A}
-}
-
-src_prepare() {
-	base_src_prepare
-
-	# Link against single-precision fftw
-	sed -i \
-		-e "s:lfftw:lsfftw:g" \
-		-e "s:lrfftw:lsrfftw:g" \
-		"${S}"/macros/clipper.m4
-
-	# So we don't need to depend on crazy old gtk and friends
-	cp "${FILESDIR}"/*.m4 "${S}"/macros/
-
-	cat >> src/svn-revision.cc <<- EOF
-	extern "C" {
-	int svn_revision() {
-		return  ${ESVN_WC_REVISION};
-	}
-	}
-
-	EOF
-
-	eautoreconf
-}
-
-src_configure() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	econf \
-		--includedir='${prefix}/include/coot' \
-		--with-gtkcanvas-prefix=/usr \
-		--with-clipper-prefix=/usr \
-		--with-mmdb-prefix=/usr \
-		--with-ssmlib-prefix=/usr \
-		--with-gtkgl-prefix=/usr \
-		--with-guile \
-		--with-python=/usr \
-		--with-guile-gtk \
-		--with-gtk2 \
-		--with-pygtk
-}
-
-src_compile() {
-#	# Regenerate wrappers, otherwise at least gtk-2 build fails
-#	pushd src
-#	rm -f coot_wrap_python.cc coot_wrap_python_pre.cc \
-#		&& emake coot_wrap_python.cc \
-#		|| die "failed to regenerate python wrapper"
-#
-#	rm -f coot_wrap_guile.cc coot_wrap_guile_pre.cc \
-#		&& emake coot_wrap_guile.cc \
-#		||die "failed to regenerate guile wrapper"
-#	popd
-#
-	emake || die "emake failed"
-
-	cp "${S}"/src/coot.py python/ || die
-}
-
-src_test() {
-#	emake check || die
-
-	mkdir "${T}"/coot_test
-
-	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
-	export COOT_SCHEME_DIR="${S}/scheme/"
-	export COOT_RESOURCES_FILE="${S}/cootrc"
-	export COOT_PIXMAPS_DIR="${S}/pixmaps"
-	export COOT_DATA_DIR="${S}"
-	export COOT_PYTHON_DIR="${S}/python"
-	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
-	export PYTHONHOME=/usr
-	export CCP4_SCR="${T}"/coot_test
-
-	export COOT_TEST_DATA_DIR="${S}"/data/greg-data
-
-	cat > command-line-greg.scm <<- EOF
-	(use-modules (ice-9 greg))
-		(set! greg-tools (list "greg-tests"))
-			(set! greg-debug #t)
-			(set! greg-verbose 5)
-			(let ((r (greg-test-run)))
-				(if r
-				(coot-real-exit 0)
-				(coot-real-exit 1)))
-	EOF
-
-	einfo "Running test with following paths ..."
-	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
-	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
-	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
-	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
-	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
-	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
-	einfo "PYTHONPATH $PYTHONPATH"
-	einfo "PYTHONHOME $PYTHONHOME"
-	einfo "CCP4_SCR ${CCP4_SCR}"
-
-	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
-}
diff --git a/sci-libs/gmsh/ChangeLog b/sci-libs/gmsh/ChangeLog
index 96080f17e..c2457f8de 100644
--- a/sci-libs/gmsh/ChangeLog
+++ b/sci-libs/gmsh/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Oct 2009; Etienne Lorriaux <etienne.lorriaux@gmail.com>
+  gmsh-9999.ebuild:
+  Removed keywords for gmsh-9999
+
 *gmsh-9999 (15 Oct 2009)
 *gmsh-2.4.2 (15 Oct 2009)
 
diff --git a/sci-libs/gmsh/Manifest b/sci-libs/gmsh/Manifest
index 1da1d7a0d..e97cb63c0 100644
--- a/sci-libs/gmsh/Manifest
+++ b/sci-libs/gmsh/Manifest
@@ -4,6 +4,6 @@ DIST gmsh-2.4.2-source.tgz 3109391 RMD160 d89906add953c28e4018b6deac7d631a10dc02
 DIST gmsh-nightly-source.tgz 3136053 RMD160 bc0ac19717ee5c8ce4a1d61e43fd79a4cf4074d0 SHA1 51648d8ed520a5882191207310b1e5f66a08aca0 SHA256 2f8b62859ccfcafb7ab77a84cbe6c7c29c643d9ee55cda82ed24a942eea34a69
 EBUILD gmsh-2.3.1-r1.ebuild 2133 RMD160 5e5a604ef569b5b750a4618e0fd7bf6698124a72 SHA1 876bb41897884ea4cdc743e27da78e1a629bafa3 SHA256 3d78c2e0e61f285474c630b64280cdbc0229cdb21d78eff075f35ae95a47e9ec
 EBUILD gmsh-2.4.2.ebuild 2312 RMD160 957034b0b7ec0821e0a7b9bae98cf96cb68384e3 SHA1 3c3d9b1e2234cc60e7c9b4f49116da4f61e793af SHA256 68678401c3e5a68986e3b41ce9615f68bd768f86b9b944799a8f5a124d9bcf1b
-EBUILD gmsh-9999.ebuild 2324 RMD160 6db33656f85b6922388947dbb05b8c9843cf25f3 SHA1 2ca1aa059a93a630807ed696cffc143a26325a7e SHA256 63105defa32fecd339ed618589c608363bde681a19d54b08c31966fd74dc2c27
-MISC ChangeLog 1696 RMD160 bd3cebcb2eeb2ede095bc2ca3a427418d823ac76 SHA1 9b6eccd1c01ba6d77df15e0d0608f7ae37154c2b SHA256 da55f7aaf2982f357d063ae06e187267f100a8235b957bc5e3b83af821134494
+EBUILD gmsh-9999.ebuild 2313 RMD160 621ca8f8e190ef1a9f490786f81dc72c58715b26 SHA1 0281dd4fefccf798ce58a2050b965ab8ae29fd17 SHA256 0d30d25060d5fc12a2c32724d33ba6dbd3678b7829ad22f42a424b221136fc7c
+MISC ChangeLog 1811 RMD160 56569301b5db9c6275fb6a2e0d1a8196c74763e7 SHA1 3bcce97156095eab8e7344a5d8189fb059ee95ab SHA256 ef3af22311c4b572f63328066c50ab5c71d6e44c1ad4b095c64a999fbcb18171
 MISC metadata.xml 450 RMD160 6eae78af85d254c48911bc974f6442c8b8dfaba6 SHA1 78d826bbdc932e4705d7a99485a809b417647f8e SHA256 ee4be918e5a7d230444ff504dbcfb12b21ddbdeea6333f2d35dae3bfeda205bc
diff --git a/sci-libs/gmsh/gmsh-9999.ebuild b/sci-libs/gmsh/gmsh-9999.ebuild
index 31da3fb85..f518e20db 100644
--- a/sci-libs/gmsh/gmsh-9999.ebuild
+++ b/sci-libs/gmsh/gmsh-9999.ebuild
@@ -12,7 +12,7 @@ SRC_URI="http://www.geuz.org/gmsh/src/${PN}-nightly-source.tgz"
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
 IUSE="blas chaco cgns doc examples jpeg med metis mpi opencascade png zlib X"
 
 RDEPEND="X? ( x11-libs/fltk:1.1 )