sci-chemistry/vmd: Drop arch specific NVCC flags

Package-Manager: portage-2.2.12/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 256 insertions, 17 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 934542be9b45..e35da6bd4d43 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/vmd
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.58 2013/10/02 11:39:48 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.59 2014/08/21 12:18:02 jlec Exp $
+
+*vmd-1.9.1-r3 (21 Aug 2014)
+
+  21 Aug 2014; Justin Lecher <jlec@gentoo.org> +vmd-1.9.1-r3.ebuild:
+  Drop arch specific NVCC flags
 
   02 Oct 2013; Justin Lecher <jlec@gentoo.org> vmd-1.9.1-r2.ebuild,
   +files/vmd-1.9.1-cuda-device_ptr.patch:
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 721e20a96ac4..c86b33d9f23a 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -8,23 +8,26 @@ DIST vmd-1.9.1-gentoo-patches.tar.xz 79240 SHA256 60fe1b017b1aed5cdd4a417d4a2dbd
 DIST vmd-1.9.1.src.tar.gz 30748110 SHA256 54aa88e03d86d763383e7b98592a152c9d68e78383e13af0dd2aca09b002491f SHA512 a54cb08e8a9ce801c2ca986f746bff0a041a25d5cffebc8d4af50813b6c05d04a3209a27830d580287230edaf3048a78923ae54bf367ab69c3d81388ab1787bd WHIRLPOOL 26d2a855c0768583cd45aed105fdd8f1ef59d59b8ce11c1903f5fc2008ea05989b8a32a0d817725e711613f8abfc22bb5301f20ea8d597efe9c7913790b25bb7
 EBUILD vmd-1.9.1-r1.ebuild 6833 SHA256 e48c5921f1904762723b10571afba42fffe4ecca6b61f261023d6df7a5c8f87f SHA512 dabb746625723b911b37c7e83b05e75fd82ced407831a4676a89d8ca2697305e06627e6707d254fd68c01c495e84e12af22e07ddb685fb715b7a4722cda2456d WHIRLPOOL c382fa4ba2db0d65c6fcc424f059d8cd2f8934d27a7f6d552db3fe12d2a408908f63286e38a441248e4c55ee5cc7444086879abaf45925a23fdcd44ddaa0f8b1
 EBUILD vmd-1.9.1-r2.ebuild 6639 SHA256 6c1ab354435510fd2366cb82cd75d9f9b14d2c449d69d96931f3abf6a00b9ae4 SHA512 5a42a368681740aa78519ca1ed181510a907ce54860565dfa73749b8ac142612847d3a63ad3a450c41d0a551681344ad392c4cafaa5731de29b820deecfac973 WHIRLPOOL b007a651ad42a42d1e7603ab88e901e9a1546d695f55c1c7e9b0dda19f6343c2dcb85a44cbadb049a1c40f0b380e1002cb3de77a3c6911a18400a665b9c6ddd0
+EBUILD vmd-1.9.1-r3.ebuild 6762 SHA256 3c1951c01251f50f0b399e62bdd72dd39fbd743411db7ca3b1dac642ae0034f3 SHA512 1e4d2605ae2d02f51c8ff8c4d15c67d4f7c3638316596cc69a3fe3340fb4e4a9c71f766328b9d28afb6eefcb07111147c1b71b2a2132caf22cda76fa2edf34fc WHIRLPOOL aa4fa2290ca82c1626ba28c4cbd8afc18fae8b19ff2060c97e644edfb25aa9391b1632d1b724a681c035fb2883b2baf093121e679cbda647572e29f39b65295b
 EBUILD vmd-1.9.1.ebuild 6488 SHA256 697574cd3122ead061f2a84b72421c3a17b1ad47cb284bb1cad7f01e87765fd6 SHA512 8a29afac2d5139778c2d26bd2e92d0c5a1ec5a6ccb5816e6b370ac14a1bf4c88ea982cb06b9684b6962498480f52e25cdf654b2849d4879b5c7c389a95349424 WHIRLPOOL 3b9bc58373a4eab84afac1d0ae455143145500e6b6ff4c21257c834ce92c8b880daab443ffb929c4df6a5cf3acf9d788129e373ea3db01f287e751475d7cd193
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+MISC ChangeLog 10116 SHA256 dc1e4bdbaee853ed8fdd7831a506a1ff41203b6dd717d58ca134781c57c5ca08 SHA512 f885a27abd4d21d4e11a6f7b832c292ef9e94b24c545862b465218afac0696aba3e4b5909059cd17b69129d8ac2e358c4589f16788c36a9a98f2463b3c8ecc05 WHIRLPOOL 7b6425ec3c933ce239e6e6fddcaaee116912b86b1f1f3fd777f26509dd1d2a4a7ec7854583218f6c46299e086efbbe785c6c93d3dedec1123f056ec9424b3eb5
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diff --git a/sci-chemistry/vmd/vmd-1.9.1-r3.ebuild b/sci-chemistry/vmd/vmd-1.9.1-r3.ebuild
new file mode 100644
index 000000000000..936ca0f69bd5
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.1-r3.ebuild
@@ -0,0 +1,231 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.1-r3.ebuild,v 1.1 2014/08/21 12:18:02 jlec Exp $
+
+EAPI=5
+
+PYTHON_DEPEND="2"
+
+inherit cuda eutils multilib prefix python toolchain-funcs
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="
+	http://dev.gentoo.org/~jlec/distifles/${P}-gentoo-patches-2.tar.xz
+	${P}.src.tar.gz"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda msms povray tachyon xinerama"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+CDEPEND="
+	|| ( =dev-lang/tk-8.5*:0=[-truetype] >=dev-lang/tk-8.6.1 )
+	dev-lang/perl
+	dev-python/numpy
+	sci-libs/netcdf
+	virtual/opengl
+	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/libXft
+	x11-libs/libXi
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	xinerama? ( x11-libs/libXinerama )"
+DEPEND="${CDEPEND}
+	dev-lang/swig"
+RDEPEND="${CDEPEND}
+	sci-biology/stride
+	sci-chemistry/surf
+	x11-terms/xterm
+	msms? ( sci-chemistry/msms-bin )
+	povray? ( media-gfx/povray )
+	tachyon? ( media-gfx/tachyon )"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+
+pkg_nofetch() {
+	elog "Please download ${P}.src.tar.gz from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and get"
+	elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches-2.tar.xz"
+	elog "Place both in ${DISTDIR}"
+}
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	use cuda && cuda_sanitize
+
+	epatch "${FILESDIR}"/${P}-cuda-device_ptr.patch
+
+	cd "${WORKDIR}"/plugins
+
+	epatch \
+		"${WORKDIR}"/${P}-gentoo-plugins.patch \
+		"${FILESDIR}"/${P}-tcl8.6.patch
+
+	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
+
+	sed \
+		-e "s:CC = gcc:CC = $(tc-getCC):" \
+		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
+		-e "s:COPTO =.*\":COPTO = -fPIC -o\":" \
+		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o\":" \
+		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
+		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
+		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
+		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
+		-e "s:-ltcl8.5:-ltcl:" \
+		-i Make-arch || die "Failed to set up plugins Makefile"
+
+	sed \
+		-e '/^AR /s:=:?=:g' \
+		-e '/^RANLIB /s:=:?=:g' \
+		-i ../plugins/*/Makefile || die
+
+	tc-export AR RANLIB
+
+	sed \
+		-e "s:\$(CXXFLAGS)::g" \
+		-i hesstrans/Makefile || die
+
+	# prepare vmd itself
+	cd "${S}"
+
+	epatch "${WORKDIR}"/${P}-gentoo-base.patch
+
+	# PREFIX
+	sed \
+		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
+		-i configure || die
+
+	sed \
+		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
+		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
+		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
+		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-gcc:$(tc-getCC):g" \
+		-e "s:gentoo-g++:$(tc-getCXX):g" \
+		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
+		-e "s:gentoo-cflags:${CFLAGS}:g" \
+		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
+		-e "s:gentoo-nvflags::g" \
+		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
+		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
+		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
+		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
+		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
+		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-i configure || die
+
+#	local NUMPY_INCLUDE="numpy/core/include"
+#	sed -e "s:gentoo-python-include:${EPREFIX}$(python_get_includedir):" \
+#		-e "s:gentoo-python-lib:${EPREFIX}$(python_get_libdir):" \
+#		-e "s:gentoo-python-link:$(PYTHON):" \
+#		-e "s:gentoo-numpy-include:${EPREFIX}$(python_get_sitedir)/${NUMPY_INCLUDE}:" \
+#		-i configure || die "failed setting up python"
+
+	if use cuda; then
+		sed \
+			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
+			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
+			-i configure src/Makefile || die
+		sed \
+			-e '/compute_/d' \
+			-i configure || die
+		sed \
+			-e 's:-gencode .*code=sm_..::' \
+			-i src/Makefile || die
+	fi
+
+	sed \
+		-e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
+		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
+		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
+		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
+}
+
+src_configure() {
+	local myconf="OPENGL FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
+	rm -f configure.options && echo $myconf >> configure.options
+
+	use cuda && myconf+=" CUDA"
+#	use mpi && myconf+=" MPI"
+#	use tachion && myconf+=" LIBTACHYON"
+	use xinerama && myconf+=" XINERAMA"
+
+	export \
+		PYTHON_INCLUDE_DIR="${EPREFIX}$(python_get_includedir)" \
+		PYTHON_LIBRARY_DIR="${EPREFIX}$(python_get_libdir)" \
+		PYTHON_LIBRARY="$(python_get_library -l)" \
+		NUMPY_INCLUDE_DIR="${EPREFIX}$(python_get_sitedir)/numpy/core/include" \
+		NUMPY_LIBRARY_DIR="${EPREFIX}$(python_get_sitedir)/numpy/core/include"
+
+	./configure LINUX \
+		${myconf} || die
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins
+
+	emake \
+		TCLINC="-I${EPREFIX}/usr/include" \
+		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" \
+		NETCDFLIB="$(pkg-config --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" \
+		NETCDFINC="$(pkg-config --cflags-only-I netcdf) ${EPREFIX}/usr/include" \
+		NETCDFLDFLAGS="$(pkg-config --libs netcdf)" \
+		LINUX
+
+	# build vmd
+	cd "${S}"/src
+	emake
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins
+	emake \
+			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
+			distrib
+
+	# install vmd
+	cd "${S}"/src
+	emake install
+
+	# install docs
+	cd "${S}"
+	dodoc Announcement README doc/ig.pdf doc/ug.pdf
+
+	# remove some of the things we don't want and need in
+	# /usr/lib
+	cd "${ED}"/usr/$(get_libdir)/vmd
+	rm -fr doc README Announcement LICENSE || \
+		die "failed to clean up /usr/lib/vmd directory"
+
+	# adjust path in vmd wrapper
+	sed \
+		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
+		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
+		|| die "failed to set up vmd wrapper script"
+
+	# install icon and generate desktop entry
+	insinto /usr/share/pixmaps
+	doins "${WORKDIR}"/vmd.png
+	eprefixify "${WORKDIR}"/vmd.desktop
+	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
+	domenu "${WORKDIR}"/vmd.desktop
+}