sci-chemistry/vmd: Use cuda.eclass and slo-operator for tcl

Package-Manager: portage-2.2.0_alpha150/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

5 files changed, 279 insertions, 18 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 70ce782d4252..cf71b1078870 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/vmd
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.52 2012/11/29 15:13:06 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.53 2013/01/11 09:29:35 jlec Exp $
+
+*vmd-1.9.1-r2 (11 Jan 2013)
+
+  11 Jan 2013; Justin Lecher <jlec@gentoo.org> +vmd-1.9.1-r2.ebuild,
+  +files/vmd-1.9.1-tcl8.6.patch, metadata.xml:
+  Use cuda.eclass and slo-operator for tcl
 
   29 Nov 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.1.ebuild,
   vmd-1.9.1-r1.ebuild:
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 1ca3c0fddb16..0d39c0705285 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,17 +1,19 @@
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 Hash: SHA256
 
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 DIST vmd-1.9.1-gentoo-patches-2.tar.xz 79212 SHA256 1249957baea6fc8d4c05b008362b185b0851d70c6eeed8fbd44d41e7e77f23a8 SHA512 b313ed92652a93647790d668bd71233708fec3e9cead8b13b31dee1277f5ef6f0e8844f563ad51bc320b83a3cda126f8ab74fe4147218c65b594ee5624b46057 WHIRLPOOL 51b8a1486c286c002d893ec4e3aa8301ec7da6b9f2de31e880c7f9523a006a06712adecd5329269c892764761da691a36e1d6e5a730fc1a32c751b7658b96903
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 EBUILD vmd-1.9.1-r1.ebuild 6769 SHA256 669057d44c15a55387fe1d0be0836e6490986aab5d16ec6737d3f549d5b07c04 SHA512 f330cffd3f3eb9591f551b8e7fb76caa6004c562f0ab28c7018069f9a164d0c405dfbcd07d85c524106d21c985968bafb17ae830cd118ab858a6b41eb3ab0953 WHIRLPOOL ed477ca36c009c6419f1fe1a6c10fc2ec332465a3564aeff0c83d2ecc5aa7e3b8fa1694c20828316a80bab14e7ee310de59e5bcb04187bda8c9d2e05a9962fa9
+EBUILD vmd-1.9.1-r2.ebuild 6612 SHA256 c39fad66714ef0464308acd43b9aa99aa6560c7aad768b173a9e84ca4531d4b8 SHA512 2ab26ba265ddd7723ef01b9af547262a695179fbbc91cda826d6a1cfb9c76f5f30887d13c57434b64a9d0dcb62ef1f900f9d55f6d9d5e8d0fd4eb2b1280b71f1 WHIRLPOOL 4b4171b2518764dd241fb5786628d89a6c32c079ed557f0712159c6c1c71e67ef41f315d2dc25a45ae26694e210044556472ff034d8959cd8a63072338a8c6e8
 EBUILD vmd-1.9.1.ebuild 6424 SHA256 94e7d41b3a4b030f77618a87f91dd028070505162640387042eb296da5be8afe SHA512 1430737231aef301612dde423c10553b17fbbd73b1481bff56761cac9be86c15613c888f78dd64db71b8a3e09a1990e28f83bb46aff8e552241bd0bc9bc12a3a WHIRLPOOL 654605fbd891f4af258ad139dd848e57cf9a889de5586bfc78a85ff16b8a689dd29224e09258930dcdbe97ab538d58deedc27f644ba6c5e75a1035cfefd8eee4
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diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch b/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch
new file mode 100644
index 000000000000..0c3e45dd39c3
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.1-tcl8.6.patch
@@ -0,0 +1,25 @@
+ plugins/molfile_plugin/src/webpdbplugin.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/plugins/molfile_plugin/src/webpdbplugin.c b/plugins/molfile_plugin/src/webpdbplugin.c
+index 80b3bb9..78597f5 100644
+--- a/plugins/molfile_plugin/src/webpdbplugin.c
++++ b/plugins/molfile_plugin/src/webpdbplugin.c
+@@ -202,7 +202,7 @@ static void *open_file_read(const char *filename, const char *filetype,
+   sprintf(url, "http://www.rcsb.org/pdb/downloadFile.do?fileFormat=pdb&compression=NO&structureId=%s",filename);
+   sprintf(cmd, "set token [::http::geturl \"%s\"]", url);
+   if (Tcl_Eval(interp, cmd) != TCL_OK) {
+-    fprintf(stderr, "Error loading PDB: %s\n",interp->result);
++    fprintf(stderr, "Error loading PDB: %s\n",Tcl_GetStringResult(interp));
+     Tcl_DeleteInterp(interp);
+     return NULL;
+   } 
+@@ -211,7 +211,7 @@ static void *open_file_read(const char *filename, const char *filetype,
+   
+   result = Tcl_GetVar2(interp, (char *)"state", "body", TCL_GLOBAL_ONLY); 
+   if (!result) {
+-    fprintf(stderr, "Error loading PDB: %s\n", interp->result);
++    fprintf(stderr, "Error loading PDB: %s\n", Tcl_GetStringResult(interp));
+     Tcl_DeleteInterp(interp);
+     return NULL;
+   } 
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
index be76141a652b..b9b5a0649de6 100644
--- a/sci-chemistry/vmd/metadata.xml
+++ b/sci-chemistry/vmd/metadata.xml
@@ -1,15 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<herd>sci-chemistry</herd>
-	<use>
-		<flag name="msms">Add support for MSMS SAS calcualtion tool</flag>
-		<flag name="povray">Add support for povray raytracer for HQ	images</flag>
-		<flag name="tachyon">Add support for tachyon raytracer for HQ images</flag>
-		<flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag>
-	</use>
+  <maintainer>
+    <email>alexxy@gentoo.org</email>
+    <name>Alexey Shvetsov</name>
+  </maintainer>
+  <herd>sci-chemistry</herd>
+  <use>
+    <flag name="msms">Add support for MSMS SAS calcualtion tool</flag>
+    <flag name="povray">Add support for povray raytracer for HQ	images</flag>
+    <flag name="tachyon">Add support for tachyon raytracer for HQ images</flag>
+    <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag>
+  </use>
 </pkgmetadata>
diff --git a/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild
new file mode 100644
index 000000000000..f87ef5f3b73d
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild
@@ -0,0 +1,228 @@
+# Copyright 1999-2013 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-r2.ebuild,v 1.1 2013/01/11 09:29:35 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
+	${P}.src.tar.gz"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda msms povray tachyon xinerama"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+CDEPEND="
+	>=dev-lang/tk-8.5:0=[-truetype]
+	dev-lang/perl
+	dev-python/numpy
+	sci-libs/netcdf
+	virtual/opengl
+	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/libXft
+	x11-libs/libXi
+	cuda? (
+		>=dev-util/nvidia-cuda-toolkit-3.1
+		|| (
+			sys-devel/gcc:4.4
+			sys-devel/gcc:4.5 )
+		)
+	xinerama? ( x11-libs/libXinerama )"
+DEPEND="${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 ${DISTDIR}"
+}
+
+pkg_setup() {
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	use cuda && cuda_sanitize
+
+	cd "${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:=:= ${NVCCFLAGS}:g" \
+			-i configure src/Makefile || die
+	fi
+
+	sed \
+		-e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-e "s:gentoo-stride:${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
+}