Version BUmp; install optional plugins, #517886

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

5 files changed, 97 insertions, 265 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 65e0c55ad45d..91c14a83b476 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/vmd
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.60 2015/02/10 02:23:22 patrick Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.61 2015/03/06 10:07:11 jlec Exp $
+
+*vmd-1.9.2 (06 Mar 2015)
+
+  06 Mar 2015; Justin Lecher <jlec@gentoo.org>
+  +files/vmd-1.9.2-format-security.patch, +vmd-1.9.2.ebuild,
+  -vmd-1.9.1-r2.ebuild, -vmd-1.9.1.ebuild, metadata.xml:
+  Version BUmp; install optional plugins, #517886
 
   10 Feb 2015; Patrick Lauer <patrick@gentoo.org> -vmd-1.9.1-r1.ebuild:
   Remove version with unsatisfiable dependencies
diff --git a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch
new file mode 100644
index 000000000000..3f9ea5c8c2ef
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch
@@ -0,0 +1,16 @@
+ plugins/molfile_plugin/src/maeffplugin.cxx | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/plugins/molfile_plugin/src/maeffplugin.cxx b/plugins/molfile_plugin/src/maeffplugin.cxx
+index cfe1223..41d92bb 100644
+--- a/plugins/molfile_plugin/src/maeffplugin.cxx
++++ b/plugins/molfile_plugin/src/maeffplugin.cxx
+@@ -1979,7 +1979,7 @@ namespace {
+       }
+     }
+     catch (std::exception &e) {
+-      fprintf(stderr, e.what());
++      fprintf(stderr, "%s", e.what());
+       return MOLFILE_ERROR;
+     }
+     return MOLFILE_SUCCESS;
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
index b9b5a0649de6..4b17d8d6b913 100644
--- a/sci-chemistry/vmd/metadata.xml
+++ b/sci-chemistry/vmd/metadata.xml
@@ -7,9 +7,10 @@
   </maintainer>
   <herd>sci-chemistry</herd>
   <use>
+    <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag>
+    <flag name="gromacs">Add support for TNG file format</flag>
     <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.ebuild b/sci-chemistry/vmd/vmd-1.9.1.ebuild
deleted file mode 100644
index 5e6d70abcd24..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.1.ebuild
+++ /dev/null
@@ -1,217 +0,0 @@
-# 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.ebuild,v 1.7 2013/03/01 08:23:03 jlec Exp $
-
-EAPI=4
-
-PYTHON_DEPEND="2"
-
-inherit eutils multilib python toolchain-funcs
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	mirror://gentoo/${P}-gentoo-patches.tar.xz
-	${P}.src.tar.gz"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda msms povray tachyon xinerama"
-
-RESTRICT="fetch"
-
-# currently, tk-8.5* with USE=truetype breaks some
-# tk apps such as Sequence Viewer or Timeline.
-CDEPEND="
-	=dev-lang/tk-8.5*[-truetype]
-	dev-lang/perl
-	dev-python/numpy
-	sci-libs/netcdf
-	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
-	x11-libs/libXft
-	x11-libs/libXi
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-3.1 )
-	xinerama? ( x11-libs/libXinerama )"
-DEPEND="${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_TEXTRELS="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
-QA_PRESTRIPPED="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64="
-	usr/lib64/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so
-	usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
-QA_FLAGS_IGNORED_x86="
-	usr/lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so
-	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.tar.xz"
-	elog "Place both in ${DISTDIR}"
-}
-
-pkg_setup() {
-	python_set_active_version 2
-	python_pkg_setup
-}
-
-src_prepare() {
-	cd "${WORKDIR}"/plugins
-
-	epatch "${WORKDIR}"/${P}-gentoo-plugins.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 = $(tc-getCXX) -shared:" \
-		-e "s:-ltcl8.5:-ltcl:" \
-		-i Make-arch || die "Failed to set up plugins Makefile"
-
-	sed \
-		-e "s:\$(CXXFLAGS)::g" \
-		-i hesstrans/Makefile || die
-
-	# prepare vmd itself
-	cd "${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: -O3 -v: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
-		local gcc44_bindir="$(ls -d ${EPREFIX}/usr/*pc-linux-gnu/gcc-bin/4.4*)"
-
-		sed \
-			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
-			-e "/^\$arch_nvccflags/s:=:= \"--compiler-bindir=${gcc44_bindir} \" . \n:1" \
-			-i configure || 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)" \
-		NETCDFINC="$(pkg-config --cflags-only-I netcdf)" \
-		NETCDFLDFLAGS="$(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 "${WORKDIR}"/vmd.png
-	domenu "${WORKDIR}"/vmd.desktop
-}
diff --git a/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild
index 58d94f044413..4805b8fe5522 100644
--- a/sci-chemistry/vmd/vmd-1.9.1-r2.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.2.ebuild
@@ -1,23 +1,23 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 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 1.5 2013/10/02 11:39:48 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.2.ebuild,v 1.1 2015/03/06 10:07:11 jlec Exp $
 
 EAPI=5
 
-PYTHON_DEPEND="2"
+PYTHON_COMPAT=( python2_7 )
 
-inherit cuda eutils multilib prefix python toolchain-funcs
+inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs
 
 DESCRIPTION="Visual Molecular Dynamics"
 HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
 SRC_URI="
-	http://dev.gentoo.org/~jlec/distifles/${P}-gentoo-patches-2.tar.xz
+	http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
 	${P}.src.tar.gz"
 
 SLOT="0"
 LICENSE="vmd"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda msms povray tachyon xinerama"
+IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
 
 RESTRICT="fetch"
 
@@ -26,15 +26,20 @@ RESTRICT="fetch"
 CDEPEND="
 	|| ( =dev-lang/tk-8.5*:0=[-truetype] >=dev-lang/tk-8.6.1 )
 	dev-lang/perl
-	dev-python/numpy
+	dev-libs/expat
+	dev-python/numpy[${PYTHON_USEDEP}]
 	sci-libs/netcdf
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1
 	x11-libs/libXft
 	x11-libs/libXi
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] )
+	sqlite? ( dev-db/sqlite:3= )
+	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
 	xinerama? ( x11-libs/libXinerama )"
 DEPEND="${CDEPEND}
+	virtual/pkgconfig
 	dev-lang/swig"
 RDEPEND="${CDEPEND}
 	sci-biology/stride
@@ -42,7 +47,7 @@ RDEPEND="${CDEPEND}
 	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!!
@@ -54,33 +59,28 @@ 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/${P}-gentoo-patches-2.tar.xz"
+	elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.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
+	epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
 
-	cd "${WORKDIR}"/plugins
+	cd "${WORKDIR}"/plugins || die
 
 	epatch \
 		"${WORKDIR}"/${P}-gentoo-plugins.patch \
-		"${FILESDIR}"/${P}-tcl8.6.patch
+		"${FILESDIR}"/${P}-format-security.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: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:" \
@@ -100,7 +100,7 @@ src_prepare() {
 		-i hesstrans/Makefile || die
 
 	# prepare vmd itself
-	cd "${S}"
+	cd "${S}" || die
 
 	epatch "${WORKDIR}"/${P}-gentoo-base.patch
 
@@ -128,18 +128,17 @@ src_prepare() {
 		-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 \
@@ -150,63 +149,89 @@ src_prepare() {
 		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
 		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
 		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
+
+	EMAKEOPTS=(
+		TCLINC="-I${EPREFIX}/usr/include"
+		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
+		TCLLDFLAGS="-shared"
+		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
+		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include"
+		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
+		NETCDFDYNAMIC=1
+		EXPATINC="-I${EPREFIX}/usr/include"
+		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
+		EXPATLDFLAGS="-shared"
+		EXPATDYNAMIC=1
+	)
+	if use gromacs; then
+		EMAKEOPTS+=(
+			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
+			TNGINC="-I${EPREFIX}/usr/include"
+			TNGLDFLAGS="-shared"
+			TNGDYNAMIC=1
+		)
+	fi
+	if use sqlite; then
+		EMAKEOPTS+=(
+			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
+			SQLITEINC="-I${EPREFIX}/usr/include"
+			SQLITELDFLAGS="-shared"
+			SQLITEDYNAMIC=1
+		)
+	fi
 }
 
 src_configure() {
-	local myconf="OPENGL FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
+	local myconf="OPENGL OPENGLPBUFFER COLVARS 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 tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon"
 	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}$(python_get_sitedir)/numpy/core/include"
+		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
+		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
+		PYTHON_LIBRARY="$(python_get_LIBS)" \
+		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
+		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
 
-	./configure LINUX \
+	perl ./configure LINUX \
 		${myconf} || die
 }
 
 src_compile() {
 	# build plugins
-	cd "${WORKDIR}"/plugins
+	cd "${WORKDIR}"/plugins || die
 
 	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)" \
+		${EMAKEOPTS[@]} \
 		LINUX
 
 	# build vmd
-	cd "${S}"/src
+	cd "${S}"/src || die
 	emake
 }
 
 src_install() {
 	# install plugins
-	cd "${WORKDIR}"/plugins
+	cd "${WORKDIR}"/plugins || die
 	emake \
 			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
 			distrib
 
 	# install vmd
-	cd "${S}"/src
+	cd "${S}"/src || die
 	emake install
 
 	# install docs
-	cd "${S}"
+	cd "${S}" || die
 	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
+	cd "${ED}"/usr/$(get_libdir)/vmd || die
 	rm -fr doc README Announcement LICENSE || \
 		die "failed to clean up /usr/lib/vmd directory"