Version BUmp; install optional plugins, #517886

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

6 files changed, 125 insertions, 270 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/Manifest b/sci-chemistry/vmd/Manifest
index 889c425bc8ce..50394098f8a9 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,10 +1,33 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
 AUX vmd-1.9.1-cuda-device_ptr.patch 934 SHA256 8d32ebe81adb4ec0186ceba08743c0b6a25c76b3c58edaefa85df38328aaa87e SHA512 274756fe17fdcc39ce471c3187f3076407d34b64e49b0006ee30525a952277b2b5c713fffa8786162dc542eef2b021f2bf7339736cf9e81b673d5146114829ed WHIRLPOOL 400959a0b52ce0026308bf2c251de9e0c87ee65c8c10844a7cd2f21b319623868316970247984a22b19dcd17a15e8cdf6959b60c5575a05f3709191a55eb4fb2
 AUX vmd-1.9.1-tcl8.6.patch 1218 SHA256 41c1c3edf77f8ffcf8b7533625471d2dc384ca9a86ab9ba6be8d083718836b33 SHA512 ef729ddadbb865024abd6a532c328fe33e667faf0a6f9b09e3fcac852c2d88713b9efce772c42549fd62e9194634e3467d76700d0d317a1bd852be7baee8c125 WHIRLPOOL 9c122bb56fa66a1dffc6aa27d3e28bcf4848c3baf8a34a048fce3c2888a5ddfc6a92a5e8f9f1fa113b19c4b7d622d290be0e5cdafaae9d0a72402ef26143aa9f
+AUX vmd-1.9.2-format-security.patch 550 SHA256 4e3fa85105117ab4c259ae6e58fb38fee668fc3000b981369841f98740c0ba61 SHA512 81a71ee4c4c438d18f3a393ebad5c9a08f1a7bb95fa58b78a8798955a34ae2494f80fa074b973a1b595862080e9103d21e509443742cfe2bc3cf77f10c0e3c9d WHIRLPOOL 8a2b64514ba9876bdbc2c4afa9ae48b4742099c1cb39b3835f4e340e0b4330cf06f28f92320c15481d4d6ed27c8491dc899572c091a952fa17eb1b0356b01aed
 DIST vmd-1.9.1-gentoo-patches-2.tar.xz 79212 SHA256 1249957baea6fc8d4c05b008362b185b0851d70c6eeed8fbd44d41e7e77f23a8 SHA512 b313ed92652a93647790d668bd71233708fec3e9cead8b13b31dee1277f5ef6f0e8844f563ad51bc320b83a3cda126f8ab74fe4147218c65b594ee5624b46057 WHIRLPOOL 51b8a1486c286c002d893ec4e3aa8301ec7da6b9f2de31e880c7f9523a006a06712adecd5329269c892764761da691a36e1d6e5a730fc1a32c751b7658b96903
-DIST vmd-1.9.1-gentoo-patches.tar.xz 79240 SHA256 60fe1b017b1aed5cdd4a417d4a2dbd20f75eae24c83d1da68c504a31bfbdbcd8 SHA512 37856d5e00d3d4452324865190aef4ac05a7a49cbddffe83f568d3190b521f17e6e1e5323dee3127aadfb446ec0871bfd06dff47d640ed862547710ec4b0a421 WHIRLPOOL b3eebffe24a96ad1c7ce9ebc565e1b88d6f52894569a6d72c22e87fb3d6975d14779bd8c4305e3e9f2ecf9d981503b8bcea78a476a1a66eb37b78c759b3bdf60
 DIST vmd-1.9.1.src.tar.gz 30748110 SHA256 54aa88e03d86d763383e7b98592a152c9d68e78383e13af0dd2aca09b002491f SHA512 a54cb08e8a9ce801c2ca986f746bff0a041a25d5cffebc8d4af50813b6c05d04a3209a27830d580287230edaf3048a78923ae54bf367ab69c3d81388ab1787bd WHIRLPOOL 26d2a855c0768583cd45aed105fdd8f1ef59d59b8ce11c1903f5fc2008ea05989b8a32a0d817725e711613f8abfc22bb5301f20ea8d597efe9c7913790b25bb7
-EBUILD vmd-1.9.1-r2.ebuild 6639 SHA256 6c1ab354435510fd2366cb82cd75d9f9b14d2c449d69d96931f3abf6a00b9ae4 SHA512 5a42a368681740aa78519ca1ed181510a907ce54860565dfa73749b8ac142612847d3a63ad3a450c41d0a551681344ad392c4cafaa5731de29b820deecfac973 WHIRLPOOL b007a651ad42a42d1e7603ab88e901e9a1546d695f55c1c7e9b0dda19f6343c2dcb85a44cbadb049a1c40f0b380e1002cb3de77a3c6911a18400a665b9c6ddd0
+DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 SHA256 91508b384cb0a8aab8d8cfc31c1e7e0bc4225dbd7cdb36fbaefcfe8baca9442c SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51 WHIRLPOOL 3f87d24ad0ca7eb60e0ae3d561da7c61e0caa9fe8bb71cd3a06731228926d4c16ee03699d80adf02e2c9b263f96ea8d5b096e64e3e94b0208b1cb618c8a8a7ca
+DIST vmd-1.9.2.src.tar.gz 34903084 SHA256 870ee1e483ad23eb7f3bb6ac816cb7be5df893879dddc0bda8423a011993ccdb SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef WHIRLPOOL e2489b4bd8f28359ee959d6ebec3a9e775fbaf7a25baa1324c99dd04c7768e002924c671c11830ec6e9589ecc9de4864f2bcf3dfaf9eb36f5a1d03d5e5841f17
 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
-MISC ChangeLog 10241 SHA256 cc150b1661cc51a6a299b01015a86f53dcb621449fff26bfc63b442f6f5c3e75 SHA512 685c018303355904b791e66a7fb7467d3e6122e8bf23c1038a3196a3aeced3631e0f804a9db24c763bb01c3311aa64340008eff5af59c65a9a0b970157f72615 WHIRLPOOL bbadeb852dc72d3f6cbf8e22ff26731846fdbee492929d33a713016b125778d2ddedc451ff40443327258feeba7546744d62ceb0927d7b050f1e3181e7f962d5
-MISC metadata.xml 597 SHA256 d2521313b36b55be1e391d0efaeb3bdb469f612c0bf00913e2f0fe83fecca3d6 SHA512 84119dffe17d4e4b12019e51df2d9dd1fc42d26f86238387f67f08e774deec21f838fd1f28eba8c69faa88002be00af97dc4b1a67d90d81d6196b91699d7e7f5 WHIRLPOOL 9eae5538aa93b3496a6dd2bfa7b1fa1a1e6da89b9e4a02e3bd383373f7031b95aa85200d40eaedd4f5121f724f9cd1e52171052e42deb81b1c201d12ad8d2164
+EBUILD vmd-1.9.2.ebuild 7229 SHA256 b949c58eb6dbf7e19ce1a3ca114837c7b337009d8324508ec074c54700c2f70f SHA512 392d40e8a0fb26f2903762958668599b51e8200292fa6c57415bccfaedc138bd5dc58b3b07fb1d6823fbdc2266ba4e37b5b03f4671d99ca2f45bd99d03a6e2f7 WHIRLPOOL bc3d2df70a3db12ca2a001bd15f24d0ddbd949f6e2db197d0ad81cf578b059a90229f63cf21f63b31c1e36c7a7baebc058ea6e27d68da49ccce3e1fc46eac77c
+MISC ChangeLog 10480 SHA256 3f3cab57dd38d545adb533c8a2c5e6f355629939b51184e0d1a8aaf5eca12a5f SHA512 7651273a4c9207d7a9e23c1c53bb61e4ba470c6fcef45dd6f6a92137f03a64afec722c88300b0ca562320ac28cefd1e387e7535d25ccccc0b43231c55630d461 WHIRLPOOL b9a89932925538574759e82707639625e222c29e5282dd26d8ab7d17228ccccab724db7576875bd6c492bfd2df5cb3172021a20ffe38b12d5de5443b173b7ef6
+MISC metadata.xml 661 SHA256 67336d8710c6fac6860af86a69d7e31c5ae7cc5f384eb8484ce0f9a5bfca4889 SHA512 6c4ace927c71786b6f8f0ac46decfc2dc1dcd50bb87caa32bba32deabe8d2990b3f0ef2d9522f458d4812f260de8f3e55cf5e583718a243a79c733f6f33ea918 WHIRLPOOL cf16561f76efa5616965b81ddab08cfd0d5ef0c57b51c599bb46d785681eb019fd93ec1a92d0c79006615bc03949ccbd89f91032b775cf52b29df445dd6bad71
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0
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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"