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jlec 15/03/06 10:07:11 |
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|
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Modified: metadata.xml ChangeLog |
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Added: vmd-1.9.2.ebuild |
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Removed: vmd-1.9.1.ebuild vmd-1.9.1-r2.ebuild |
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Log: |
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Version BUmp; install optional plugins, #517886 |
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|
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(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
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|
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Revision Changes Path |
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1.9 sci-chemistry/vmd/metadata.xml |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/metadata.xml?rev=1.9&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/metadata.xml?rev=1.9&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/metadata.xml?r1=1.8&r2=1.9 |
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|
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Index: metadata.xml |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/metadata.xml,v |
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retrieving revision 1.8 |
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retrieving revision 1.9 |
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diff -u -r1.8 -r1.9 |
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--- metadata.xml 11 Jan 2013 09:29:35 -0000 1.8 |
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+++ metadata.xml 6 Mar 2015 10:07:11 -0000 1.9 |
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@@ -7,9 +7,10 @@ |
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</maintainer> |
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<herd>sci-chemistry</herd> |
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<use> |
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+ <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag> |
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+ <flag name="gromacs">Add support for TNG file format</flag> |
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<flag name="msms">Add support for MSMS SAS calcualtion tool</flag> |
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<flag name="povray">Add support for povray raytracer for HQ images</flag> |
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<flag name="tachyon">Add support for tachyon raytracer for HQ images</flag> |
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- <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag> |
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</use> |
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</pkgmetadata> |
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|
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|
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|
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1.61 sci-chemistry/vmd/ChangeLog |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/ChangeLog?rev=1.61&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/ChangeLog?rev=1.61&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/ChangeLog?r1=1.60&r2=1.61 |
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|
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Index: ChangeLog |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v |
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retrieving revision 1.60 |
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retrieving revision 1.61 |
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diff -u -r1.60 -r1.61 |
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--- ChangeLog 10 Feb 2015 02:23:22 -0000 1.60 |
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+++ ChangeLog 6 Mar 2015 10:07:11 -0000 1.61 |
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@@ -1,6 +1,13 @@ |
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# ChangeLog for sci-chemistry/vmd |
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# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.60 2015/02/10 02:23:22 patrick Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.61 2015/03/06 10:07:11 jlec Exp $ |
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+ |
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+*vmd-1.9.2 (06 Mar 2015) |
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+ |
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+ 06 Mar 2015; Justin Lecher <jlec@g.o> |
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+ +files/vmd-1.9.2-format-security.patch, +vmd-1.9.2.ebuild, |
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+ -vmd-1.9.1-r2.ebuild, -vmd-1.9.1.ebuild, metadata.xml: |
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+ Version BUmp; install optional plugins, #517886 |
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|
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10 Feb 2015; Patrick Lauer <patrick@g.o> -vmd-1.9.1-r1.ebuild: |
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Remove version with unsatisfiable dependencies |
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|
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|
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|
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1.1 sci-chemistry/vmd/vmd-1.9.2.ebuild |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/vmd-1.9.2.ebuild?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/vmd-1.9.2.ebuild?rev=1.1&content-type=text/plain |
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|
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Index: vmd-1.9.2.ebuild |
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=================================================================== |
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# Copyright 1999-2015 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.2.ebuild,v 1.1 2015/03/06 10:07:11 jlec Exp $ |
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|
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EAPI=5 |
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|
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PYTHON_COMPAT=( python2_7 ) |
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|
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inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs |
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|
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DESCRIPTION="Visual Molecular Dynamics" |
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HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" |
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SRC_URI=" |
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http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz |
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${P}.src.tar.gz" |
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|
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SLOT="0" |
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LICENSE="vmd" |
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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IUSE="cuda gromacs msms povray sqlite tachyon xinerama" |
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|
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RESTRICT="fetch" |
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|
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# currently, tk-8.5* with USE=truetype breaks some |
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# tk apps such as Sequence Viewer or Timeline. |
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CDEPEND=" |
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|| ( =dev-lang/tk-8.5*:0=[-truetype] >=dev-lang/tk-8.6.1 ) |
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dev-lang/perl |
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dev-libs/expat |
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dev-python/numpy[${PYTHON_USEDEP}] |
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sci-libs/netcdf |
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virtual/opengl |
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>=x11-libs/fltk-1.1.10-r2:1 |
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x11-libs/libXft |
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x11-libs/libXi |
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cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
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gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] ) |
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sqlite? ( dev-db/sqlite:3= ) |
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tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) |
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xinerama? ( x11-libs/libXinerama )" |
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DEPEND="${CDEPEND} |
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virtual/pkgconfig |
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dev-lang/swig" |
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RDEPEND="${CDEPEND} |
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sci-biology/stride |
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sci-chemistry/surf |
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x11-terms/xterm |
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msms? ( sci-chemistry/msms-bin ) |
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povray? ( media-gfx/povray ) |
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" |
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|
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VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" |
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# Binary only plugin!! |
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QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" |
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QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" |
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QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" |
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|
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pkg_nofetch() { |
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elog "Please download ${P}.src.tar.gz from" |
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elog "${VMD_DOWNLOAD}" |
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elog "after agreeing to the license and get" |
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elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" |
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elog "Place both in ${DISTDIR}" |
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} |
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|
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src_prepare() { |
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use cuda && cuda_sanitize |
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|
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epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch |
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|
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cd "${WORKDIR}"/plugins || die |
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|
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epatch \ |
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"${WORKDIR}"/${P}-gentoo-plugins.patch \ |
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"${FILESDIR}"/${P}-format-security.patch |
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|
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[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) |
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|
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sed \ |
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-e "s:CC = gcc:CC = $(tc-getCC):" \ |
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-e "s:CXX = g++:CXX = $(tc-getCXX):" \ |
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-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ |
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-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ |
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-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ |
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-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ |
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-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ |
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-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ |
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-e "s:-ltcl8.5:-ltcl:" \ |
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-i Make-arch || die "Failed to set up plugins Makefile" |
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|
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sed \ |
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-e '/^AR /s:=:?=:g' \ |
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-e '/^RANLIB /s:=:?=:g' \ |
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-i ../plugins/*/Makefile || die |
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|
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tc-export AR RANLIB |
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|
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sed \ |
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-e "s:\$(CXXFLAGS)::g" \ |
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-i hesstrans/Makefile || die |
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|
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# prepare vmd itself |
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cd "${S}" || die |
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|
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epatch "${WORKDIR}"/${P}-gentoo-base.patch |
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|
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# PREFIX |
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sed \ |
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-e "s:/usr/include/:${EPREFIX}/usr/include:g" \ |
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-i configure || die |
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|
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sed \ |
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-e "s:gentoo-bindir:${ED}/usr/bin:g" \ |
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-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ |
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-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ |
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-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ |
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-e "s:gentoo-gcc:$(tc-getCC):g" \ |
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-e "s:gentoo-g++:$(tc-getCXX):g" \ |
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-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ |
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-e "s:gentoo-cflags:${CFLAGS}:g" \ |
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-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ |
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-e "s:gentoo-nvflags::g" \ |
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-e "s:gentoo-ldflags:${LDFLAGS}:g" \ |
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-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ |
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-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ |
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-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ |
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-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ |
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-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ |
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-i configure || die |
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|
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if use cuda; then |
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sed \ |
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-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ |
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-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ |
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-i configure src/Makefile || die |
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sed \ |
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-e '/compute_/d' \ |
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-i configure || die |
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sed \ |
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-e 's:-gencode .*code=sm_..::' \ |
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-i src/Makefile || die |
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fi |
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|
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sed \ |
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-e "s:LINUXPPC:LINUX:g" \ |
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-e "s:LINUXALPHA:LINUX:g" \ |
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-e "s:LINUXAMD64:LINUX:g" \ |
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-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ |
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-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ |
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-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ |
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-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" |
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|
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EMAKEOPTS=( |
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TCLINC="-I${EPREFIX}/usr/include" |
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TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" |
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TCLLDFLAGS="-shared" |
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NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" |
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NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include" |
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NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" |
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NETCDFDYNAMIC=1 |
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EXPATINC="-I${EPREFIX}/usr/include" |
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EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" |
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EXPATLDFLAGS="-shared" |
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EXPATDYNAMIC=1 |
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) |
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if use gromacs; then |
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EMAKEOPTS+=( |
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TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" |
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TNGINC="-I${EPREFIX}/usr/include" |
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TNGLDFLAGS="-shared" |
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TNGDYNAMIC=1 |
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) |
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fi |
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if use sqlite; then |
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EMAKEOPTS+=( |
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SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" |
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SQLITEINC="-I${EPREFIX}/usr/include" |
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SQLITELDFLAGS="-shared" |
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SQLITEDYNAMIC=1 |
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) |
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fi |
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} |
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|
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src_configure() { |
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local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" |
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rm -f configure.options && echo $myconf >> configure.options |
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|
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use cuda && myconf+=" CUDA" |
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# use mpi && myconf+=" MPI" |
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use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon" |
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use xinerama && myconf+=" XINERAMA" |
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|
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export \ |
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PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ |
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PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ |
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PYTHON_LIBRARY="$(python_get_LIBS)" \ |
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NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ |
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NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" |
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|
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perl ./configure LINUX \ |
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${myconf} || die |
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} |
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|
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src_compile() { |
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# build plugins |
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cd "${WORKDIR}"/plugins || die |
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|
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emake \ |
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${EMAKEOPTS[@]} \ |
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LINUX |
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|
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# build vmd |
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cd "${S}"/src || die |
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emake |
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} |
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|
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src_install() { |
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# install plugins |
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cd "${WORKDIR}"/plugins || die |
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emake \ |
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PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ |
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distrib |
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|
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# install vmd |
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cd "${S}"/src || die |
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emake install |
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|
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# install docs |
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cd "${S}" || die |
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dodoc Announcement README doc/ig.pdf doc/ug.pdf |
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|
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# remove some of the things we don't want and need in |
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# /usr/lib |
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cd "${ED}"/usr/$(get_libdir)/vmd || die |
| 314 |
rm -fr doc README Announcement LICENSE || \ |
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die "failed to clean up /usr/lib/vmd directory" |
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|
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# adjust path in vmd wrapper |
| 318 |
sed \ |
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-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ |
| 320 |
-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ |
| 321 |
|| die "failed to set up vmd wrapper script" |
| 322 |
|
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# install icon and generate desktop entry |
| 324 |
insinto /usr/share/pixmaps |
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doins "${WORKDIR}"/vmd.png |
| 326 |
eprefixify "${WORKDIR}"/vmd.desktop |
| 327 |
sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die |
| 328 |
domenu "${WORKDIR}"/vmd.desktop |
| 329 |
} |
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