Version bump. Also removed some of the old ebuilds.

(Portage version: 2.1.1_pre5-r3)

4 files changed, 267 insertions, 1 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index b96cf4168098..655dfbf7264d 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/vmd
 # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.6 2006/08/13 17:48:01 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.7 2006/08/26 14:56:33 markusle Exp $
+
+*vmd-1.8.5 (26 Aug 2006)
+
+  26 Aug 2006; Markus Dittrich <markusle@gentoo.org>
+  -files/vmd-1.8.3-config-gentoo.patch,
+  +files/vmd-1.8.5-config-gentoo.patch, -vmd-1.8.3.ebuild,
+  +vmd-1.8.5.ebuild:
+  Version bump. Also removed some of the old ebuilds.
 
 *vmd-1.8.4-r1 (13 Aug 2006)
 
diff --git a/sci-chemistry/vmd/files/digest-vmd-1.8.5 b/sci-chemistry/vmd/files/digest-vmd-1.8.5
new file mode 100644
index 000000000000..f6aa451ff4ad
--- /dev/null
+++ b/sci-chemistry/vmd/files/digest-vmd-1.8.5
@@ -0,0 +1,3 @@
+MD5 a8f28ef4a69717a9ed348825f659836b vmd-1.8.5.src.tar.gz 17106456
+RMD160 70087a42ae20180f2ed18cc4492764ed24b19aa4 vmd-1.8.5.src.tar.gz 17106456
+SHA256 208d7829e4fc2744e30c778e1485b96d35018b1e0dbc02388630ce4a2733c30b vmd-1.8.5.src.tar.gz 17106456
diff --git a/sci-chemistry/vmd/files/vmd-1.8.5-config-gentoo.patch b/sci-chemistry/vmd/files/vmd-1.8.5-config-gentoo.patch
new file mode 100644
index 000000000000..55a22ed9862f
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.8.5-config-gentoo.patch
@@ -0,0 +1,103 @@
+diff -Naur vmd-1.8.5/configure vmd-1.8.5-new/configure
+--- vmd-1.8.5/configure	2006-08-25 16:39:51.000000000 -0400
++++ vmd-1.8.5-new/configure	2006-08-26 09:57:30.000000000 -0400
+@@ -13,10 +13,10 @@
+ $install_name = "vmd";
+ 
+ # Directory where VMD startup script is installed, should be in users' paths.
+-$install_bin_dir="/usr/local/bin";
++$install_bin_dir="gentoo-bindir";
+ 
+ # Directory where VMD files and executables are installed
+-$install_library_dir="/usr/local/lib/$install_name";
++$install_library_dir="gentoo-libdir/$install_name";
+ 
+ 
+ # optionally override hard-coded defaults above with environment variables
+@@ -121,29 +121,6 @@
+ # Configure script code begins here
+ ############################################################################
+ 
+-## Test for existence of a properly compiled plugin tree
+-if (!(-e "plugins")) {
+-  print "\n";
+-  print "VMD plugin directory not found.\n";
+-  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
+-  print "into a 'plugins' directory linked or located in this directory.\n";
+-  print "Be sure your PLUGINDIR environment variable is set before running\n";
+-  print "'make distrib' in the plugin build area.\n";
+-  print "\n";
+-  die "Halting configuration until VMD plugins are built.\n";
+-} else {
+-  if (!(-e "plugins/include/vmdplugin.h")) {
+-    print "\n";
+-    print "VMD plugin include files or directory not found.\n";
+-    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
+-    print "into a 'plugins' directory linked or located in this directory.\n";
+-    print "Be sure your PLUGINDIR environment variable is set before running\n";
+-    print "'make distrib' in the plugin build area.\n";
+-    print "\n";
+-    die "Halting configuration until VMD plugins are built.\n";
+-  }
+-} 
+-
+ #################### Parse command line options   ###########
+ # list of allowed architectures
+ @archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'MACOSX', 'MACOSXX86', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
+@@ -409,8 +386,8 @@
+ 
+ ################ Plugin options
+ #
+-$plugin_dir	= "../plugins";
+-$molfile_dir = "$plugin_dir/$config_arch/molfile";
++$plugin_dir	= "gentoo-plugindir";
++$molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
+ $plugin_include = "-I$plugin_dir/include -I$molfile_dir";
+ $plugin_library = "-L$molfile_dir";
+ $plugin_libs    = "-lmolfile_plugin";
+@@ -510,8 +487,8 @@
+ ################ FLTK GUI
+ $fltk_defines     = "-DVMDGUI -DVMDFLTK";
+ $fltk_dir         = "$vmd_library_dir/fltk";
+-$fltk_include     = "-I$fltk_dir/include";
+-$fltk_library     = "-L$fltk_dir/$config_arch";
++$fltk_include     = "-Igentoo-fltk-include";
++$fltk_library     = "-Lgentoo-fltk-libs";
+ $fltk_libs        = "-lfltk -lX11";
+ #@fltk_cc          = ('forms_ui.c');
+ @fltk_ccpp        = ( 'ColorFltkMenu.C',
+@@ -859,9 +836,9 @@
+ ###################
+ $python_defines     = "-DVMDPYTHON";
+ $python_dir         = "$vmd_library_dir/python";
+-$python_include     = "-I$python_dir/lib_$config_arch/include/python2.2";
+-$python_library     = "-L$python_dir/lib_$config_arch/lib/python2.2/config";
+-$python_libs        = "-lpython2.2 -lpthread";
++$python_include     = "-Igentoo-python-include";
++$python_library     = "-Lgentoo-python-lib";
++$python_libs        = "-lgentoo-python-link -lpthread";
+ @python_h           = ('PythonTextInterp.h',
+                        'VMDTkinterMenu.h',
+ 		       'py_commands.h',
+@@ -1441,8 +1418,8 @@
+     $opengl_libs        = "-lGL -lGLU"; 
+     # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
+ 
+-    $arch_cc          = "gcc";
+-    $arch_ccpp        = "g++";
++    $arch_cc          = "gentoo-gcc";
++    $arch_ccpp        = "gentoo-g++";
+     # test hack to statically link libstd++
+     # $arch_ccpp        = "gcc";
+     $arch_depend_flag = "-MM";
+@@ -1451,8 +1428,8 @@
+     $arch_shcppopts   = "-fPIC";
+     $arch_shldopts    = "";
+ 
+-    $arch_opt_flag    = "-m32 -fno-for-scope -Wno-deprecated -Wall -O3";
+-    $arch_copts       = "-m32 -Wall -O3";
++    $arch_opt_flag    = "gentoo-cflags";
++    $arch_copts       = "gentoo-cflags";
+ 
+     if ($config_static) {
+       $arch_lopts       = "-static";
diff --git a/sci-chemistry/vmd/vmd-1.8.5.ebuild b/sci-chemistry/vmd/vmd-1.8.5.ebuild
new file mode 100644
index 000000000000..c10a3bd2b417
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.8.5.ebuild
@@ -0,0 +1,152 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.5.ebuild,v 1.1 2006/08/26 14:56:33 markusle Exp $
+
+inherit eutils toolchain-funcs python
+
+DESCRIPTION="Visual Molecular Dynamics"
+LICENSE="vmd"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="${P}.src.tar.gz"
+
+SLOT="0"
+KEYWORDS="~ppc ~x86"
+IUSE="hardened"
+
+RESTRICT="fetch"
+
+DEPEND="app-shells/tcsh
+	|| ( x11-libs/libXft virtual/x11 )
+	virtual/opengl
+	x11-libs/fltk
+	sci-libs/netcdf
+	=dev-lang/tcl-8.4*
+	=dev-lang/tk-8.4*
+	>=dev-lang/python-2.3
+	sci-biology/stride
+	hardened? ( sys-apps/paxctl )"
+
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+
+pkg_nofetch() {
+	echo
+	einfo "Please download ${SRC_URI} from"
+	einfo "${VMD_DOWNLOAD}"
+	einfo "after agreeing to the license and then move it to "
+	einfo "${DISTDIR}"
+	echo
+}
+
+src_unpack() {
+	unpack ${A}
+
+	# apply LINUX-arch patches to vmd configure
+	epatch "${FILESDIR}"/${P}-config-gentoo.patch
+#	epatch "${FILESDIR}"/${P}-plugin-autopsf.patch
+
+	# prepare the plugins 
+
+	cd "${WORKDIR}"/plugins
+
+	sed -e "s/CC = gcc/CC = $(tc-getCC)/" \
+	    -e "s/CXX = g++/CXX = $(tc-getCXX)/" \
+		-e "s/COPTO = -o /COPTO = -fPIC -o /" \
+		-e "s/LOPTO = -o /LOPTO = -fPIC -o /" \
+		-e "s/CCFLAGS = -O2 -Wall/CCFLAGS = ${CFLAGS}/" \
+		-e "s/CXXFLAGS = -O2 -Wall/CXXFLAGS = ${CXXFLAGS}/" \
+		-e "s/SHLD = gcc/SHLD = $(tc-getCC)/" \
+	    -i Make-arch || die "Failed to set up plugins Makefile"
+
+	# prepare vmd itself
+
+	cd "${S}"
+
+	sed -e "s:gentoo-bindir:${D}/usr/bin:" \
+		-e "s:gentoo-libdir:${D}/usr/$(get_libdir):" \
+		-i configure || die "failed to adjust install paths"
+
+
+	sed -e "s:gentoo-gcc:$(tc-getCC):" \
+		-e "s:gentoo-g++:$(tc-getCXX):" \
+		-e "s:gentoo-cflags:${CFLAGS}:" \
+		-i configure || die "Failed to adjust C compiler/flags"
+
+
+	sed -e "s:gentoo-plugindir:${WORKDIR}/plugins:" \
+		-i configure || die "Failed to set up linking to plugin files"
+
+	sed -e "s:gentoo-fltk-include:/usr/include/fltk-1.1:" \
+		-e "s:gentoo-fltk-libs:/usr/$(get_libdir)/fltk-1.1:" \
+		-i configure || die "failed setting up fltk"
+
+
+	# get installed python version
+	python_version
+	local PY="python${PYVER}"
+
+	sed -e "s:gentoo-python-include:/usr/include/${PY}:" \
+		-e "s:gentoo-python-lib:/usr/$(get_libdir)/${PY}:" \
+		-e "s:gentoo-python-link:${PY}:" \
+		-i configure || die "failed setting up python"
+
+	sed -e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-i ${S}/bin/vmd || die "failed setting up vmd wrapper script"
+
+	local myconfig="LINUX OPENGL FLTK TK TCL PTHREADS PYTHON"
+
+	rm -f configure.options && echo $myconfig >> configure.options
+
+	./configure &> /dev/null || die "failed to configure"
+
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins
+	make LINUX TCLINC="-I/usr/include" \
+		TCLLIB="-L/usr/$(get_libdir)/tcl8.4" || \
+		die "failed to build plugins"
+
+	# build vmd
+	cd "${S}"/src
+	make || die "failed to build vmd"
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins
+	PLUGINDIR=${D}/usr/$(get_libdir)/${PN}/plugins make distrib || \
+		die "failed to install plugins"
+
+	# install vmd 
+	cd "${S}"/src
+	make install || die "failed to install vmd"
+
+	# export STRIDE_BIN so VMD find stride
+	echo "STRIDE_BIN=/usr/bin/stride" > ${T}/99${PN} || \
+		die "Failed to create vmd env file"
+	doenvd ${T}/99${PN} || die "Failed to install vmd env file"
+
+	# install docs
+	cd "${S}"
+	dodoc Announcement README doc/ig.pdf doc/ug.pdf
+
+	# remove some of the things we don't want and need in 
+	# /usr/lib
+	cd "${D}"/usr/$(get_libdir)/vmd
+	rm -fr doc README Announcement LICENSE || \
+		die "failed to clean up /usr/lib/vmd directory"
+
+	# adjust path in vmd wrapper
+	sed -e "s:${D}::" -i "${D}"/usr/bin/${PN} \
+		|| die "failed to set up vmd wrapper script"
+
+	# adjust paxctl settings on hardened systems
+	if use hardened; then
+		/sbin/paxctl -pemrxs ${D}/usr/$(get_libdir)/${PN}/${PN}_LINUX
+	fi
+}
+