Version bump.

Package-Manager: portage-2.1_pre7-r5

6 files changed, 298 insertions, 4 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 359202e82bea..28399a35d133 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.3 2006/03/21 08:37:58 spyderous Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.4 2006/04/18 02:04:56 markusle Exp $
+
+*vmd-1.8.4 (18 Apr 2006)
+
+  18 Apr 2006; Markus Dittrich <markusle@gentoo.org>
+  +files/vmd-1.8.4-config-gentoo.patch,
+  +files/vmd-1.8.4-plugin-autopsf.patch, +vmd-1.8.4.ebuild:
+  Version bump.
 
   21 Mar 2006; Donnie Berkholz <spyderous@gentoo.org>; vmd-1.8.3.ebuild:
   Keyword ~ppc, and make changes to the wrapper script that may also fix amd64
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 9cb082698bcd..6058c89ca834 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,15 +1,27 @@
-MD5 9e362ddc8ad99c0fe2cbad395f295bfb ChangeLog 663
-RMD160 adeb0ae7c03bd36828a60e9300cd7507de5c6293 ChangeLog 663
-SHA256 987a193b9c864fb0b2dedcfecfc682a8bf27cb19d5128e55a741595fdb1f3e0a ChangeLog 663
+MD5 69d2126b17865e4c0d4731033c72bbe0 ChangeLog 858
+RMD160 7c70627061115b261a22583998db3330d15b024f ChangeLog 858
+SHA256 4e615db7d98e805a08af83b1bfbc2f09b7ba38160ec3398a88b7b65b0b4db3b6 ChangeLog 858
 MD5 369e1a4fc4a190880b7bcd1847da843f files/digest-vmd-1.8.3 244
 RMD160 99396b8dda8d7fc4a45c128cde3773103be4c5a4 files/digest-vmd-1.8.3 244
 SHA256 afb2b7701f35aeaedd2191351e44ba399d7c2b449edfd8b3d9adac47fd266734 files/digest-vmd-1.8.3 244
+MD5 6938330c3067d798a3014e5b9808d45d files/digest-vmd-1.8.4 247
+RMD160 64861c785c0dc69121006bec5a4ee50b2680c15d files/digest-vmd-1.8.4 247
+SHA256 bceb65dcbf7a1b074af7434b7d32dc5624361862aa5a96b7a279cdaded08c732 files/digest-vmd-1.8.4 247
 MD5 c2f7407b24ab8fee80f913a2b31e79f5 files/vmd-1.8.3-config-gentoo.patch 2849
 RMD160 6bfdf7aa6f19839578b9dd08833f5af9a934514a files/vmd-1.8.3-config-gentoo.patch 2849
 SHA256 ee812af9c130d93b795c3f6967a1cc84a03fd56c16fcf9308636c3285a86ed73 files/vmd-1.8.3-config-gentoo.patch 2849
+MD5 6325ce1d0cbfe7731240deef3d69efa5 files/vmd-1.8.4-config-gentoo.patch 4246
+RMD160 61aa7bff404a775e5e6be01c42654eeb69a7711f files/vmd-1.8.4-config-gentoo.patch 4246
+SHA256 0be5b5d67a5198929b4c3db8c0dfa3a7a69150f02b075d7bafe0255825bdcbb9 files/vmd-1.8.4-config-gentoo.patch 4246
+MD5 94569757919baac0e2b61400d356cb74 files/vmd-1.8.4-plugin-autopsf.patch 723
+RMD160 6ccb492685cdeedc762f16e6f8ba010e2833908a files/vmd-1.8.4-plugin-autopsf.patch 723
+SHA256 7230d8f5f4281b7b8615cc7ff60fc3b77432b3ec12cc507f3016566178b07fae files/vmd-1.8.4-plugin-autopsf.patch 723
 MD5 df166a2ae1cb64196abc394d4fa522ed metadata.xml 272
 RMD160 42331a21c1e7a31cfe105f705fe3073de14b6b14 metadata.xml 272
 SHA256 36ae23839abbf283daf51b7f9585af067c0504484f5ca61e2f08113912becb77 metadata.xml 272
 MD5 7b4f1380ec72e3ec6ab436d3c557e33b vmd-1.8.3.ebuild 3615
 RMD160 2bbeaf3e7ebb73ce89aa4c8d56269790f9900071 vmd-1.8.3.ebuild 3615
 SHA256 afb3dc12dfbaab4cd9bcf14e3908b26d824a1d19dd932bdb6c5d9e887e059924 vmd-1.8.3.ebuild 3615
+MD5 e494359bcb14b7fe3f295f118c7c5f7b vmd-1.8.4.ebuild 3744
+RMD160 feaaa172c06211db51b474f60cc8abfc97aef4ea vmd-1.8.4.ebuild 3744
+SHA256 bcf706a28add41d94d5ac2120d448c8210203f67fada754161f116955bc24d8b vmd-1.8.4.ebuild 3744
diff --git a/sci-chemistry/vmd/files/digest-vmd-1.8.4 b/sci-chemistry/vmd/files/digest-vmd-1.8.4
new file mode 100644
index 000000000000..9ea1e6202b57
--- /dev/null
+++ b/sci-chemistry/vmd/files/digest-vmd-1.8.4
@@ -0,0 +1,3 @@
+MD5 3cf6f2e23898ace4ffe022115470ec28 vmd-1.8.4.src.tar.gz 12042149
+RMD160 f49a68ae63a607cd37a58d894df2f22d7df55b85 vmd-1.8.4.src.tar.gz 12042149
+SHA256 29b046767f1efe90d5f3e3dbbdcd4988d5335d1db226405f5ddb9f171c811cac vmd-1.8.4.src.tar.gz 12042149
diff --git a/sci-chemistry/vmd/files/vmd-1.8.4-config-gentoo.patch b/sci-chemistry/vmd/files/vmd-1.8.4-config-gentoo.patch
new file mode 100755
index 000000000000..fc117bee18d5
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.8.4-config-gentoo.patch
@@ -0,0 +1,102 @@
+--- vmd-1.8.4/configure	2006-04-17 03:12:36.000000000 -0500
++++ vmd-1.8.4-new/configure	2006-04-17 16:22:09.000000000 -0500
+@@ -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/$install_name";
+ 
+ 
+ # optionally override hard-coded defaults above with environment variables
+@@ -121,29 +121,6 @@
+ # Configure script code begins here
+ ############################################################################
+ 
+-## Test for existence of a properly compiled plugin tree
+-if (!(-e "plugins")) {
+-  print "\n";
+-  print "VMD plugin directory not found.\n";
+-  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
+-  print "into a 'plugins' directory linked or located in this directory.\n";
+-  print "Be sure your PLUGINDIR environment variable is set before running\n";
+-  print "'make distrib' in the plugin build area.\n";
+-  print "\n";
+-  die "Halting configuration until VMD plugins are built.\n";
+-} else {
+-  if (!(-e "plugins/include/vmdplugin.h")) {
+-    print "\n";
+-    print "VMD plugin include files or directory not found.\n";
+-    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
+-    print "into a 'plugins' directory linked or located in this directory.\n";
+-    print "Be sure your PLUGINDIR environment variable is set before running\n";
+-    print "'make distrib' in the plugin build area.\n";
+-    print "\n";
+-    die "Halting configuration until VMD plugins are built.\n";
+-  }
+-} 
+-
+ #################### Parse command line options   ###########
+ # list of allowed architectures
+ @archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'MACOSX', 'MACOSXX86', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
+@@ -406,8 +383,8 @@
+ 
+ ################ Plugin options
+ #
+-$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";
+@@ -507,8 +484,8 @@
+ ################ 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',
+@@ -856,9 +833,9 @@
+ ###################
+ $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',
+@@ -1428,8 +1405,8 @@
+     $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";
+@@ -1438,8 +1415,8 @@
+     $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/files/vmd-1.8.4-plugin-autopsf.patch b/sci-chemistry/vmd/files/vmd-1.8.4-plugin-autopsf.patch
new file mode 100644
index 000000000000..c07e6477b0f0
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.8.4-plugin-autopsf.patch
@@ -0,0 +1,24 @@
+diff -Naur plugins/autopsf/src/psftype.C plugins-new/autopsf/src/psftype.C
+--- plugins/autopsf/src/psftype.C	2005-11-07 11:01:31.000000000 -0600
++++ plugins-new/autopsf/src/psftype.C	2006-04-17 18:50:15.000000000 -0500
+@@ -31,7 +31,7 @@
+ 	}
+ }
+ 
+-bool PsfType::equals(PsfType compatom) {
++bool PsfType::equals(PsfType &compatom) {
+ 	return (strcmp(compatom.type(),atomtype) == 0);
+ }
+ 
+diff -Naur plugins/autopsf/src/psftype.h plugins-new/autopsf/src/psftype.h
+--- plugins/autopsf/src/psftype.h	2005-09-07 16:12:27.000000000 -0500
++++ plugins-new/autopsf/src/psftype.h	2006-04-17 18:50:02.000000000 -0500
+@@ -9,7 +9,7 @@
+ 
+ 		~PsfType(); 
+ 
+-		bool equals(PsfType);
++		bool equals(PsfType&);
+ 
+ 		void setnext(PsfType*);
+ 
diff --git a/sci-chemistry/vmd/vmd-1.8.4.ebuild b/sci-chemistry/vmd/vmd-1.8.4.ebuild
new file mode 100644
index 000000000000..3f922a75aa9b
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.8.4.ebuild
@@ -0,0 +1,146 @@
+# 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-1.8.4.ebuild,v 1.1 2006/04/18 02:04:56 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
+	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 = ${CXXFLAGS}/" \
+	    -i Make-arch || die "Failed to set up plugins Makefile"
+
+	# prepare vmd itself
+
+	cd "${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 "${S}"/src
+	make install || die "failed to install vmd"
+
+	# install docs
+	cd "${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
+}
+