Version bump (fixes bug #174595).

(Portage version: 2.1.2.3)

6 files changed, 185 insertions, 66 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 6743d34340d1..20f8cb8bdf3e 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/vmd
 # Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.14 2007/01/08 00:07:38 kugelfang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.15 2007/04/16 12:47:57 markusle Exp $
+
+*vmd-1.8.6 (15 Apr 2007)
+
+  15 Apr 2007; Markus Dittrich <markusle@gentoo.org>
+  -files/vmd-1.8.4-config-gentoo.patch, -files/vmd-1.8.4-paratool.patch,
+  -files/vmd-1.8.4-plugin-autopsf.patch,
+  +files/vmd-1.8.6-config-gentoo.patch, +vmd-1.8.6.ebuild:
+  Version bump (fixes bug #174595). Thanks much to Jeffrey Gardner
+  <je_fro@gentoo.org> for his patch and ebuild.
 
   08 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -vmd-1.8.4.ebuild,
   -vmd-1.8.4-r1.ebuild:
diff --git a/sci-chemistry/vmd/files/digest-vmd-1.8.6 b/sci-chemistry/vmd/files/digest-vmd-1.8.6
new file mode 100644
index 000000000000..1c72cc7d9805
--- /dev/null
+++ b/sci-chemistry/vmd/files/digest-vmd-1.8.6
@@ -0,0 +1,3 @@
+MD5 cb344a3d6e90f4561c37c9ea1518cdab vmd-1.8.6.src.tar.gz 18045341
+RMD160 66f8ee5a0313000ea8dd3cb79881fd26a2836a79 vmd-1.8.6.src.tar.gz 18045341
+SHA256 fe2bcf7ffea1ed6b3a7f2402d6e1cb1d6def588a8b09a5d0943c0a9f3426ead2 vmd-1.8.6.src.tar.gz 18045341
diff --git a/sci-chemistry/vmd/files/vmd-1.8.4-paratool.patch b/sci-chemistry/vmd/files/vmd-1.8.4-paratool.patch
deleted file mode 100644
index d0d5e63bcf5b..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.4-paratool.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-diff -Naur plugins/paratool/paratool_readwrite.tcl plugins-new/paratool/paratool_readwrite.tcl
---- plugins/paratool/paratool_readwrite.tcl	2006-04-05 18:53:03.000000000 -0400
-+++ plugins-new/paratool/paratool_readwrite.tcl	2006-08-01 22:05:50.000000000 -0400
-@@ -651,12 +651,8 @@
- ##########################################################
- 
- proc ::Paratool::load_basemolecule { file {file2 {}}} {
--<<<<<<< paratool_readwrite.tcl
--    puts "Files $file $file2"
--=======
-    puts "Loading base molecule $file"
- 
-->>>>>>> 1.20
-    save_viewpoint_orig
-    set newmolid [mol new $file]
-    if {[llength $file2]} {
-diff -Naur plugins/resptool/resptool.tcl plugins-new/resptool/resptool.tcl
---- plugins/resptool/resptool.tcl	2005-12-20 11:08:16.000000000 -0500
-+++ plugins-new/resptool/resptool.tcl	2006-08-01 22:06:00.000000000 -0400
-@@ -14,7 +14,7 @@
- # * Clear selection button
- 
- package provide resptool 1.0
--package require paratool
-+#package require paratool
- 
- namespace eval ::RESPTool:: {
-   variable w
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
deleted file mode 100644
index c07e6477b0f0..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.4-plugin-autopsf.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-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/files/vmd-1.8.4-config-gentoo.patch b/sci-chemistry/vmd/files/vmd-1.8.6-config-gentoo.patch
index fc117bee18d5..950b2f6b1836 100755..100644
--- a/sci-chemistry/vmd/files/vmd-1.8.4-config-gentoo.patch
+++ b/sci-chemistry/vmd/files/vmd-1.8.6-config-gentoo.patch
@@ -1,5 +1,5 @@
---- 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
+--- ../vmd-1.8.6-orig/configure	2007-04-14 17:08:43.000000000 -0500
++++ vmd-1.8.6/configure	2007-04-14 17:30:28.000000000 -0500
 @@ -13,10 +13,10 @@
  $install_name = "vmd";
  
@@ -13,7 +13,7 @@
  
  
  # optionally override hard-coded defaults above with environment variables
-@@ -121,29 +121,6 @@
+@@ -123,29 +123,6 @@
  # Configure script code begins here
  ############################################################################
  
@@ -43,18 +43,18 @@
  #################### 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 @@
+@@ -423,8 +400,8 @@
  
  ################ Plugin options
  #
 -$plugin_dir	= "../plugins";
 -$molfile_dir = "$plugin_dir/$config_arch/molfile";
-+$plugin_dir	= "gentoo-plugindir";
++$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 @@
+@@ -529,8 +506,8 @@
  ################ FLTK GUI
  $fltk_defines     = "-DVMDGUI -DVMDFLTK";
  $fltk_dir         = "$vmd_library_dir/fltk";
@@ -64,8 +64,19 @@
 +$fltk_library     = "-Lgentoo-fltk-libs";
  $fltk_libs        = "-lfltk -lX11";
  #@fltk_cc          = ('forms_ui.c');
- @fltk_ccpp        = ( 'ColorFltkMenu.C',
-@@ -856,9 +833,9 @@
+ @fltk_cu          = ();
+@@ -886,8 +863,8 @@
+ #######################
+ $netcdf_defines     = "";
+ $netcdf_dir         = "$vmd_library_dir/netcdf";
+-$netcdf_include     = "-I$netcdf_dir/include";
+-$netcdf_library     = "-L$netcdf_dir/lib_$config_arch";
++$netcdf_include     = "-Igentoo-netcdf-include";
++$netcdf_library     = "-Lgentoo-netcdf-libs";
+ $netcdf_libs        = "-lnetcdf";
+ @netcdf_cc          = ();
+ @netcdf_cu          = ();
+@@ -954,9 +931,9 @@
  ###################
  $python_defines     = "-DVMDPYTHON";
  $python_dir         = "$vmd_library_dir/python";
@@ -78,7 +89,7 @@
  @python_h           = ('PythonTextInterp.h',
                         'VMDTkinterMenu.h',
  		       'py_commands.h',
-@@ -1428,8 +1405,8 @@
+@@ -1555,8 +1532,8 @@
      $opengl_libs        = "-lGL -lGLU"; 
      # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
  
@@ -89,7 +100,7 @@
      # test hack to statically link libstd++
      # $arch_ccpp        = "gcc";
      $arch_depend_flag = "-MM";
-@@ -1438,8 +1415,8 @@
+@@ -1565,8 +1542,8 @@
      $arch_shcppopts   = "-fPIC";
      $arch_shldopts    = "";
  
@@ -97,6 +108,6 @@
 -    $arch_copts       = "-m32 -Wall -O3";
 +    $arch_opt_flag    = "gentoo-cflags";
 +    $arch_copts       = "gentoo-cflags";
- 
-     if ($config_static) {
-       $arch_lopts       = "-static";
+     if ($config_swig) {
+       $swig_cflags     .= " -fno-strict-aliasing";
+     }
diff --git a/sci-chemistry/vmd/vmd-1.8.6.ebuild b/sci-chemistry/vmd/vmd-1.8.6.ebuild
new file mode 100644
index 000000000000..3fe08f0efcd7
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.8.6.ebuild
@@ -0,0 +1,148 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.6.ebuild,v 1.1 2007/04/16 12:47:57 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="~amd64 ~ppc ~x86"
+IUSE=""
+
+RESTRICT="fetch"
+
+DEPEND="app-shells/tcsh
+	|| ( x11-libs/libXft virtual/x11 )
+	virtual/opengl
+	x11-libs/fltk
+	=dev-lang/tcl-8.4*
+	=dev-lang/tk-8.4*
+	>=dev-lang/python-2.3
+	sci-biology/stride
+	sci-libs/netcdf"
+
+
+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}"/${P}-config-gentoo.patch
+
+	# prepare the plugins 
+
+	cd "${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"
+
+	sed -e "s:gentoo-netcdf-include:/usr/include:" \
+		-e "s:gentoo-netcdf-libs:/usr/$(get_libdir):" \
+		-i configure || die "failed to set up netcdf"
+
+	# get installed python version
+	python_version
+	local PY="python${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 IMD NETCDF"
+
+	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 knows where to 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"
+}
+