Make it really prefix ready, don't mix CFLAGS/CXXFLAGS,clean old patches

(Portage version: 2.2_rc67/cvs/Linux x86_64)

11 files changed, 262 insertions, 525 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 0e80ffc282bb..338052d7cd77 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,18 @@
 # ChangeLog for sci-chemistry/vmd
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.30 2010/07/24 17:27:05 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.31 2010/07/27 18:47:37 jlec Exp $
+
+*vmd-1.8.7-r2 (27 Jul 2010)
+
+  27 Jul 2010; Justin Lecher <jlec@gentoo.org>
+  -files/vmd-1.8.5-config-gentoo.patch,
+  -files/vmd-1.8.6-config-gentoo.patch,
+  -files/vmd-1.8.6-fix-crash-on-tcl8.5.patch,
+  -files/vmd-1.8.6-python-2.5.patch, -files/vmd-1.8.6-tcltk8.5.patch,
+  vmd-1.8.7-r1.ebuild, +vmd-1.8.7-r2.ebuild, -files/vmd-1.8.7-config.patch,
+  files/vmd-1.8.7-gentoo.patch, +files/vmd-1.8.7-respect-flags.patch,
+  -files/vmd-1.8.7-use-bash-startup.patch:
+  Make it really prefix ready, don't mix CFLAGS/CXXFLAGS,clean old patches
 
   24 Jul 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r1.ebuild:
   Added prefix changes, thanks rei4dan #327517; keyworded for ~-linux prefix
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
deleted file mode 100644
index 754977954aaa..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.5-config-gentoo.patch
+++ /dev/null
@@ -1,114 +0,0 @@
-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	2006-12-22 08:26:32.000000000 -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/$install_name";
- 
- 
- # optionally override hard-coded defaults above with environment variables
-@@ -121,29 +121,6 @@
- # Configure script code begins here
- ############################################################################
- 
--## Test for existence of a properly compiled plugin tree
--if (!(-e "plugins")) {
--  print "\n";
--  print "VMD plugin directory not found.\n";
--  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--  print "into a 'plugins' directory linked or located in this directory.\n";
--  print "Be sure your PLUGINDIR environment variable is set before running\n";
--  print "'make distrib' in the plugin build area.\n";
--  print "\n";
--  die "Halting configuration until VMD plugins are built.\n";
--} else {
--  if (!(-e "plugins/include/vmdplugin.h")) {
--    print "\n";
--    print "VMD plugin include files or directory not found.\n";
--    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--    print "into a 'plugins' directory linked or located in this directory.\n";
--    print "Be sure your PLUGINDIR environment variable is set before running\n";
--    print "'make distrib' in the plugin build area.\n";
--    print "\n";
--    die "Halting configuration until VMD plugins are built.\n";
--  }
--} 
--
- #################### Parse command line options   ###########
- # list of allowed architectures
- @archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'MACOSX', 'MACOSXX86', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
-@@ -409,8 +386,8 @@
- 
- ################ Plugin options
- #
--$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',
-@@ -797,8 +774,8 @@
- #######################
- $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_ccpp        = ();
-@@ -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/files/vmd-1.8.6-config-gentoo.patch b/sci-chemistry/vmd/files/vmd-1.8.6-config-gentoo.patch
deleted file mode 100644
index 950b2f6b1836..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.6-config-gentoo.patch
+++ /dev/null
@@ -1,113 +0,0 @@
---- ../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 @@
- $install_name = "vmd";
- 
- # Directory where VMD startup script is installed, should be in users' paths.
--$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/$install_name";
- 
- 
- # optionally override hard-coded defaults above with environment variables
-@@ -123,29 +123,6 @@
- # Configure script code begins here
- ############################################################################
- 
--## Test for existence of a properly compiled plugin tree
--if (!(-e "plugins")) {
--  print "\n";
--  print "VMD plugin directory not found.\n";
--  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--  print "into a 'plugins' directory linked or located in this directory.\n";
--  print "Be sure your PLUGINDIR environment variable is set before running\n";
--  print "'make distrib' in the plugin build area.\n";
--  print "\n";
--  die "Halting configuration until VMD plugins are built.\n";
--} else {
--  if (!(-e "plugins/include/vmdplugin.h")) {
--    print "\n";
--    print "VMD plugin include files or directory not found.\n";
--    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--    print "into a 'plugins' directory linked or located in this directory.\n";
--    print "Be sure your PLUGINDIR environment variable is set before running\n";
--    print "'make distrib' in the plugin build area.\n";
--    print "\n";
--    die "Halting configuration until VMD plugins are built.\n";
--  }
--} 
--
- #################### Parse command line options   ###########
- # list of allowed architectures
- @archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'MACOSX', 'MACOSXX86', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
-@@ -423,8 +400,8 @@
- 
- ################ Plugin options
- #
--$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";
-@@ -529,8 +506,8 @@
- ################ 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_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";
--$python_include     = "-I$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',
-@@ -1555,8 +1532,8 @@
-     $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";
-@@ -1565,8 +1542,8 @@
-     $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_swig) {
-       $swig_cflags     .= " -fno-strict-aliasing";
-     }
diff --git a/sci-chemistry/vmd/files/vmd-1.8.6-fix-crash-on-tcl8.5.patch b/sci-chemistry/vmd/files/vmd-1.8.6-fix-crash-on-tcl8.5.patch
deleted file mode 100644
index db83164ce710..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.6-fix-crash-on-tcl8.5.patch
+++ /dev/null
@@ -1,49 +0,0 @@
---- vmd-1.8.6/src/TclTextInterp.C.orig	2009-02-02 23:24:27.000000000 +0300
-+++ vmd-1.8.6/src/TclTextInterp.C	2009-02-02 23:35:33.000000000 +0300
-@@ -100,7 +100,9 @@
- 
- TclTextInterp::TclTextInterp(VMDApp *vmdapp)
- : app(vmdapp) {
--  
-+#if 0
-+	Tcl_InitMemory(interp); // enable Tcl memory debugging features when compiled with TCL_MEM_DEBUG
-+#endif
-   interp = Tcl_CreateInterp();
-   commandPtr = Tcl_NewObj();
-   Tcl_IncrRefCount(commandPtr);
-@@ -310,8 +312,16 @@
-     callLevel++;
-     Tcl_RecordAndEvalObj(interp, commandPtr, 0);
-     callLevel--;
--
-+#if TCL_MINOR_VERSION >= 5
-+	if (Tcl_IsShared(commandPtr)) {
-+		Tcl_DecrRefCount(commandPtr);
-+		commandPtr = Tcl_NewObj();
-+		Tcl_IncrRefCount(commandPtr);
-+	}
-+#else
-+// XXX this crashes Tcl 8.5.[46] with an internal panic
-     Tcl_SetObjLength(commandPtr, 0);
-+#endif
-     
-     // if ok, send to stdout; if not, send to stderr
-     Tcl_Obj *resultPtr = Tcl_GetObjResult(interp);
-@@ -388,8 +398,16 @@
-     if (app->exitFlag) break;
- 
-     Tcl_RecordAndEvalObj(interp, cmdPtr, 0);
-+#if TCL_MINOR_VERSION >= 5
-+	if (Tcl_IsShared(cmdPtr)) {
-+		Tcl_DecrRefCount(cmdPtr);
-+		cmdPtr = Tcl_NewObj();
-+		Tcl_IncrRefCount(cmdPtr);
-+	}
-+#else
-+ // XXX this crashes Tcl 8.5.[46] with an internal panic
-     Tcl_SetObjLength(cmdPtr, 0);
--
-+#endif
-     // XXX what's this here for?
-     app->display_update();
- 
diff --git a/sci-chemistry/vmd/files/vmd-1.8.6-python-2.5.patch b/sci-chemistry/vmd/files/vmd-1.8.6-python-2.5.patch
deleted file mode 100644
index ad8d0ae9b51a..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.6-python-2.5.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- vmd-1.8.6/src/py_atomsel.C	2007-04-08 07:04:03.000000000 +0200
-+++ vmd-1.8.6.new/src/py_atomsel.C	2007-09-20 19:30:41.000000000 +0200
-@@ -25,6 +25,10 @@
- #include "py_commands.h"
- #include "BondSearch.h"
- 
-+#if PY_VERSION_HEX < ((2<<24)|(5<<16))
-+typedef int Py_ssize_t;
-+#endif
-+
- typedef struct {
-   PyObject_HEAD
-   AtomSel *atomSel;
-@@ -915,9 +919,11 @@
-  * Support for mapping protocol 
-  */
- 
--static int
--atomselection_length( PyAtomSelObject *a ) {
--  return a->atomSel->selected;
-+
-+static Py_ssize_t
-+atomselection_length(PyObject *a)
-+{
-+  return ((PyAtomSelObject *)a)->atomSel->selected;
- }
- 
- // for integer argument, return True or False if index in in selection
-@@ -935,7 +941,7 @@
- }
- 
- static PyMappingMethods atomsel_mapping = {
--  (inquiry)atomselection_length,
-+  atomselection_length,
-   (binaryfunc)atomselection_subscript,
-   0
- };
diff --git a/sci-chemistry/vmd/files/vmd-1.8.6-tcltk8.5.patch b/sci-chemistry/vmd/files/vmd-1.8.6-tcltk8.5.patch
deleted file mode 100644
index abb9be3e3431..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.6-tcltk8.5.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-diff -Naur vmd-1.8.6/configure vmd-1.8.6.new/configure
---- vmd-1.8.6/configure	2007-04-08 01:03:49.000000000 -0400
-+++ vmd-1.8.6.new/configure	2008-03-11 09:53:43.000000000 -0400
-@@ -591,8 +591,8 @@
- if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
- $tcl_library      = "-L$stock_tcl_library_dir";
- if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
--$tcl_libs         = "-ltcl8.4";  
--if ($config_tk) { $tcl_libs = "-ltk8.4 -lX11 " . $tcl_libs; }
-+$tcl_libs         = "-ltcl";  
-+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
- 
- @tcl_cc           = ();
- @tcl_cu           = ();
-@@ -1843,8 +1843,8 @@
-       $fltk_libs        = "-lfltk-x11 -lX11";
-       $opengl_include   = $opengl_include . " -I/usr/X11R6/include";
-       $opengl_libs      = "-L/usr/X11R6/lib -lGLU -lGL -framework Carbon -lXext -lX11";
--      $tcl_libs         = "-ltcl8.4-x11";
--      if ($config_tk) { $tcl_libs = "-ltk8.4-x11 -lX11 " . $tcl_libs; }
-+      $tcl_libs         = "-ltcl-x11";
-+      if ($config_tk) { $tcl_libs = "-ltk-x11 -lX11 " . $tcl_libs; }
-       $vmd_libs          = "$tcl_libs";
-     } else {
-       ##
-@@ -1936,8 +1936,8 @@
-       $fltk_libs        = "-lfltk-x11 -lX11";
-       $opengl_include   = $opengl_include . " -I/usr/X11R6/include";
-       $opengl_libs      = "-L/usr/X11R6/lib -lGLU -lGL -framework Carbon -lXext -lX11";
--      $tcl_libs         = "-ltcl8.4-x11";
--      if ($config_tk) { $tcl_libs = "-ltk8.4-x11 -lX11 " . $tcl_libs; }
-+      $tcl_libs         = "-ltcl-x11";
-+      if ($config_tk) { $tcl_libs = "-ltk-x11 -lX11 " . $tcl_libs; }
-       $vmd_libs          = "$tcl_libs";
-     } else {
-       ##
-diff -Naur vmd-1.8.6/src/cmd_render.C vmd-1.8.6.new/src/cmd_render.C
---- vmd-1.8.6/src/cmd_render.C	2007-04-08 01:04:03.000000000 -0400
-+++ vmd-1.8.6.new/src/cmd_render.C	2008-03-11 09:53:12.000000000 -0400
-@@ -211,8 +211,8 @@
-   // likely to lead to memory leaks in various scripts.  There's also currently
-   // no way to read out the size of the display in VMD (sad, I know), so
-   // it's just easier to set it here.
--  Tk_PhotoSetSize(handle, xs, ys);
--  Tk_PhotoPutBlock(handle, &blk, 0, 0, xs, ys, TK_PHOTO_COMPOSITE_SET);
-+  Tk_PhotoSetSize(interp, handle, xs, ys);
-+  Tk_PhotoPutBlock(interp, handle, &blk, 0, 0, xs, ys, TK_PHOTO_COMPOSITE_SET);
-   free(img);
-   return TCL_OK;
- }
diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-config.patch b/sci-chemistry/vmd/files/vmd-1.8.7-config.patch
deleted file mode 100644
index 7850e9f32b6b..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.7-config.patch
+++ /dev/null
@@ -1,142 +0,0 @@
-diff -Naur vmd-1.8.7/configure vmd-1.8.7.new/configure
---- vmd-1.8.7/configure	2009-08-01 03:19:34.000000000 -0400
-+++ vmd-1.8.7.new/configure	2009-08-07 09:12:43.000000000 -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/$install_name";
- 
- 
- # optionally override hard-coded defaults above with environment variables
-@@ -128,29 +128,6 @@
- # Configure script code begins here
- ############################################################################
- 
--## Test for existence of a properly compiled plugin tree
--if (!(-e "plugins")) {
--  print "\n";
--  print "VMD plugin directory not found.\n";
--  print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--  print "into a 'plugins' directory linked or located in this directory.\n";
--  print "Be sure your PLUGINDIR environment variable is set before running\n";
--  print "'make distrib' in the plugin build area.\n";
--  print "\n";
--  die "Halting configuration until VMD plugins are built.\n";
--} else {
--  if (!(-e "plugins/include/vmdplugin.h")) {
--    print "\n";
--    print "VMD plugin include files or directory not found.\n";
--    print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
--    print "into a 'plugins' directory linked or located in this directory.\n";
--    print "Be sure your PLUGINDIR environment variable is set before running\n";
--    print "'make distrib' in the plugin build area.\n";
--    print "\n";
--    die "Halting configuration until VMD plugins are built.\n";
--  }
--} 
--
- #################### Parse command line options   ###########
- # list of allowed architectures
- @archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'AIX6_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
-@@ -435,7 +412,7 @@
- 
- ################ Plugin options
- #
--$plugin_dir	= "../plugins";
-+$plugin_dir	= "gentoo-plugindir";
- $plugin_include = "-I$plugin_dir/include";
- $plugin_library = "";
- $plugin_libs    = "";
-@@ -448,7 +425,7 @@
- @plugin_extra   = ();
- 
- if ($config_staticplugin) {
--  $molfile_dir = "$plugin_dir/$config_arch/molfile";
-+  $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
-   $plugin_include .= " -I$molfile_dir";
-   $plugin_library .= " -L$molfile_dir";
-   $plugin_libs    .= " -lmolfile_plugin";
-@@ -550,8 +527,8 @@
- ################ 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";
- $fltk_libs        = "-lfltk -lX11";
- #@fltk_cc          = ('forms_ui.c');
- @fltk_cu          = ();
-@@ -612,8 +589,8 @@
- if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
- $tcl_library      = "-L$stock_tcl_library_dir";
- if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
--$tcl_libs         = "-ltcl8.5";  
--if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
-+$tcl_libs         = "-ltcl";  
-+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
- 
- @tcl_cc           = ();
- @tcl_cu           = ();
-@@ -938,8 +915,8 @@
- #######################
- $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          = ();
-@@ -1007,9 +984,9 @@
- $python_defines     = "-DVMDPYTHON";
- $python_dir         = "$vmd_library_dir/python";
- $numpy_dir          = "$vmd_library_dir/numpy";
--$python_include     = "-I$python_dir/lib_$config_arch/include/python2.5 -I$numpy_dir/lib_$config_arch/include -I$python_dir/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include";
--$python_library     = "-L$python_dir/lib_$config_arch/lib/python2.5/config";
--$python_libs        = "-lpython2.5 -lpthread";
-+$python_include     = "-Igentoo-python-include -Igentoo-numpy-include";
-+$python_library     = "-Lgentoo-python-lib";
-+$python_libs        = "-lgentoo-python-link -lpthread";
- @python_h           = ('PythonTextInterp.h',
-                        'VMDTkinterMenu.h',
- 		       'py_commands.h',
-@@ -1621,8 +1598,8 @@
- 
-     # XFree 4.0 Direct Rendering Interface and GLX 
-     $opengl_dir         = "/usr/X11R6";
--    $opengl_include     = "-I$opengl_dir/include";
--    $opengl_library     = "-L$opengl_dir/lib";
-+    $opengl_include     = "-Igentoo-opengl-include";
-+    $opengl_library     = "-Lgentoo-opengl-libs";
-     $opengl_libs        = "-lGL -lGLU"; 
-     # $opengl_libs      = "-L/usr/X11R6/lib -lGL -lGLU -lXext -lX11";
- 
-@@ -1650,15 +1627,15 @@
-       $arch_lopts       .= "-i-static ";
-     } else {
-       # compling with GCC
--      $arch_cc          = "gcc";
--      $arch_ccpp        = "g++";
-+      $arch_cc          = "gentoo-gcc";
-+      $arch_ccpp        = "gentoo-g++";
-       $arch_depend_flag = "-MM";
--      $arch_shld        = "g++ -shared";
-+      $arch_shld        = "gentoo-g++ -shared";
-       $arch_shlibname   = "so";
-       $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-1.8.7-gentoo.patch b/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch
index c80ed09be17b..e8c82c2bf872 100644
--- a/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch
+++ b/sci-chemistry/vmd/files/vmd-1.8.7-gentoo.patch
@@ -40,7 +40,7 @@ index 1b6ea67..d13aca1 100644
 +++ b/plugins/Makefile.rej
 @@ -3,7 +3,6 @@
    # Makefile for molecule file readers
-   # $Id: vmd-1.8.7-gentoo.patch,v 1.1 2010/05/18 07:22:51 jlec Exp $
+   # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $
    
 -- .SILENT:
    
@@ -48,7 +48,7 @@ index 1b6ea67..d13aca1 100644
    
 @@ -17,7 +16,6 @@
    # Makefile for molecule file readers
-   # $Id: vmd-1.8.7-gentoo.patch,v 1.1 2010/05/18 07:22:51 jlec Exp $
+   # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $
    
 -+ .SILENT:
    
@@ -543,19 +543,30 @@ index 96e70dc..8d10ef4 100644
  VMFILES = molefacture.tcl molefacture_builder.tcl \
  	molefacture_edit.tcl molefacture_geometry.tcl molefacture_gui.tcl \
 diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile
-index 18fb6dc..f17bdda 100644
+index 18fb6dc..e32b130 100644
 --- a/plugins/molfile_plugin/Makefile
 +++ b/plugins/molfile_plugin/Makefile
 @@ -1,7 +1,6 @@
  # Makefile for molecule file readers
- # $Id: vmd-1.8.7-gentoo.patch,v 1.1 2010/05/18 07:22:51 jlec Exp $
+ # $Id: vmd-1.8.7-gentoo.patch,v 1.2 2010/07/27 18:47:33 jlec Exp $
  
 -.SILENT:
  
  .SUFFIXES:
  
+@@ -14,8 +13,8 @@ INCDIR = -I../include -I${SRCDIR}
+ 
+ VPATH = src ../include ${ARCHDIR}
+ 
+-SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
+-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
++SCCFLAGS = $(CFLAGS) $(DEF)"STATIC_PLUGIN"
++SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
+ 
+ #
+ # Rules
 diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile
-index 1dfa768..88f4b7b 100644
+index 1dfa768..e3f380b 100644
 --- a/plugins/molfile_plugin/src/cifplugin/Makefile
 +++ b/plugins/molfile_plugin/src/cifplugin/Makefile
 @@ -1,6 +1,5 @@
@@ -565,6 +576,15 @@ index 1dfa768..88f4b7b 100644
  
  .SUFFIXES:
  
+@@ -14,7 +13,7 @@ INCDIR = -I../include -I${SRCDIR}
+ VPATH = src ../include ${ARCHDIR}
+ 
+ SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
+-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
++SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
+ 
+ #
+ # Rules
 diff --git a/plugins/moltoptools/Makefile b/plugins/moltoptools/Makefile
 index 3599cb7..8d80ec2 100644
 --- a/plugins/moltoptools/Makefile
@@ -1018,7 +1038,7 @@ index aa95b41..66ee516 100644
  VMFILES = zoomseq.tcl pkgIndex.tcl
  VMVERSION = 1.1
 diff --git a/vmd-1.8.7/configure b/vmd-1.8.7/configure
-index f01944a..2763347 100755
+index f01944a..b04bade 100755
 --- a/vmd-1.8.7/configure
 +++ b/vmd-1.8.7/configure
 @@ -13,10 +13,10 @@
@@ -1170,6 +1190,22 @@ index f01944a..2763347 100755
  
        if ($config_static) {
          # link everything statically (this won't work due to libGL issues)
+@@ -2714,11 +2691,11 @@ LIBDIRS     = $LIBDIRS
+ DEFINES     = $DEFINES
+ 
+ # compiler and compiler directives 
+-CC          = $arch_cc
+-CFLAGS      = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
++CC          = gentoo-gcc
++CFLAGS      = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+ 
+-CCPP	    = $arch_ccpp
+-CPPFLAGS    = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
++CCPP	    = gentoo-g++
++CPPFLAGS    = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+ 
+ NVCC        = $arch_nvcc
+ NVCCFLAGS   = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
 @@ -2766,7 +2743,7 @@ $config_progname: y.tab.h \$(VMD_OBJS)
  	if [ ! -r ./$arch_template_repository ]; then \\
  	  ln -s $vmd_src_dir/$arch_template_repository ./$arch_template_repository ; \\
diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-respect-flags.patch b/sci-chemistry/vmd/files/vmd-1.8.7-respect-flags.patch
new file mode 100644
index 000000000000..cd1281e3b682
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.8.7-respect-flags.patch
@@ -0,0 +1,28 @@
+diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile
+index 18fb6dc..8659573 100644
+--- a/plugins/molfile_plugin/Makefile
++++ b/plugins/molfile_plugin/Makefile
+@@ -14,8 +14,8 @@ INCDIR = -I../include -I${SRCDIR}
+ 
+ VPATH = src ../include ${ARCHDIR}
+ 
+-SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
+-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
++SCCFLAGS = $(CFLAGS) $(DEF)"STATIC_PLUGIN"
++SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
+ 
+ #
+ # Rules
+diff --git a/plugins/molfile_plugin/src/cifplugin/Makefile b/plugins/molfile_plugin/src/cifplugin/Makefile
+index 1dfa768..9de3f6b 100644
+--- a/plugins/molfile_plugin/src/cifplugin/Makefile
++++ b/plugins/molfile_plugin/src/cifplugin/Makefile
+@@ -14,7 +14,7 @@ INCDIR = -I../include -I${SRCDIR}
+ VPATH = src ../include ${ARCHDIR}
+ 
+ SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
+-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN"
++SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN"
+ 
+ #
+ # Rules
diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-use-bash-startup.patch b/sci-chemistry/vmd/files/vmd-1.8.7-use-bash-startup.patch
deleted file mode 100644
index 422d95c69d11..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.8.7-use-bash-startup.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff -Naur vmd-1.8.7.old/configure vmd-1.8.7/configure
---- vmd-1.8.7.old/configure	2009-08-01 03:19:34.000000000 -0400
-+++ vmd-1.8.7/configure	2009-08-05 09:30:33.000000000 -0400
-@@ -2804,8 +2804,7 @@
- 	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
- 	\$(CD) $vmd_bin_dir ; \\
- 	if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
--	if [ ! -x "/bin/csh" ]; then \\
--		\$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
-+	if [ -x "/bin/bash" ]; then \\
- 		\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
- 		\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
- 		\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
diff --git a/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild b/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild
new file mode 100644
index 000000000000..bfe487b72169
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild
@@ -0,0 +1,179 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.8.7-r2.ebuild,v 1.1 2010/07/27 18:47:38 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit eutils multilib python toolchain-funcs
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="${P}.src.tar.gz"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="tachyon"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+DEPEND="
+	|| (
+		>=dev-lang/tk-8.5[-truetype]
+		=dev-lang/tk-8.4*
+	)
+	dev-lang/perl
+	dev-python/numpy
+	sci-biology/stride
+	sci-libs/netcdf
+	virtual/opengl
+	x11-libs/fltk:1.1
+	x11-libs/libXft"
+
+RDEPEND="${DEPEND}
+	x11-terms/xterm
+	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_DT_HASH_amd64="usr/lib64/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_DT_HASH_x86="usr/lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+
+pkg_nofetch() {
+	elog "Please download ${A} from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and then move it to "
+	elog "${DISTDIR}"
+}
+
+src_prepare() {
+	# apply LINUX-arch patches to vmd configure
+	cd "${WORKDIR}" && epatch "${FILESDIR}/${P}-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 =.*\":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 = $(tc-getCC):" \
+		-e "s:-ltcl8.5:-ltcl:" \
+		-i Make-arch || die "Failed to set up plugins Makefile"
+
+	# prepare vmd itself
+	cd "${S}"
+
+	# PREFIX
+	sed \
+		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
+		-i configure || die
+
+	sed -e "s:gentoo-bindir:${ED}/usr/bin:" \
+		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):" \
+		-i configure || die "failed to adjust install paths"
+
+	sed -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:" \
+		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):" \
+		-i configure || die "failed to adjust OpenGL paths"
+
+	sed -e "s:gentoo-gcc:$(tc-getCC):" \
+		-e "s:gentoo-g++:$(tc-getCXX):" \
+		-e "s:gentoo-cflags:${CFLAGS}:" \
+		-e "s:gentoo-cxxflags:${CXXFLAGS}:" \
+		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
+		-i configure || die "Failed to adjust C compiler/flags"
+
+	sed -e "s:gentoo-plugindir:${WORKDIR}/plugins:" \
+		-i configure || die "Failed to set up linking to plugin files"
+
+	sed -e "s:gentoo-fltk-include:${EPREFIX}/usr/include/fltk-1.1:" \
+		-e "s:gentoo-fltk-libs:${EPREFIX}/usr/$(get_libdir)/fltk-1.1 -Wl,-rpath,${EPREFIX}/usr/$(get_libdir)/fltk-1.1:" \
+		-i configure || die "failed setting up fltk"
+
+	sed -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:" \
+		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):" \
+		-i configure || die "failed to set up netcdf"
+
+	local NUMPY_INCLUDE="numpy/core/include"
+	sed -e "s:gentoo-python-include:${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)/${NUMPY_INCLUDE}:" \
+		-i configure || die "failed setting up python"
+
+	sed -e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
+}
+
+src_configure() {
+	local myconfig="LINUX OPENGL FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT"
+	rm -f configure.options && echo $myconfig >> configure.options
+
+	./configure &> /dev/null || die "failed to configure"
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins
+
+	emake -j1 \
+		LINUX TCLINC="-I${EPREFIX}/usr/include" \
+		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" \
+		NETCDFLIB="-L${EPREFIX}/usr/$(get_libdir)" \
+		NETCDFINC="-I${EPREFIX}/usr/include" \
+		NETCDFLDFLAGS="-lnetcdf" \
+		|| die "failed to build plugins"
+
+	# build vmd
+	cd "${S}"/src
+	emake || die "failed to build vmd"
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins
+	PLUGINDIR=${ED}/usr/$(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=${EPREFIX}/usr/bin/stride" > "${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 "${ED}"/usr/$(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)/${PN}\":g" \
+		|| die "failed to set up vmd wrapper script"
+
+	# install icon and generate desktop entry
+	insinto /usr/share/pixmaps
+	doins "${FILESDIR}"/vmd.png || die "Failed to install vmd icon"
+	insinto /usr/share/applications
+	doins "${FILESDIR}"/vmd.desktop || die "Failed to install desktop entry"
+}