Version bump (fixes bug #262275).

Package-Manager: portage-2.1.6.13/cvs/Linux x86_64

5 files changed, 313 insertions, 12 deletions

diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 2b86734de4dd..854a80b5321d 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/vmd
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.22 2009/07/07 22:54:52 flameeyes Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.23 2009/08/06 14:19:15 markusle Exp $
+
+*vmd-1.8.7 (05 Aug 2009)
+
+  05 Aug 2009; Markus Dittrich <markusle@gentoo.org> +vmd-1.8.7.ebuild,
+  +files/vmd-1.8.7-config.patch, +files/vmd-1.8.7-use-bash-startup.patch:
+  Version bump (fixes bug #262275).
 
   07 Jul 2009; Diego E. Pettenò <flameeyes@gentoo.org> vmd-1.8.6-r1.ebuild:
   Use elog for fetch error.
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 4564e82279ad..5fb5a5b3da7c 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,20 +1,14 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 AUX vmd-1.8.5-config-gentoo.patch 4714 RMD160 192224a4a05e249c357f08e13d0811dcfb60f7ea SHA1 9b008b3313c969517dacf1c721e894151d0771f7 SHA256 8e7ac5124de52dbef9469c8416b1f011ffe3420043c5a58c2183b67dd66a6be9
 AUX vmd-1.8.6-config-gentoo.patch 4666 RMD160 1fb149ab58292f42abbe4d658aff0334d3fe73f9 SHA1 27a7ea51772e93e858ef23bf09d819e75d6418b5 SHA256 6dc232ee1c01a56bb94bdf193f024e868f957a22b6c1c8666d2d443801a36f03
 AUX vmd-1.8.6-fix-crash-on-tcl8.5.patch 1355 RMD160 19f86942aabda74eb5726346b84012b6509b67f1 SHA1 921c554d9a6e296251ce01e22f5bf03c7bcc8841 SHA256 98bcd0c524f0392a12149c5d6ab15cff489edf1092315a74110f655de482ca4e
 AUX vmd-1.8.6-python-2.5.patch 860 RMD160 4f9f83800e0f5083fcd32a016404c909da4042a6 SHA1 bb401cccbb18428cc0fdce5cf4b5fd3a910a9cea SHA256 652e5dbb44d2c14c13886e9e7bc2677287bfdd520e7489547cffc2331b39d7ec
 AUX vmd-1.8.6-tcltk8.5.patch 2348 RMD160 d1661e1effd1ab35def56cbd53601801427f96a0 SHA1 b7b7fd68cb6e9c8fea12c4544179daaada5dd36b SHA256 d1e39f5d67af22281ccf1bf56e1360778e03d1b1ea6c6c184a0d269f49edee2c
+AUX vmd-1.8.7-config.patch 5519 RMD160 68d3648978db8c23e4df08dd7757018b6a6d6f88 SHA1 1a93053099ba364538463b5a06a31e96f3224e5a SHA256 0f39351b856ba5a828344e0ae8ec6451ace8a3d0f491639564cb53ac6935ef9d
+AUX vmd-1.8.7-use-bash-startup.patch 717 RMD160 f061a9e4c90115b3eab42d754e66f62240b3fb69 SHA1 73001ba99f97ce484610593b50bafcbed7943889 SHA256 3f9a8c9f8f0f461b8dd3985d71265c942e655e56e1745b75c25f547821d4228c
 DIST vmd-1.8.6.src.tar.gz 18045341 RMD160 66f8ee5a0313000ea8dd3cb79881fd26a2836a79 SHA1 62ceaab06c7fec7c2c8e9a2d7f08c83ba662679d SHA256 fe2bcf7ffea1ed6b3a7f2402d6e1cb1d6def588a8b09a5d0943c0a9f3426ead2
+DIST vmd-1.8.7.src.tar.gz 23853864 RMD160 1c4751552d7b3f376f91a4b28ee9d4a028ded01a SHA1 409b6f8959d551f581991073f98885b47c21c25c SHA256 72fe2fb7eff4c805a886ea929c7e143a3a1be57cc817b5d1719d29e591d80316
 EBUILD vmd-1.8.6-r1.ebuild 4349 RMD160 6fcb070cb84f90164db8554a0596f208a1a6490b SHA1 46b06a0c0b8decf35e379f8bbaa96774733ef847 SHA256 071f247254b1941dcb05e949e08c4d3d97568bdb8fbe3ebe480bbb764682da9c
 EBUILD vmd-1.8.6.ebuild 4299 RMD160 1e4bee161856b5996bbd1b61de1d5575c030804e SHA1 1a943a032e8699ea41b7aa135a2550e05fbfc77a SHA256 d5f4d08855fc4095bfd58099aae3a3e56c1db064e06bf9569f8ef71334f4734a
-MISC ChangeLog 4089 RMD160 4ed4f46cd5edf052002c8b48d3e1a59bf65967e6 SHA1 971f8a7d6be16c31982ff1ecd8c7889b3b0cf1ac SHA256 57dd7ecc93800b9b7ced0a6f229c4f86318a03f3216849122fd8f351387b515e
+EBUILD vmd-1.8.7.ebuild 4366 RMD160 fdbd2955360f4e591bc18ed61333b8b36e2c2a41 SHA1 40b301b697fa3c854258d4b48c63af1fa7620446 SHA256 fd2f5ffdd93b58b3a3b18aad8b2a3051130eded6b562b1a28633e392abfb8507
+MISC ChangeLog 4297 RMD160 682d4c3ad918647bf013bc7f587d09a188041bdc SHA1 55968bc11e4ee07c86fe7756cb17995d374b2519 SHA256 428ae8093899224ee135bfd253bdd63c9b430dbb1c33a20b20abc9b721eb0676
 MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349
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diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-config.patch b/sci-chemistry/vmd/files/vmd-1.8.7-config.patch
new file mode 100644
index 000000000000..633337105e97
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.8.7-config.patch
@@ -0,0 +1,131 @@
+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	2009-08-05 09:07:08.000000000 -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          = ();
+@@ -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) {
+         $arch_lopts       = "-static";
diff --git a/sci-chemistry/vmd/files/vmd-1.8.7-use-bash-startup.patch b/sci-chemistry/vmd/files/vmd-1.8.7-use-bash-startup.patch
new file mode 100644
index 000000000000..422d95c69d11
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.8.7-use-bash-startup.patch
@@ -0,0 +1,13 @@
+diff -Naur vmd-1.8.7.old/configure vmd-1.8.7/configure
+--- vmd-1.8.7.old/configure	2009-08-01 03:19:34.000000000 -0400
++++ vmd-1.8.7/configure	2009-08-05 09:30:33.000000000 -0400
+@@ -2804,8 +2804,7 @@
+ 	-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$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.ebuild b/sci-chemistry/vmd/vmd-1.8.7.ebuild
new file mode 100644
index 000000000000..359d045909bc
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.8.7.ebuild
@@ -0,0 +1,157 @@
+# Copyright 1999-2009 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.ebuild,v 1.1 2009/08/06 14:19:15 markusle Exp $
+
+EAPI="2"
+
+inherit eutils toolchain-funcs python
+
+DESCRIPTION="Visual Molecular Dynamics"
+LICENSE="vmd"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="${P}.src.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+
+RESTRICT="fetch"
+
+DEPEND="x11-libs/libXft
+	virtual/opengl
+	x11-libs/fltk:1.1
+	>=dev-lang/tcl-8.4
+	>=dev-lang/tk-8.4[-truetype]
+	=dev-lang/python-2*
+	dev-lang/perl
+	dev-python/numpy
+	sci-biology/stride
+	sci-libs/netcdf"
+
+RDEPEND="${DEPEND}
+	x11-terms/xterm"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+
+pkg_nofetch() {
+	echo
+	elog "Please download ${SRC_URI} from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and then move it to "
+	elog "${DISTDIR}"
+	echo
+}
+
+src_prepare() {
+	# apply LINUX-arch patches to vmd configure
+	epatch "${FILESDIR}/${P}-config.patch"
+	epatch "${FILESDIR}/${P}-use-bash-startup.patch"
+
+	# prepare the plugins
+	cd "${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 = -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}"
+
+	sed -e "s:gentoo-bindir:${D}/usr/bin:" \
+		-e "s:gentoo-libdir:${D}/usr/$(get_libdir):" \
+		-i configure || die "failed to adjust install paths"
+
+	sed -e "s:gentoo-opengl-include:/usr/include/GL:" \
+		-e "s:gentoo-opengl-libs:/usr/$(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:${CFLAGS}:" \
+		-i configure || die "Failed to adjust C compiler/flags"
+
+	sed -e "s:gentoo-plugindir:${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${PYVER}"
+
+	local NUMPY_INCLUDE="site-packages/numpy/core/include"
+	sed -e "s:gentoo-python-include:/usr/include/${PY}:" \
+		-e "s:gentoo-python-lib:/usr/$(get_libdir)/${PY}:" \
+		-e "s:gentoo-python-link:${PY}:" \
+		-e "s:gentoo-numpy-include:/usr/$(get_libdir)/${PY}/${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"
+	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/$(get_libdir)" \
+		|| die "failed to build plugins"
+
+	# build vmd
+	cd "${S}"/src
+	emake || 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"
+}