# 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:
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-AUX vmd-1.8.4-config-gentoo.patch 4246 RMD160 61aa7bff404a775e5e6be01c42654eeb69a7711f SHA1 51e80f1887cb7a00b554359c809a960b22851b57 SHA256 0be5b5d67a5198929b4c3db8c0dfa3a7a69150f02b075d7bafe0255825bdcbb9
-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
-AUX vmd-1.8.4-paratool.patch 1008 RMD160 40e707894c50fee586b2f3c042086c03c53ca97e SHA1 4c90456cd5bb41de60ed14b7397375d21ab4384f SHA256 e6853e4f260c91777adccac10fde29e1b3f9bec2231f47d15e92ac7d845f178b
-MD5 5885e749cea5fdb0e819d16d48159040 files/vmd-1.8.4-paratool.patch 1008
-RMD160 40e707894c50fee586b2f3c042086c03c53ca97e files/vmd-1.8.4-paratool.patch 1008
-SHA256 e6853e4f260c91777adccac10fde29e1b3f9bec2231f47d15e92ac7d845f178b files/vmd-1.8.4-paratool.patch 1008
-AUX vmd-1.8.4-plugin-autopsf.patch 723 RMD160 6ccb492685cdeedc762f16e6f8ba010e2833908a SHA1 a05dd68ac178b75bfdc7c1b4d8b079557837195e SHA256 7230d8f5f4281b7b8615cc7ff60fc3b77432b3ec12cc507f3016566178b07fae
-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
AUX vmd-1.8.5-config-gentoo.patch 4714 RMD160 192224a4a05e249c357f08e13d0811dcfb60f7ea SHA1 9b008b3313c969517dacf1c721e894151d0771f7 SHA256 8e7ac5124de52dbef9469c8416b1f011ffe3420043c5a58c2183b67dd66a6be9
MD5 d6b046bc901c4b95ac869c6298c03f3e files/vmd-1.8.5-config-gentoo.patch 4714
RMD160 192224a4a05e249c357f08e13d0811dcfb60f7ea files/vmd-1.8.5-config-gentoo.patch 4714
SHA256 8e7ac5124de52dbef9469c8416b1f011ffe3420043c5a58c2183b67dd66a6be9 files/vmd-1.8.5-config-gentoo.patch 4714
+AUX vmd-1.8.6-config-gentoo.patch 4666 RMD160 1fb149ab58292f42abbe4d658aff0334d3fe73f9 SHA1 27a7ea51772e93e858ef23bf09d819e75d6418b5 SHA256 6dc232ee1c01a56bb94bdf193f024e868f957a22b6c1c8666d2d443801a36f03
+MD5 f71b1bfc5279a8654b3366e9d24f3ccf files/vmd-1.8.6-config-gentoo.patch 4666
+RMD160 1fb149ab58292f42abbe4d658aff0334d3fe73f9 files/vmd-1.8.6-config-gentoo.patch 4666
+SHA256 6dc232ee1c01a56bb94bdf193f024e868f957a22b6c1c8666d2d443801a36f03 files/vmd-1.8.6-config-gentoo.patch 4666
DIST vmd-1.8.5.src.tar.gz 17106456 RMD160 70087a42ae20180f2ed18cc4492764ed24b19aa4 SHA1 c3da36d75262b75423ddd2a07c17415b9859504a SHA256 208d7829e4fc2744e30c778e1485b96d35018b1e0dbc02388630ce4a2733c30b
+DIST vmd-1.8.6.src.tar.gz 18045341 RMD160 66f8ee5a0313000ea8dd3cb79881fd26a2836a79 SHA1 62ceaab06c7fec7c2c8e9a2d7f08c83ba662679d SHA256 fe2bcf7ffea1ed6b3a7f2402d6e1cb1d6def588a8b09a5d0943c0a9f3426ead2
EBUILD vmd-1.8.5.ebuild 4118 RMD160 32fe8507cbab20939a01ac8df1a2cde388223ce6 SHA1 f1b02ea48248eeef051c3c48004ef5e47d9bb3a9 SHA256 7a21e404aaaebf1d3c3ebd6a259f4af704a22b8586e3d98dda6978211d5a147b
MD5 424d8c1a087c47c1e24f47ef6f4cd0c9 vmd-1.8.5.ebuild 4118
RMD160 32fe8507cbab20939a01ac8df1a2cde388223ce6 vmd-1.8.5.ebuild 4118
SHA256 7a21e404aaaebf1d3c3ebd6a259f4af704a22b8586e3d98dda6978211d5a147b vmd-1.8.5.ebuild 4118
-MISC ChangeLog 2521 RMD160 a986021ffabfd109829223b19fb715186803e927 SHA1 eef0b1f6cc2baaf64b6fcf9fd271886cf75a33b5 SHA256 dba0f86d6116e0ea7944ac6ccf423dfe55a014d607e41ca7606e5a6c592a9994
-MD5 057a363ef58730f5dcf07ed357121c41 ChangeLog 2521
-RMD160 a986021ffabfd109829223b19fb715186803e927 ChangeLog 2521
-SHA256 dba0f86d6116e0ea7944ac6ccf423dfe55a014d607e41ca7606e5a6c592a9994 ChangeLog 2521
+EBUILD vmd-1.8.6.ebuild 3956 RMD160 a1462c5669f926d7a628c9f226414509623770f0 SHA1 6542ab3209d6e6b61a2d1cf57be26085410c1aa1 SHA256 f6a4a9ff1d231593bbbccb3b318155c1b8a15262301b2b08b555464705428f19
+MD5 00d8e08b9c78a4feb6c19746b45162bd vmd-1.8.6.ebuild 3956
+RMD160 a1462c5669f926d7a628c9f226414509623770f0 vmd-1.8.6.ebuild 3956
+SHA256 f6a4a9ff1d231593bbbccb3b318155c1b8a15262301b2b08b555464705428f19 vmd-1.8.6.ebuild 3956
+MISC ChangeLog 2888 RMD160 016ebb6210ea5b06cfc59e2a7c6da3e13ce0eb0f SHA1 3dd52b197ef2aba6643ca03901a6a0cdfe4409c6 SHA256 d8cc572836b299a7bd1ef860250282844a1c348f5ff4fa00e1ca8cab5a2ed4e0
+MD5 fe52458ae4ca2b353ed2a31eb5f49796 ChangeLog 2888
+RMD160 016ebb6210ea5b06cfc59e2a7c6da3e13ce0eb0f ChangeLog 2888
+SHA256 d8cc572836b299a7bd1ef860250282844a1c348f5ff4fa00e1ca8cab5a2ed4e0 ChangeLog 2888
MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349
MD5 cf7436fe44a27481d1001082eb06326e metadata.xml 282
RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 metadata.xml 282
MD5 147e30ebf64237e28be760bc5504caaf files/digest-vmd-1.8.5 247
RMD160 6841d16295791a86c1e65c14593aec2bc3156cc4 files/digest-vmd-1.8.5 247
SHA256 d4d4f88e2ab30537dc0995069a237ba823ac798e6d37a84ad7bbf7aecfd179d7 files/digest-vmd-1.8.5 247
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+MD5 1d5a461b901a2cf0179a3f192d9c133a files/digest-vmd-1.8.6 247
+RMD160 6387755bf0fce21fbcf107e63730f4767e417647 files/digest-vmd-1.8.6 247
+SHA256 91402ac4e4075d5775e4eba29482b77c89b098ae8a2f01e999415795c4863dd0 files/digest-vmd-1.8.6 247
--- /dev/null
+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
+++ /dev/null
-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
+++ /dev/null
-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*);
-
---- 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 @@
$install_name = "vmd";
# optionally override hard-coded defaults above with environment variables
-@@ -121,29 +121,6 @@
+@@ -123,29 +123,6 @@
# Configure script code begins here
############################################################################
#################### Parse command line options ###########
# list of allowed architectures
@archlist=('IRIX6', 'IRIX6_64', 'FREEBSD', 'HPUX11', 'AIX4', 'AIX5', 'AIX5_64', 'LINUX', 'LINUXALPHA', 'LINUXAMD64', 'LINUXIA64', 'LINUXPPC', 'MACOSX', 'MACOSXX86', 'TRU64', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
-@@ -406,8 +383,8 @@
+@@ -423,8 +400,8 @@
################ Plugin options
#
-$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";
+$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";
@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";
# 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 = "";
- $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";
+ }
--- /dev/null
+# 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"
+}
+
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