diff options
Diffstat (limited to 'sci-chemistry/vmd')
| -rw-r--r-- | sci-chemistry/vmd/ChangeLog | 11 | ||||
| -rw-r--r-- | sci-chemistry/vmd/files/digest-vmd-1.8.6 | 3 | ||||
| -rw-r--r-- | sci-chemistry/vmd/files/vmd-1.8.4-paratool.patch | 28 | ||||
| -rw-r--r-- | sci-chemistry/vmd/files/vmd-1.8.4-plugin-autopsf.patch | 24 | ||||
| -rw-r--r--[-rwxr-xr-x] | sci-chemistry/vmd/files/vmd-1.8.6-config-gentoo.patch (renamed from sci-chemistry/vmd/files/vmd-1.8.4-config-gentoo.patch) | 37 | ||||
| -rw-r--r-- | sci-chemistry/vmd/vmd-1.8.6.ebuild | 148 |
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" +} + |