From 9d46232b51b154befd652a1a78a88d6af6529bba Mon Sep 17 00:00:00 2001 From: Markus Dittrich Date: Thu, 6 Aug 2009 14:19:15 +0000 Subject: Version bump (fixes bug #262275). (Portage version: 2.1.6.13/cvs/Linux x86_64) --- sci-chemistry/vmd/ChangeLog | 8 +- sci-chemistry/vmd/files/vmd-1.8.7-config.patch | 131 +++++++++++++++++ .../vmd/files/vmd-1.8.7-use-bash-startup.patch | 13 ++ sci-chemistry/vmd/vmd-1.8.7.ebuild | 157 +++++++++++++++++++++ 4 files changed, 308 insertions(+), 1 deletion(-) create mode 100644 sci-chemistry/vmd/files/vmd-1.8.7-config.patch create mode 100644 sci-chemistry/vmd/files/vmd-1.8.7-use-bash-startup.patch create mode 100644 sci-chemistry/vmd/vmd-1.8.7.ebuild (limited to 'sci-chemistry/vmd') 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 +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 vmd-1.8.6-r1.ebuild: Use elog for fetch error. 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" +} -- cgit v1.2.3-65-gdbad