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author | 2021-05-02 21:22:03 +0200 | |
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committer | 2021-05-02 21:22:23 +0200 | |
commit | 8c9499c1d811547d4d69f60d5b78ae7edacdd922 (patch) | |
tree | e5208d22e3202acef813f7021ad5326959fb012d /sci-chemistry/vmd/files | |
parent | sci-chemistry/pymol: Re-host distfiles (diff) | |
download | gentoo-8c9499c1d811547d4d69f60d5b78ae7edacdd922.tar.gz gentoo-8c9499c1d811547d4d69f60d5b78ae7edacdd922.tar.bz2 gentoo-8c9499c1d811547d4d69f60d5b78ae7edacdd922.zip |
sci-chemistry/vmd: Drop old
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Pacho Ramos <pacho@gentoo.org>
Diffstat (limited to 'sci-chemistry/vmd/files')
-rw-r--r-- | sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch | 276 | ||||
-rw-r--r-- | sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch | 11 |
2 files changed, 0 insertions, 287 deletions
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch deleted file mode 100644 index ca74b868d8f4..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch +++ /dev/null @@ -1,276 +0,0 @@ ---- a/bin/vmd.sh.old 2020-09-09 18:02:09.135798193 +0200 -+++ b/bin/vmd.sh 2020-09-09 18:37:22.355511675 +0200 -@@ -436,6 +436,7 @@ - - # set the path to a few external programs - # Stride -- used to generate cartoon representations etc. -+export STRIDE_BIN="gentoo-stride" - if [ -z "$STRIDE_BIN" ] - then - if [ -x "$MASTERVMDDIR/stride_$ARCH" ] -@@ -446,6 +447,7 @@ - fi - - # Surf -- used to generate molecular surfaces -+export SURF_BIN="gentoo-surf" - if [ -z "$SURF_BIN" ] - then - if [ -x "$MASTERVMDDIR/surf_$ARCH" ] -@@ -456,6 +458,7 @@ - fi - - # Tachyon -- used to generate ray traced graphics -+export TACHYON_BIN="gentoo-tachyon" - if [ -z "$TACHYON_BIN" ] - then - if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ] ---- a/configure.old 2020-09-09 18:05:55.778655084 +0200 -+++ b/configure 2020-09-09 18:38:01.607083112 +0200 -@@ -13,11 +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/$install_name"; - - # optionally override hard-coded defaults above with environment variables - if ($ENV{VMDINSTALLNAME}) { -@@ -143,29 +142,6 @@ - # 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=('AIX6_64', 'ANDROIDARMV7A', 'BLUEGENEQ', 'BLUEWATERS', 'CRAY_XC', 'CRAY_XK', 'FREEBSD', 'FREEBSDAMD64', 'LINUX', 'LINUXAMD64', 'LINUXARM64', 'LINUXCARMA', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'OPENPOWER', 'SUMMIT', 'SUMMITDEV', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64'); -@@ -493,7 +469,7 @@ - - $arch_cc = "cc"; - $arch_ccpp = "CC"; --$arch_nvcc = "/usr/local/cuda-10.2/bin/nvcc"; -+$arch_nvcc = "gentoo-nvcc"; - $arch_nvccflags = "-lineinfo --ptxas-options=-v " . - "-gencode arch=compute_30,code=compute_30 " . - "-gencode arch=compute_30,code=sm_35 " . -@@ -537,7 +513,7 @@ - - ################ Plugin options - # --$plugin_dir = "../plugins"; -+$plugin_dir = "gentoo-plugindir"; - $plugin_include = "-I$plugin_dir/include"; - $plugin_library = ""; - $plugin_libs = ""; -@@ -550,7 +526,7 @@ - @plugin_extra = (); - - if ($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"; -@@ -715,8 +691,8 @@ - ################ 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"; - $fltk_libs = "-lfltk -lX11"; - #@fltk_cc = ('forms_ui.c'); - @fltk_cu = (); -@@ -777,8 +753,8 @@ - if ($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 = (); -@@ -1289,8 +1265,8 @@ - # This may be commented out if not required. - $libtachyon_defines = "-DVMDLIBTACHYON"; - $libtachyon_dir = "$vmd_library_dir/tachyon"; --$libtachyon_include = "-I$libtachyon_dir/include"; --$libtachyon_library = "-L$libtachyon_dir/lib_$config_arch"; -+$libtachyon_include = "-Igentoo-libtachyon-include"; -+$libtachyon_library = "-Lgentoo-libtachyon-libs"; - $libtachyon_libs = "-ltachyon"; - @libtachyon_cc = (); - @libtachyon_cu = (); -@@ -1541,8 +1517,8 @@ - ####################### - $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"; - $netcdf_libs = "-lnetcdf"; - @netcdf_cc = (); - @netcdf_cu = (); -@@ -1595,6 +1571,7 @@ - #$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib"; - $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.5"; - $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config"; -+$stock_python_library=$ENV{"PYTHON_LIBRARY"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config"; - - #$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include"; - #$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib"; -@@ -1604,7 +1581,7 @@ - $python_defines = "-DVMDPYTHON"; - $python_include = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir"; - $python_library = "-L$stock_python_library_dir"; --$python_libs = "-lpython2.5 -lpthread"; -+$python_libs = "$stock_python_library -lpthread"; - @python_h = ('PythonTextInterp.h', - 'VMDTkinterMenu.h', - 'py_commands.h', -@@ -2350,8 +2327,8 @@ - - # XFree 4.0 Direct Rendering Interface and GLX - $opengl_dep_dir = "/usr/X11R6"; -- $opengl_dep_include = "-I$opengl_dep_dir/include"; -- $opengl_dep_library = "-L$opengl_dep_dir/lib"; -+ $opengl_dep_include = "-Igentoo-opengl-include"; -+ $opengl_dep_library = "-Lgentoo-opengl-libs"; - $opengl_dep_libs = "-lGL"; - # $opengl_dep_libs = "-L/usr/X11R6/lib -lGL -lXext -lX11"; - -@@ -2381,15 +2358,15 @@ - $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 -Wno-unknown-pragmas -O3"; -- $arch_copts = "-m32 -Wall -Wno-unknown-pragmas -O3"; -+ $arch_shldopts = "gentoo-ldflags"; -+ $arch_opt_flag = "gentoo-cflags"; -+ $arch_copts = "gentoo-cflags"; - - if ($config_static) { - $arch_lopts = "-static"; -@@ -2407,14 +2384,13 @@ - - $arch_cppopts = ""; - if ($config_cuda) { -- $arch_nvcc = "/usr/local/cuda-4.0/bin/nvcc"; - $arch_nvccflags = "--ptxas-options=-v " . - "-gencode arch=compute_13,code=sm_13 " . - "-gencode arch=compute_20,code=sm_20 " . - "-gencode arch=compute_20,code=compute_20 " . - "--ftz=true "; -- $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include"; -- $cuda_library = "-L/usr/local/cuda-4.0/lib"; -+ $arch_nvccflags .= "gentoo-nvflags $cuda_include"; -+ $cuda_library = "-Lgentoo-cuda-lib"; - $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart"; - } - # this is to make tcl happy -@@ -2513,7 +2489,7 @@ - - if ($config_cuda) { - $arch_nvccflags .= " --machine 64 -O3 $cuda_include"; -- $cuda_library = "-L/usr/local/cuda-10.2/lib64"; -+ $cuda_library = "-Lgentoo-cuda-lib"; - } - - $arch_lex = "flex"; # has problems with vendor lex -@@ -3502,11 +3478,11 @@ - 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) -@@ -3555,7 +3531,7 @@ - $config_progname: y.tab.h \$(VMD_OBJS) \$(VMD_PTX) - \$(ECHO) "Linking " \$\@ "..."; \\ - \$(CD) $vmd_arch_dir ; \\ -- \$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; -+ \$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; - \$(COMPILERC) \$(RCFLAGS) - - install: -@@ -3596,8 +3572,7 @@ - -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$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 ; \\ ---- a/src/Makefile.old 2020-09-09 18:22:46.234818925 +0200 -+++ b/src/Makefile 2020-09-09 18:37:22.356511690 +0200 -@@ -647,7 +647,7 @@ - vmd_LINUXAMD64: y.tab.h $(VMD_OBJS) $(VMD_PTX) - $(ECHO) "Linking " $@ "..."; \ - $(CD) ../LINUXAMD64 ; \ -- $(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; -+ $(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; - $(COMPILERC) $(RCFLAGS) - - install: -@@ -660,10 +660,6 @@ - if [ ! -d "/usr/local/lib/vmd"/doc ]; then \ - $(MAKEDIR) "/usr/local/lib/vmd"/doc; \ - fi -- -$(COPY) ../Announcement "/usr/local/lib/vmd" -- -$(COPY) ../README "/usr/local/lib/vmd" -- -$(COPY) ../LICENSE "/usr/local/lib/vmd" -- -$(COPY) ../doc/ug.pdf "/usr/local/lib/vmd"/doc - if [ -f /usr/local/lib/vmd/vmd_LINUXAMD64 ]; then \ - $(MOVE) "/usr/local/lib/vmd/vmd_LINUXAMD64" "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi - -$(COPY) ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd" diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch deleted file mode 100644 index 295811db0580..000000000000 --- a/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/scripts/vmd/chemical2vmd.old 2020-09-09 18:40:56.795215443 +0200 -+++ b/scripts/vmd/chemical2vmd 2020-09-09 18:41:09.648348701 +0200 -@@ -61,7 +61,7 @@ - - - # Make a temp. file to store the load command --$ENV{'TMPDIR'} = '/usr/tmp' if !$ENV{'TMPDIR'}; -+$ENV{'TMPDIR'} = '/tmp' if !$ENV{'TMPDIR'}; - sub tmpfile { - local ($tempfile) = $ENV{'TMPDIR'} . '/chemical2vmd.' . $$; - local ($i); |