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authorPacho Ramos <pacho@gentoo.org>2021-05-02 21:22:03 +0200
committerPacho Ramos <pacho@gentoo.org>2021-05-02 21:22:23 +0200
commit8c9499c1d811547d4d69f60d5b78ae7edacdd922 (patch)
treee5208d22e3202acef813f7021ad5326959fb012d /sci-chemistry/vmd/files
parentsci-chemistry/pymol: Re-host distfiles (diff)
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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.patch276
-rw-r--r--sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch11
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);