1 |
commit: 8c9499c1d811547d4d69f60d5b78ae7edacdd922 |
2 |
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org> |
3 |
AuthorDate: Sun May 2 19:22:03 2021 +0000 |
4 |
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org> |
5 |
CommitDate: Sun May 2 19:22:23 2021 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8c9499c1 |
7 |
|
8 |
sci-chemistry/vmd: Drop old |
9 |
|
10 |
Package-Manager: Portage-3.0.18, Repoman-3.0.3 |
11 |
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org> |
12 |
|
13 |
sci-chemistry/vmd/Manifest | 3 - |
14 |
.../vmd/files/vmd-1.9.4-gentoo-paths.patch | 276 -------------------- |
15 |
sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch | 11 - |
16 |
sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild | 277 --------------------- |
17 |
4 files changed, 567 deletions(-) |
18 |
|
19 |
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest |
20 |
index a94593a65fc..dbb4249c928 100644 |
21 |
--- a/sci-chemistry/vmd/Manifest |
22 |
+++ b/sci-chemistry/vmd/Manifest |
23 |
@@ -1,5 +1,2 @@ |
24 |
-DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1 |
25 |
-DIST vmd-1.9.4-gentoo-plugins.patch 24618 BLAKE2B 6fbcf2e3bb59765e0980a5ed46f02e29d7b72a313865849c15891f2398d2aaf9afe6069f993a61257572d031556ce523c622858e29611ca6795be6030f4bb186 SHA512 9b8675811992d6392e9ec49cdcbcfd0da99dce1e164be4f8bf9bd07e0582b6b1e1d25f3e90fbc91cad7f94984bd091e644713c136628d0e4cc60e782a855fb63 |
26 |
DIST vmd-1.9.4_alpha51-gentoo-patches.tar.xz 14604 BLAKE2B f8621956785d365cc056ba53373120d8f99da1476ab9789af6bb8ef00b8dd8c2a4c3599d75e13eba2fc5630b291aed966ce64f7f408504b079e3e994e45da243 SHA512 c57fd81e667e405ab1208a4e4a1d63710e593c07f554420c32980becd3547c2df98fbf6e439a53a626121fc361559f1ba53ab7b7235c97422bba61ece59d23bc |
27 |
-DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0 |
28 |
DIST vmd-1.9.4a51.src.tar.gz 42826371 BLAKE2B 239d87f975c41a71096083028c1db8bf40cc058fc687fd9fff3c14c97c9b12bd68818d4c2eaeefd8c95c661409f1f056bce42178d0ba9271aa344fdce6f81ea9 SHA512 b42af6a4a7b1d2f0d242f89bff3a1c25a608ff59b9902b90154ba82a40439afb802a2d319363fa388a5211420fdaf0ee9bfd1f0a0e6e85d89d1dd506b373ba40 |
29 |
|
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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 |
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deleted file mode 100644 |
32 |
index ca74b868d8f..00000000000 |
33 |
--- a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch |
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+++ /dev/null |
35 |
@@ -1,276 +0,0 @@ |
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---- a/bin/vmd.sh.old 2020-09-09 18:02:09.135798193 +0200 |
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-+++ b/bin/vmd.sh 2020-09-09 18:37:22.355511675 +0200 |
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-@@ -436,6 +436,7 @@ |
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- |
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- # set the path to a few external programs |
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- # Stride -- used to generate cartoon representations etc. |
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-+export STRIDE_BIN="gentoo-stride" |
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- if [ -z "$STRIDE_BIN" ] |
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- then |
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- if [ -x "$MASTERVMDDIR/stride_$ARCH" ] |
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-@@ -446,6 +447,7 @@ |
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- fi |
48 |
- |
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- # Surf -- used to generate molecular surfaces |
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-+export SURF_BIN="gentoo-surf" |
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- if [ -z "$SURF_BIN" ] |
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- then |
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- if [ -x "$MASTERVMDDIR/surf_$ARCH" ] |
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-@@ -456,6 +458,7 @@ |
55 |
- fi |
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- |
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- # Tachyon -- used to generate ray traced graphics |
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-+export TACHYON_BIN="gentoo-tachyon" |
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- if [ -z "$TACHYON_BIN" ] |
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- then |
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- if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ] |
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---- a/configure.old 2020-09-09 18:05:55.778655084 +0200 |
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-+++ b/configure 2020-09-09 18:38:01.607083112 +0200 |
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-@@ -13,11 +13,10 @@ |
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- $install_name = "vmd"; |
66 |
- |
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- # Directory where VMD startup script is installed, should be in users' paths. |
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--$install_bin_dir="/usr/local/bin"; |
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-+$install_bin_dir="gentoo-bindir"; |
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- |
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- # Directory where VMD files and executables are installed |
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--$install_library_dir="/usr/local/lib/$install_name"; |
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-- |
74 |
-+$install_library_dir="gentoo-libdir/$install_name"; |
75 |
- |
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- # optionally override hard-coded defaults above with environment variables |
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- if ($ENV{VMDINSTALLNAME}) { |
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-@@ -143,29 +142,6 @@ |
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- # Configure script code begins here |
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- ############################################################################ |
81 |
- |
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--## Test for existence of a properly compiled plugin tree |
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--if (!(-e "plugins")) { |
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-- print "\n"; |
85 |
-- print "VMD plugin directory not found.\n"; |
86 |
-- print "Please compile the VMD plugins and do 'make distrib' to copy them\n"; |
87 |
-- print "into a 'plugins' directory linked or located in this directory.\n"; |
88 |
-- print "Be sure your PLUGINDIR environment variable is set before running\n"; |
89 |
-- print "'make distrib' in the plugin build area.\n"; |
90 |
-- print "\n"; |
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-- die "Halting configuration until VMD plugins are built.\n"; |
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--} else { |
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-- if (!(-e "plugins/include/vmdplugin.h")) { |
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-- print "\n"; |
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-- print "VMD plugin include files or directory not found.\n"; |
96 |
-- print "Please compile the VMD plugins and do 'make distrib' to copy them\n"; |
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-- print "into a 'plugins' directory linked or located in this directory.\n"; |
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-- print "Be sure your PLUGINDIR environment variable is set before running\n"; |
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-- print "'make distrib' in the plugin build area.\n"; |
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-- print "\n"; |
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-- die "Halting configuration until VMD plugins are built.\n"; |
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-- } |
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--} |
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-- |
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- #################### Parse command line options ########### |
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- # list of allowed architectures |
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- @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'); |
108 |
-@@ -493,7 +469,7 @@ |
109 |
- |
110 |
- $arch_cc = "cc"; |
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- $arch_ccpp = "CC"; |
112 |
--$arch_nvcc = "/usr/local/cuda-10.2/bin/nvcc"; |
113 |
-+$arch_nvcc = "gentoo-nvcc"; |
114 |
- $arch_nvccflags = "-lineinfo --ptxas-options=-v " . |
115 |
- "-gencode arch=compute_30,code=compute_30 " . |
116 |
- "-gencode arch=compute_30,code=sm_35 " . |
117 |
-@@ -537,7 +513,7 @@ |
118 |
- |
119 |
- ################ Plugin options |
120 |
- # |
121 |
--$plugin_dir = "../plugins"; |
122 |
-+$plugin_dir = "gentoo-plugindir"; |
123 |
- $plugin_include = "-I$plugin_dir/include"; |
124 |
- $plugin_library = ""; |
125 |
- $plugin_libs = ""; |
126 |
-@@ -550,7 +526,7 @@ |
127 |
- @plugin_extra = (); |
128 |
- |
129 |
- if ($config_staticplugin) { |
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-- $molfile_dir = "$plugin_dir/$config_arch/molfile"; |
131 |
-+ $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile"; |
132 |
- $plugin_include .= " -I$molfile_dir"; |
133 |
- $plugin_library .= " -L$molfile_dir"; |
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- $plugin_libs .= " -lmolfile_plugin"; |
135 |
-@@ -715,8 +691,8 @@ |
136 |
- ################ FLTK GUI |
137 |
- $fltk_defines = "-DVMDGUI -DVMDFLTK"; |
138 |
- $fltk_dir = "$vmd_library_dir/fltk"; |
139 |
--$fltk_include = "-I$fltk_dir/include"; |
140 |
--$fltk_library = "-L$fltk_dir/$config_arch"; |
141 |
-+$fltk_include = "-Igentoo-fltk-include"; |
142 |
-+$fltk_library = "-Lgentoo-fltk-libs"; |
143 |
- $fltk_libs = "-lfltk -lX11"; |
144 |
- #@fltk_cc = ('forms_ui.c'); |
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- @fltk_cu = (); |
146 |
-@@ -777,8 +753,8 @@ |
147 |
- if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; } |
148 |
- $tcl_library = "-L$stock_tcl_library_dir"; |
149 |
- if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; } |
150 |
--$tcl_libs = "-ltcl8.5"; |
151 |
--if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; } |
152 |
-+$tcl_libs = "-ltcl"; |
153 |
-+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; } |
154 |
- |
155 |
- @tcl_cc = (); |
156 |
- @tcl_cu = (); |
157 |
-@@ -1289,8 +1265,8 @@ |
158 |
- # This may be commented out if not required. |
159 |
- $libtachyon_defines = "-DVMDLIBTACHYON"; |
160 |
- $libtachyon_dir = "$vmd_library_dir/tachyon"; |
161 |
--$libtachyon_include = "-I$libtachyon_dir/include"; |
162 |
--$libtachyon_library = "-L$libtachyon_dir/lib_$config_arch"; |
163 |
-+$libtachyon_include = "-Igentoo-libtachyon-include"; |
164 |
-+$libtachyon_library = "-Lgentoo-libtachyon-libs"; |
165 |
- $libtachyon_libs = "-ltachyon"; |
166 |
- @libtachyon_cc = (); |
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- @libtachyon_cu = (); |
168 |
-@@ -1541,8 +1517,8 @@ |
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- ####################### |
170 |
- $netcdf_defines = ""; |
171 |
- $netcdf_dir = "$vmd_library_dir/netcdf"; |
172 |
--$netcdf_include = "-I$netcdf_dir/include"; |
173 |
--$netcdf_library = "-L$netcdf_dir/lib_$config_arch"; |
174 |
-+$netcdf_include = "-Igentoo-netcdf-include"; |
175 |
-+$netcdf_library = "-Lgentoo-netcdf-libs"; |
176 |
- $netcdf_libs = "-lnetcdf"; |
177 |
- @netcdf_cc = (); |
178 |
- @netcdf_cu = (); |
179 |
-@@ -1595,6 +1571,7 @@ |
180 |
- #$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib"; |
181 |
- $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.5"; |
182 |
- $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config"; |
183 |
-+$stock_python_library=$ENV{"PYTHON_LIBRARY"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config"; |
184 |
- |
185 |
- #$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include"; |
186 |
- #$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib"; |
187 |
-@@ -1604,7 +1581,7 @@ |
188 |
- $python_defines = "-DVMDPYTHON"; |
189 |
- $python_include = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir"; |
190 |
- $python_library = "-L$stock_python_library_dir"; |
191 |
--$python_libs = "-lpython2.5 -lpthread"; |
192 |
-+$python_libs = "$stock_python_library -lpthread"; |
193 |
- @python_h = ('PythonTextInterp.h', |
194 |
- 'VMDTkinterMenu.h', |
195 |
- 'py_commands.h', |
196 |
-@@ -2350,8 +2327,8 @@ |
197 |
- |
198 |
- # XFree 4.0 Direct Rendering Interface and GLX |
199 |
- $opengl_dep_dir = "/usr/X11R6"; |
200 |
-- $opengl_dep_include = "-I$opengl_dep_dir/include"; |
201 |
-- $opengl_dep_library = "-L$opengl_dep_dir/lib"; |
202 |
-+ $opengl_dep_include = "-Igentoo-opengl-include"; |
203 |
-+ $opengl_dep_library = "-Lgentoo-opengl-libs"; |
204 |
- $opengl_dep_libs = "-lGL"; |
205 |
- # $opengl_dep_libs = "-L/usr/X11R6/lib -lGL -lXext -lX11"; |
206 |
- |
207 |
-@@ -2381,15 +2358,15 @@ |
208 |
- $arch_lopts .= "-i-static "; |
209 |
- } else { |
210 |
- # compling with GCC |
211 |
-- $arch_cc = "gcc"; |
212 |
-- $arch_ccpp = "g++"; |
213 |
-+ $arch_cc = "gentoo-gcc"; |
214 |
-+ $arch_ccpp = "gentoo-g++"; |
215 |
- $arch_depend_flag = "-MM"; |
216 |
-- $arch_shld = "g++ -shared"; |
217 |
-+ $arch_shld = "gentoo-g++ -shared"; |
218 |
- $arch_shlibname = "so"; |
219 |
- $arch_shcppopts = "-fPIC"; |
220 |
-- $arch_shldopts = ""; |
221 |
-- $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3"; |
222 |
-- $arch_copts = "-m32 -Wall -Wno-unknown-pragmas -O3"; |
223 |
-+ $arch_shldopts = "gentoo-ldflags"; |
224 |
-+ $arch_opt_flag = "gentoo-cflags"; |
225 |
-+ $arch_copts = "gentoo-cflags"; |
226 |
- |
227 |
- if ($config_static) { |
228 |
- $arch_lopts = "-static"; |
229 |
-@@ -2407,14 +2384,13 @@ |
230 |
- |
231 |
- $arch_cppopts = ""; |
232 |
- if ($config_cuda) { |
233 |
-- $arch_nvcc = "/usr/local/cuda-4.0/bin/nvcc"; |
234 |
- $arch_nvccflags = "--ptxas-options=-v " . |
235 |
- "-gencode arch=compute_13,code=sm_13 " . |
236 |
- "-gencode arch=compute_20,code=sm_20 " . |
237 |
- "-gencode arch=compute_20,code=compute_20 " . |
238 |
- "--ftz=true "; |
239 |
-- $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include"; |
240 |
-- $cuda_library = "-L/usr/local/cuda-4.0/lib"; |
241 |
-+ $arch_nvccflags .= "gentoo-nvflags $cuda_include"; |
242 |
-+ $cuda_library = "-Lgentoo-cuda-lib"; |
243 |
- $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart"; |
244 |
- } |
245 |
- # this is to make tcl happy |
246 |
-@@ -2513,7 +2489,7 @@ |
247 |
- |
248 |
- if ($config_cuda) { |
249 |
- $arch_nvccflags .= " --machine 64 -O3 $cuda_include"; |
250 |
-- $cuda_library = "-L/usr/local/cuda-10.2/lib64"; |
251 |
-+ $cuda_library = "-Lgentoo-cuda-lib"; |
252 |
- } |
253 |
- |
254 |
- $arch_lex = "flex"; # has problems with vendor lex |
255 |
-@@ -3502,11 +3478,11 @@ |
256 |
- DEFINES = $DEFINES |
257 |
- |
258 |
- # compiler and compiler directives |
259 |
--CC = $arch_cc |
260 |
--CFLAGS = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags |
261 |
-+CC = gentoo-gcc |
262 |
-+CFLAGS = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags |
263 |
- |
264 |
--CCPP = $arch_ccpp |
265 |
--CPPFLAGS = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags |
266 |
-+CCPP = gentoo-g++ |
267 |
-+CPPFLAGS = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags |
268 |
- |
269 |
- NVCC = $arch_nvcc |
270 |
- NVCCFLAGS = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) |
271 |
-@@ -3555,7 +3531,7 @@ |
272 |
- $config_progname: y.tab.h \$(VMD_OBJS) \$(VMD_PTX) |
273 |
- \$(ECHO) "Linking " \$\@ "..."; \\ |
274 |
- \$(CD) $vmd_arch_dir ; \\ |
275 |
-- \$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; |
276 |
-+ \$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ; |
277 |
- \$(COMPILERC) \$(RCFLAGS) |
278 |
- |
279 |
- install: |
280 |
-@@ -3596,8 +3572,7 @@ |
281 |
- -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir" |
282 |
- \$(CD) $vmd_bin_dir ; \\ |
283 |
- if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\ |
284 |
-- if [ ! -x "/bin/csh" ]; then \\ |
285 |
-- \$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\ |
286 |
-+ if [ -x "/bin/bash" ]; then \\ |
287 |
- \$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\ |
288 |
- \$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\ |
289 |
- \$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\ |
290 |
---- a/src/Makefile.old 2020-09-09 18:22:46.234818925 +0200 |
291 |
-+++ b/src/Makefile 2020-09-09 18:37:22.356511690 +0200 |
292 |
-@@ -647,7 +647,7 @@ |
293 |
- vmd_LINUXAMD64: y.tab.h $(VMD_OBJS) $(VMD_PTX) |
294 |
- $(ECHO) "Linking " $@ "..."; \ |
295 |
- $(CD) ../LINUXAMD64 ; \ |
296 |
-- $(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; |
297 |
-+ $(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ; |
298 |
- $(COMPILERC) $(RCFLAGS) |
299 |
- |
300 |
- install: |
301 |
-@@ -660,10 +660,6 @@ |
302 |
- if [ ! -d "/usr/local/lib/vmd"/doc ]; then \ |
303 |
- $(MAKEDIR) "/usr/local/lib/vmd"/doc; \ |
304 |
- fi |
305 |
-- -$(COPY) ../Announcement "/usr/local/lib/vmd" |
306 |
-- -$(COPY) ../README "/usr/local/lib/vmd" |
307 |
-- -$(COPY) ../LICENSE "/usr/local/lib/vmd" |
308 |
-- -$(COPY) ../doc/ug.pdf "/usr/local/lib/vmd"/doc |
309 |
- if [ -f /usr/local/lib/vmd/vmd_LINUXAMD64 ]; then \ |
310 |
- $(MOVE) "/usr/local/lib/vmd/vmd_LINUXAMD64" "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi |
311 |
- -$(COPY) ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd" |
312 |
|
313 |
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch |
314 |
deleted file mode 100644 |
315 |
index 295811db058..00000000000 |
316 |
--- a/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch |
317 |
+++ /dev/null |
318 |
@@ -1,11 +0,0 @@ |
319 |
---- a/scripts/vmd/chemical2vmd.old 2020-09-09 18:40:56.795215443 +0200 |
320 |
-+++ b/scripts/vmd/chemical2vmd 2020-09-09 18:41:09.648348701 +0200 |
321 |
-@@ -61,7 +61,7 @@ |
322 |
- |
323 |
- |
324 |
- # Make a temp. file to store the load command |
325 |
--$ENV{'TMPDIR'} = '/usr/tmp' if !$ENV{'TMPDIR'}; |
326 |
-+$ENV{'TMPDIR'} = '/tmp' if !$ENV{'TMPDIR'}; |
327 |
- sub tmpfile { |
328 |
- local ($tempfile) = $ENV{'TMPDIR'} . '/chemical2vmd.' . $$; |
329 |
- local ($i); |
330 |
|
331 |
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild |
332 |
deleted file mode 100644 |
333 |
index 417828a3209..00000000000 |
334 |
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild |
335 |
+++ /dev/null |
336 |
@@ -1,277 +0,0 @@ |
337 |
-# Copyright 1999-2020 Gentoo Authors |
338 |
-# Distributed under the terms of the GNU General Public License v2 |
339 |
- |
340 |
-EAPI=7 |
341 |
-PYTHON_COMPAT=( python3_{7..9} ) |
342 |
- |
343 |
-inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg |
344 |
- |
345 |
-DESCRIPTION="Visual Molecular Dynamics" |
346 |
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" |
347 |
- |
348 |
-MY_PV="${PV/_alpha/a}" |
349 |
-MY_P="${PN}-${MY_PV}" |
350 |
-SRC_URI=" |
351 |
- ${MY_P}.src.tar |
352 |
- https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz |
353 |
- https://dev.gentoo.org/~juippis/distfiles/tmp/vmd-1.9.4-gentoo-plugins.patch |
354 |
-" |
355 |
- |
356 |
-SLOT="0" |
357 |
-LICENSE="vmd" |
358 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
359 |
- |
360 |
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama" |
361 |
-REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
362 |
- |
363 |
-RESTRICT="fetch" |
364 |
- |
365 |
-CDEPEND=" |
366 |
- >=dev-lang/tk-8.6.1:0= |
367 |
- dev-lang/perl |
368 |
- dev-libs/expat |
369 |
- $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_MULTI_USEDEP}]') |
370 |
- sci-libs/netcdf:0= |
371 |
- virtual/opengl |
372 |
- >=x11-libs/fltk-1.1.10-r2:1 |
373 |
- x11-libs/libXft |
374 |
- x11-libs/libXi |
375 |
- ${PYTHON_DEPS} |
376 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) |
377 |
- gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) |
378 |
- sqlite? ( dev-db/sqlite:3= ) |
379 |
- tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) |
380 |
- xinerama? ( x11-libs/libXinerama ) |
381 |
-" |
382 |
-DEPEND="${CDEPEND}" |
383 |
-BDEPEND=" |
384 |
- virtual/pkgconfig |
385 |
- dev-lang/swig |
386 |
-" |
387 |
-RDEPEND="${CDEPEND} |
388 |
- sci-biology/stride |
389 |
- sci-chemistry/chemical-mime-data |
390 |
- sci-chemistry/surf |
391 |
- x11-terms/xterm |
392 |
- msms? ( sci-chemistry/msms-bin ) |
393 |
- povray? ( media-gfx/povray ) |
394 |
-" |
395 |
- |
396 |
-S="${WORKDIR}/${MY_P}" |
397 |
- |
398 |
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" |
399 |
-# Binary only plugin!! |
400 |
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf/bin/intersurf.so" |
401 |
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil" |
402 |
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil" |
403 |
- |
404 |
-pkg_nofetch() { |
405 |
- elog "Please download ${MY_P}.src.tar from" |
406 |
- elog "${VMD_DOWNLOAD}" |
407 |
- elog "after agreeing to the license and get" |
408 |
- elog "https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz" |
409 |
- elog "https://dev.gentoo.org/~juippis/distfiles/tmp/vmd-1.9.4-gentoo-plugins.patch" |
410 |
- elog "Place them into your DISTDIR directory" |
411 |
- elog |
412 |
- elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources" |
413 |
- elog "file may get downloaded as a compressed tarball or not. In that case" |
414 |
- elog "you will need to ensure you uncompress the file and rename it" |
415 |
- elog "to ${MY_P}.src.tar" |
416 |
-} |
417 |
- |
418 |
-src_prepare() { |
419 |
- # Apply user patches from ${WORKDIR} to allow patching on patches |
420 |
- # subdir too |
421 |
- cd "${WORKDIR}" |
422 |
- xdg_src_prepare |
423 |
- |
424 |
- # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html |
425 |
- # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html |
426 |
- eapply "${DISTDIR}"/${PN}-1.9.4-gentoo-plugins.patch |
427 |
- |
428 |
- use cuda && cuda_sanitize |
429 |
- |
430 |
- # Prepare plugins |
431 |
- cd plugins || die |
432 |
- |
433 |
- sed '/^.SILENT/d' -i $(find -name Makefile) |
434 |
- |
435 |
- sed \ |
436 |
- -e "s:CC = gcc:CC = $(tc-getCC):" \ |
437 |
- -e "s:CXX = g++:CXX = $(tc-getCXX):" \ |
438 |
- -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ |
439 |
- -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ |
440 |
- -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ |
441 |
- -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ |
442 |
- -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ |
443 |
- -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ |
444 |
- -e "s:-ltcl8.5:-ltcl:" \ |
445 |
- -i Make-arch || die "Failed to set up plugins Makefile" |
446 |
- |
447 |
- sed \ |
448 |
- -e '/^AR /s:=:?=:g' \ |
449 |
- -e '/^RANLIB /s:=:?=:g' \ |
450 |
- -i ../plugins/*/Makefile || die |
451 |
- |
452 |
- tc-export AR RANLIB |
453 |
- |
454 |
- sed \ |
455 |
- -e "s:\$(CXXFLAGS)::g" \ |
456 |
- -i hesstrans/Makefile || die |
457 |
- |
458 |
- # prepare vmd itself |
459 |
- cd "${S}" || die |
460 |
- |
461 |
- eapply "${FILESDIR}"/${PN}-1.9.4-gentoo-paths.patch |
462 |
- |
463 |
- # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html |
464 |
- eapply "${FILESDIR}"/${PN}-1.9.4-tmpdir.patch |
465 |
- |
466 |
- # PREFIX |
467 |
- sed \ |
468 |
- -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ |
469 |
- -i configure || die |
470 |
- |
471 |
- sed \ |
472 |
- -e "s:gentoo-bindir:${ED}/usr/bin:g" \ |
473 |
- -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ |
474 |
- -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ |
475 |
- -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ |
476 |
- -e "s:gentoo-gcc:$(tc-getCC):g" \ |
477 |
- -e "s:gentoo-g++:$(tc-getCXX):g" \ |
478 |
- -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ |
479 |
- -e "s:gentoo-cflags:${CFLAGS}:g" \ |
480 |
- -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ |
481 |
- -e "s:gentoo-nvflags::g" \ |
482 |
- -e "s:gentoo-ldflags:${LDFLAGS}:g" \ |
483 |
- -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ |
484 |
- -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ |
485 |
- -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ |
486 |
- -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ |
487 |
- -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ |
488 |
- -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ |
489 |
- -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ |
490 |
- -i configure || die |
491 |
- |
492 |
- if use cuda; then |
493 |
- sed \ |
494 |
- -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ |
495 |
- -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ |
496 |
- -i configure src/Makefile || die |
497 |
- sed \ |
498 |
- -e '/compute_/d' \ |
499 |
- -i configure || die |
500 |
- sed \ |
501 |
- -e 's:-gencode .*code=sm_..::' \ |
502 |
- -i src/Makefile || die |
503 |
- fi |
504 |
- |
505 |
- sed \ |
506 |
- -e "s:LINUXPPC:LINUX:g" \ |
507 |
- -e "s:LINUXALPHA:LINUX:g" \ |
508 |
- -e "s:LINUXAMD64:LINUX:g" \ |
509 |
- -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ |
510 |
- -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ |
511 |
- -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ |
512 |
- -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" |
513 |
- |
514 |
- EMAKEOPTS=( |
515 |
- TCLINC="-I${EPREFIX}/usr/include" |
516 |
- TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" |
517 |
- TCLLDFLAGS="-shared" |
518 |
- NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" |
519 |
- NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" |
520 |
- NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" |
521 |
- NETCDFDYNAMIC=1 |
522 |
- EXPATINC="-I${EPREFIX}/usr/include" |
523 |
- EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" |
524 |
- EXPATLDFLAGS="-shared" |
525 |
- EXPATDYNAMIC=1 |
526 |
- ) |
527 |
- if use gromacs; then |
528 |
- EMAKEOPTS+=( |
529 |
- TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" |
530 |
- TNGINC="-I${EPREFIX}/usr/include" |
531 |
- TNGLDFLAGS="-shared" |
532 |
- TNGDYNAMIC=1 |
533 |
- ) |
534 |
- fi |
535 |
- if use sqlite; then |
536 |
- EMAKEOPTS+=( |
537 |
- SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" |
538 |
- SQLITEINC="-I${EPREFIX}/usr/include" |
539 |
- SQLITELDFLAGS="-shared" |
540 |
- SQLITEDYNAMIC=1 |
541 |
- ) |
542 |
- fi |
543 |
-} |
544 |
- |
545 |
-src_configure() { |
546 |
- local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" |
547 |
- rm -f configure.options && echo $myconf >> configure.options |
548 |
- |
549 |
- use cuda && myconf+=" CUDA" |
550 |
-# use mpi && myconf+=" MPI" |
551 |
- use tachyon && myconf+=" LIBTACHYON" |
552 |
- use xinerama && myconf+=" XINERAMA" |
553 |
- |
554 |
- export \ |
555 |
- PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ |
556 |
- PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ |
557 |
- PYTHON_LIBRARY="$(python_get_LIBS)" \ |
558 |
- NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ |
559 |
- NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" |
560 |
- |
561 |
- perl ./configure LINUX \ |
562 |
- ${myconf} || die |
563 |
-} |
564 |
- |
565 |
-src_compile() { |
566 |
- # build plugins |
567 |
- cd "${WORKDIR}"/plugins || die |
568 |
- |
569 |
- emake \ |
570 |
- ${EMAKEOPTS[@]} \ |
571 |
- LINUX |
572 |
- |
573 |
- # build vmd |
574 |
- cd "${S}"/src || die |
575 |
- emake |
576 |
-} |
577 |
- |
578 |
-src_install() { |
579 |
- # install plugins |
580 |
- cd "${WORKDIR}"/plugins || die |
581 |
- emake \ |
582 |
- PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ |
583 |
- distrib |
584 |
- |
585 |
- # install vmd |
586 |
- cd "${S}"/src || die |
587 |
- emake install |
588 |
- |
589 |
- # install docs |
590 |
- cd "${S}" || die |
591 |
- dodoc Announcement README doc/ig.pdf doc/ug.pdf |
592 |
- |
593 |
- # remove some of the things we don't want and need in |
594 |
- # /usr/lib |
595 |
- cd "${ED}"/usr/$(get_libdir)/vmd || die |
596 |
- rm -fr doc README Announcement LICENSE || \ |
597 |
- die "failed to clean up /usr/lib/vmd directory" |
598 |
- |
599 |
- # adjust path in vmd wrapper |
600 |
- sed \ |
601 |
- -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ |
602 |
- -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ |
603 |
- || die "failed to set up vmd wrapper script" |
604 |
- |
605 |
- # install icon and generate desktop entry |
606 |
- insinto /usr/share/pixmaps |
607 |
- doins "${WORKDIR}"/vmd.png |
608 |
- eprefixify "${WORKDIR}"/vmd.desktop |
609 |
- sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die |
610 |
- # Open PDB files with VMD |
611 |
- echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die |
612 |
- domenu "${WORKDIR}"/vmd.desktop |
613 |
-} |