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Installation issue: netcdf-cxx4 on MacOS BigSur #26559
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Steps to reproduce the issue
% spack install --jobs 1 netcdf-cxx4
[+] /Users/cessenat/Softs/spack/opt/spack/darwin-bigsur-skylake/apple-clang-11.0.0/netcdf-c-4.8.1-nhspe6pdexngkivhww4yqdpqifpthssa
==> Installing netcdf-cxx4-4.3.1-cqmoty4pwryblx4c2xhipqesqtuvywvy
==> No binary for netcdf-cxx4-4.3.1-cqmoty4pwryblx4c2xhipqesqtuvywvy found: installing from source
/Users/cessenat/Softs/spack/lib/spack/spack/target.py:137: UserWarning: microarchitecture specific optimizations are not supported yet on mixed compiler toolchains [check [email protected] for further details]
warnings.warn(msg.format(compiler))
==> Using cached archive: /Users/cessenat/Softs/spack/var/spack/cache/_source-cache/archive/6a/6a1189a181eed043b5859e15d5c080c30d0e107406fbb212c8fb9814e90f3445.tar.gz
==> No patches needed for netcdf-cxx4
==> netcdf-cxx4: Executing phase: 'autoreconf'
==> netcdf-cxx4: Executing phase: 'configure'
==> netcdf-cxx4: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' 'V=1'
22 errors found in build log:
204 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
205 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
206 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
207 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:639:
208 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/initializer_list:46:
209 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:37:
>> 210 ../version:1:1: error: expected external declaration
211 -n 4.3.1
212 ^
>> 213 ../version:1:2: error: unknown type name 'n'
214 -n 4.3.1
215 ^
>> 216 ../version:1:4: error: expected unqualified-id
217 -n 4.3.1
218 ^
219 In file included from ncAtt.cpp:1:
220 In file included from ./ncAtt.h:1:
221 In file included from ./ncType.h:1:
222 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
223 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
224 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
225 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:639:
226 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/initializer_list:46:
>> 227 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:49:9: error: no member named 'ptrdiff_t
' in the global namespace
228 using ::ptrdiff_t;
229 ~~^
230 In file included from ncAtt.cpp:1:
231 In file included from ./ncAtt.h:1:
232 In file included from ./ncType.h:1:
233 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
234 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
235 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
236 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:640:
237 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:418:
>> 238 ../version:1:1: error: expected external declaration
239 -n 4.3.1
240 ^
>> 241 ../version:1:2: error: unknown type name 'n'
242 -n 4.3.1
243 ^
>> 244 ../version:1:4: error: expected unqualified-id
245 -n 4.3.1
246 ^
247 In file included from ncAtt.cpp:1:
248 In file included from ./ncAtt.h:1:
249 In file included from ./ncType.h:1:
250 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
251 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
252 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
253 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:642:
254 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/utility:205:
>> 255 ../version:1:1: error: expected external declaration
256 -n 4.3.1
257 ^
>> 258 ../version:1:2: error: unknown type name 'n'
259 -n 4.3.1
260 ^
>> 261 ../version:1:4: error: expected unqualified-id
262 -n 4.3.1
263 ^
264 In file included from ncAtt.cpp:1:
265 In file included from ./ncAtt.h:1:
266 In file included from ./ncType.h:1:
267 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
268 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
269 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
270 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
271 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:668:
272 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/typeinfo:60:
273 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:83:
>> 274 ../version:1:1: error: expected external declaration
275 -n 4.3.1
276 ^
>> 277 ../version:1:2: error: unknown type name 'n'
278 -n 4.3.1
279 ^
>> 280 ../version:1:4: error: expected unqualified-id
281 -n 4.3.1
282 ^
283 In file included from ncAtt.cpp:1:
284 In file included from ./ncAtt.h:1:
285 In file included from ./ncType.h:1:
286 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
287 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
288 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
289 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
290 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:671:
291 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/new:93:
>> 292 ../version:1:1: error: expected external declaration
293 -n 4.3.1
294 ^
>> 295 ../version:1:2: error: unknown type name 'n'
296 -n 4.3.1
297 ^
>> 298 ../version:1:4: error: expected unqualified-id
299 -n 4.3.1
300 ^
301 In file included from ncAtt.cpp:1:
302 In file included from ./ncAtt.h:1:
303 In file included from ./ncType.h:1:
304 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506:
305 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175:
306 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57:
307 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:643:
308 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory:673:
309 In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:121:
>> 310 ../version:1:1: error: expected external declaration
311 -n 4.3.1
312 ^
>> 313 ../version:1:2: error: unknown type name 'n'
314 -n 4.3.1
315 ^
>> 316 ../version:1:4: error: expected unqualified-id
317 -n 4.3.1
318 ^
319 fatal error: too many errors emitted, stopping now [-ferror-limit=]
320 20 errors generated.
>> 321 make[2]: *** [ncAtt.lo] Error 1
>> 322 make[1]: *** [all-recursive] Error 1
>> 323 make: *** [all] Error 2
See build log for details:
/var/folders/53/vwnr5jhj4h3cgvt1y6w3wgmh0000gn/T/cessenat/spack-stage/spack-stage-netcdf-cxx4-4.3.1-cqmoty4pwryblx4c2xhipqesqtuvywvy/spack-build-out.txt
Information on your system
% spack debug report
- Spack: 0.16.1-4783-199bd9f8f8
- Python: 3.8.2
- Platform: darwin-bigsur-skylake
- Concretizer: clingo
Additional information
% spack maintainers netcdf-cxx4
@WardF
spack-build-env.txt
spack-build-out.txt
General information
- I have run
spack debug reportand reported the version of Spack/Python/Platform - I have run
spack maintainers <name-of-the-package>and @mentioned any maintainers - I have uploaded the build log and environment files
- I have searched the issues of this repo and believe this is not a duplicate
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