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Installation issue: netcdf-cxx4 on MacOS BigSur #26559

@cessenat

Description

@cessenat

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 report and 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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