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problem installation MacOS #215

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jbwoillard opened this issue Mar 22, 2024 · 1 comment
Open

problem installation MacOS #215

jbwoillard opened this issue Mar 22, 2024 · 1 comment
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bug Something isn't working mac Related to Pmetrics running on macOS

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@jbwoillard
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Hi Julian, I have trouble to install Pmetrics on my new MacBook Pro
I installed gFortran and try to install Pmetrics, I have the following error
`── R CMD build ───────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/m5/9q7ccw491nl307gdl50xlrz40000gp/T/RtmpxLc8oG/remotes80df66127df2/LAPKB-Pmetrics-dc8f519/DESCRIPTION’ ...
─ preparing ‘Pmetrics’: (370ms)
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Removed empty directory ‘Pmetrics/inst/Examples/Runs’
─ building ‘Pmetrics_2.1.1.tar.gz’

  • installing source package ‘Pmetrics’ ...
    ** using staged installation
    ** libs
    clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c knn.cpp -o knn.o
    In file included from knn.cpp:9:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/queue:272:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/deque:2999:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:526:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:27:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:321:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
    /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:966:34: error: too many arguments provided to function-like macro invocation
    int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
    ^
    /Library/Frameworks/R.framework/Resources/include/Rinternals.h:969:9: note: macro 'length' defined here
    #define length(x) Rf_length(x)
    ^
    In file included from knn.cpp:9:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/queue:272:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/deque:2999:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:526:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:27:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:321:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
    In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
    /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:965:5: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
    _LIBCPP_INLINE_VISIBILITY
    ^
    /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:891:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'

define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI

                                ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:870:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
^
In file included from knn.cpp:9:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/queue:272:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/deque:2999:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:526:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:321:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:966:15: error: expected ';' at end of declaration list
int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1052:34: error: too many arguments provided to function-like macro invocation
int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:969:9: note: macro 'length' defined here
#define length(x) Rf_length(x)
^
In file included from knn.cpp:9:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/queue:272:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/deque:2999:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:526:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:321:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1051:5: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:891:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'

define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI

                                ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:870:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
^
In file included from knn.cpp:9:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/queue:272:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/deque:2999:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:526:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:321:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1052:15: error: expected ';' at end of declaration list
int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1137:34: error: too many arguments provided to function-like macro invocation
int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:969:9: note: macro 'length' defined here
#define length(x) Rf_length(x)
^
In file included from knn.cpp:9:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/queue:272:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/deque:2999:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:526:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:321:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1136:5: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:891:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'

define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI

                                ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:870:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
^
In file included from knn.cpp:9:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/queue:272:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/deque:2999:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:526:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:321:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1137:15: error: expected ';' at end of declaration list
int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1313:34: error: too many arguments provided to function-like macro invocation
int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:969:9: note: macro 'length' defined here
#define length(x) Rf_length(x)
^
In file included from knn.cpp:9:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/queue:272:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/deque:2999:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:526:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:321:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1312:5: error: 'abi_tag' attribute only applies to structs, variables, functions, and namespaces
_LIBCPP_INLINE_VISIBILITY
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:891:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'

define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI

                                ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:870:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
^
In file included from knn.cpp:9:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/queue:272:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/deque:2999:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:526:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/vector:321:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:202:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:1313:15: error: expected ';' at end of declaration list
int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
^
12 errors generated.
make: *** [knn.o] Error 1
ERROR: compilation failed for package ‘Pmetrics’

  • removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Pmetrics’
    Warning message:
    In i.p(...) :
    installation of package ‘/var/folders/m5/9q7ccw491nl307gdl50xlrz40000gp/T//RtmpxLc8oG/file80df68b36cde/Pmetrics_2.1.1.tar.gz’ had non-zero exit status`
    Many thanks in advance for your help
    Best
    jb
@Siel
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Siel commented Mar 22, 2024

Hi @jbwoillard

I actually had exactly the same issue a couple of days ago, it is not gfortran the one that tis failing but the C++ compiler. Apple's Clang seems to be broken since the last update.

What I did to fix it was to force R to use GCC instead of Clang.

To do this, create this file in your system ~/.R/Makevars

Then copy this into that file:

CC=gcc-13
CXX=g++-13

This changes the C and C++ compilers to the GNU ones (like Gfortran).

Hope it works!

Julian

@mhovd mhovd added bug Something isn't working mac Related to Pmetrics running on macOS labels Mar 22, 2024
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@Siel @jbwoillard @mhovd