Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

problem installation MacOS #215

Open
jbwoillard opened this issue Mar 22, 2024 · 2 comments
Open

problem installation MacOS #215

jbwoillard opened this issue Mar 22, 2024 · 2 comments
Labels
bug Something isn't working mac Related to Pmetrics running on macOS

Comments

@jbwoillard
Copy link

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
Copy link
Member

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
@mnneely
Copy link
Contributor

mnneely commented Nov 15, 2024

In the current release (2.1.1), we removed the dependency on C++, so hopefully this is no longer an issue.

@Siel Siel mentioned this issue Dec 12, 2024
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working mac Related to Pmetrics running on macOS
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
4 participants
@Siel @mnneely @jbwoillard @mhovd