Siel
commented
7 months ago 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++-13This changes the C and C++ compilers to the GNU ones (like Gfortran).
Hope it works!
Julian
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’
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’