Problem Installing Mac M3 Sonoma #207

joshuagmedina · 2024-01-13T02:01:45Z

UPDATE:
Resolved the issue.
The Makevars file appeared to be the issue. Using additional variables seemed to be conflicting.
The file had to contain only this:

CXX_STD = CXX11
PKG_CXXFLAGS= $(SHLIB_OPENMP_CXXFLAGS)
PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
PKG_LIBS=-lboost_filesystem -lboost_system   -lstdc++ $(LAPACK_LIBS) $(BLAS_LIBS)  $(SHLIB_OPENMP_CFLAGS) $(FLIBS) -L /opt/homebrew/Cellar/boost/1.83.0/lib/

And gfortran had to be located at /opt/gfortran

Hi,
I've been trying to install velocyto.R in a M3 Mac running Sonoma OS but have not been successful.

Here is what I've tried so far:

Installing everything using brew (llvm, gcc, boost, gfortran, etc.)
Followed this #167 and this Installing Conos guide

My ~/.R/Makevars has:

CXX_STD = CXX11
PKG_CXXFLAGS= $(SHLIB_OPENMP_CXXFLAGS)
PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
PKG_LIBS=-lboost_filesystem -lboost_system   -lstdc++ $(LAPACK_LIBS) $(BLAS_LIBS)  $(SHLIB_OPENMP_CFLAGS) $(FLIBS) -L /opt/homebrew/Cellar/boost/1.83.0/lib/

CC=/opt/homebrew/opt/llvm/bin/clang -fopenmp
CXX=/opt/homebrew/opt/llvm/bin/clang++ -fopenmp
CXX11=/opt/homebrew/opt/llvm/bin/clang++ -fopenmp
CXX14=/opt/homebrew/opt/llvm/bin/clang++ -fopenmp
CXX17=/opt/homebrew/opt/llvm/bin/clang++ -fopenmp
CXX1X=/opt/homebrew/opt/llvm/bin/clang++ -fopenmp
CXX98=/opt/homebrew/opt/llvm/bin/clang++ -fopenmp

FC = /opt/R/arm64/gfortran/bin -fopenmp
F77 = /opt/R/arm64/gfortran/bin -fopenmp
FLIBS = -L/opt/homebrew/opt/gcc/lib/gcc/13/ -lm

Also, included the following in my .zshrc

export LDFLAGS="-L/opt/homebrew/opt/llvm/lib"
export CPPFLAGS="-I/opt/homebrew/opt/llvm/include"

I also included these to the Makevars file but did not make any difference.

Still I continue to have the following error:

* installing *source* package ‘velocyto.R’ ...
** using staged installation
** libs
using C++ compiler: ‘Homebrew clang version 17.0.6’
using C++11
using SDK: ‘MacOSX14.2.sdk’
/opt/homebrew/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' "-I/opt/homebrew/opt/llvm/include"    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
/opt/homebrew/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' "-I/opt/homebrew/opt/llvm/include"    -fPIC  -falign-functions=64 -Wall -g -O2  -c points_within.cpp -o points_within.o
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:962:34: error: too many arguments provided to function-like macro invocation
  962 |     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:968:9: note: macro 'length' defined here
  968 | #define length(x)               Rf_length(x)
      |         ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:961:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
  961 |     _LIBCPP_INLINE_VISIBILITY
      |     ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:841:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
  841 | #  define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
      |                                     ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:820:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  820 |           __attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
      |                          ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:962:15: error: expected ';' at end of declaration list
  962 |     int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
      |               ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1048:34: error: too many arguments provided to function-like macro invocation
 1048 |     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:968:9: note: macro 'length' defined here
  968 | #define length(x)               Rf_length(x)
      |         ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1047:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
 1047 |     _LIBCPP_INLINE_VISIBILITY
      |     ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:841:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
  841 | #  define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
      |                                     ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:820:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  820 |           __attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
      |                          ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1048:15: error: expected ';' at end of declaration list
 1048 |     int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
      |               ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1133:34: error: too many arguments provided to function-like macro invocation
 1133 |     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:968:9: note: macro 'length' defined here
  968 | #define length(x)               Rf_length(x)
      |         ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1132:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
 1132 |     _LIBCPP_INLINE_VISIBILITY
      |     ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:841:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
  841 | #  define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
      |                                     ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:820:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  820 |           __attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
      |                          ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1133:15: error: expected ';' at end of declaration list
 1133 |     int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
      |               ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1309:34: error: too many arguments provided to function-like macro invocation
 1309 |     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:968:9: note: macro 'length' defined here
  968 | #define length(x)               Rf_length(x)
      |         ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1308:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces
 1308 |     _LIBCPP_INLINE_VISIBILITY
      |     ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:841:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
  841 | #  define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
      |                                     ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:820:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
  820 |           __attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
      |                          ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1309:15: error: expected ';' at end of declaration list
 1309 |     int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
      |               ^
12 errors generated.
make: *** [points_within.o] Error 1
ERROR: compilation failed for package ‘velocyto.R’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/velocyto.R’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/mk/2zf6m29j5kn9km15d_5cc4cw0000gn/T//RtmpgrfvIC/file81dc2f079bc7/velocyto.R_0.6.tar.gz’ had non-zero exit status

Any suggestions?
PS. I also tried downgrading the llvm brew install to version 11.1.0, but got a different error.

Thanks!

The text was updated successfully, but these errors were encountered:

BenjaminDEMAILLE · 2024-04-03T14:24:22Z

Same problem for. Do the devs can quickly resolve it ? this problem is here this many month

adri-biochem · 2024-04-22T21:50:10Z

Thank you for posting your solution. I am on Apple M1 Sonoma 14.4.1 and cannot install the package.

My Makevars file has this:
CXX_STD = CXX11 PKG_CXXFLAGS= $(SHLIB_OPENMP_CXXFLAGS) PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS) PKG_LIBS=-lboost_filesystem -lboost_system -lstdc++ $(LAPACK_LIBS) $(BLAS_LIBS) $(SHLIB_OPENMP_CFLAGS) $(FLIBS) -L/opt/homebrew/Cellar/boost/1.84.0_1/lib

And I do have gfortran at opt/gfortran

I then ran:
git clone https://github.com/velocyto-team/velocyto.R
R CMD build velocyto.R
R CMD INSTALL velocyto.R_0.6.tar.gz

However, I am getting the same error as your did above:

Any insight on how to fix this would be great! Using brew, I have gcc, gfortran, llvm, and boost. Wondering what else I should try. Thanks!

`* installing source package ‘velocyto.R’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c points_within.cpp -o points_within.o
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:962:34: error: too many arguments provided to function-like macro invocation
962 | 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
969 | #define length(x) Rf_length(x)
| ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:961:5: error: 'abi_tag' attribute only applies to structs, variables, functions, and
namespaces
961 | _LIBCPP_INLINE_VISIBILITY
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:841:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
841 | # define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:820:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
820 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
| ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:962:15: error: expected ';' at end of declaration list
962 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1048:34: error: too many arguments provided to function-like macro invocation
1048 | 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
969 | #define length(x) Rf_length(x)
| ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1047:5: error: 'abi_tag' attribute only applies to structs, variables, functions, and
namespaces
1047 | _LIBCPP_INLINE_VISIBILITY
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:841:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
841 | # define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:820:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
820 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
| ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1048:15: error: expected ';' at end of declaration list
1048 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1133:34: error: too many arguments provided to function-like macro invocation
1133 | 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
969 | #define length(x) Rf_length(x)
| ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1132:5: error: 'abi_tag' attribute only applies to structs, variables, functions, and
namespaces
1132 | _LIBCPP_INLINE_VISIBILITY
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:841:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
841 | # define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:820:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
820 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
| ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1133:15: error: expected ';' at end of declaration list
1133 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1309:34: error: too many arguments provided to function-like macro invocation
1309 | 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
969 | #define length(x) Rf_length(x)
| ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1308:5: error: 'abi_tag' attribute only applies to structs, variables, functions, and
namespaces
1308 | _LIBCPP_INLINE_VISIBILITY
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:841:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY'
841 | # define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI
| ^
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__config:820:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI'
820 | attribute((abi_tag(_LIBCPP_TOSTRING(_LIBCPP_ODR_SIGNATURE))))
| ^
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1761:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:321:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:32:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:1309:15: error: expected ';' at end of declaration list
1309 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const
| ^
12 errors generated.
make: *** [points_within.o] Error 1
ERROR: compilation failed for package ‘velocyto.R’

removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/velocyto.R’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/z4/d9dxjxp54g760dgphtt7mk4c0000gn/T//RtmpLDWvHJ/file1472d31eec929/velocyto.R_0.6.tar.gz’ had non-zero exit status`

gvogler · 2024-05-07T00:26:47Z

I am also facing this problem (on Apple M1):

Installing package into ‘/Users/Geo/Library/R/arm64/4.3/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘velocyto.R’ ...
** using staged installation
** libs
using C++ compiler: ‘Homebrew clang version 18.1.5’
using C++11
using SDK: ‘’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c points_within.cpp -o points_within.o
In file included from points_within.cpp:3:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/set:1499:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/functional:526:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/vector:325:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_bool.h:20:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/__format/formatter_integral.h:35:
In file included from /opt/homebrew/opt/llvm/bin/../include/c++/v1/locale:202:
/opt/homebrew/opt/llvm/bin/../include/c++/v1/__locale:804:28: error: too many arguments provided to function-like macro invocation
  804 |   length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const {
      |                            ^

Compiler and libs seem to be there and in place:

> pkgbuild::check_build_tools(debug = TRUE)
Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Homebrew clang version 18.1.5’
using SDK: ‘’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o foo.so foo.o -lboost_filesystem -lboost_system -lstdc++ -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -L /opt/homebrew/Cellar/boost/1.85.0/lib/ -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
 
Your system is ready to build packages!

garci1294 · 2024-10-04T04:16:19Z

I believe I've identified the issue, which occurred during the C++ compilation. I added the following to the top of the points_within.cpp file located in the /src directory, and the installation was successful.

I have an M3 device.

#include <R.h>
#include <Rinternals.h>

// Undefine the 'length' macro to prevent conflicts
#undef length

#include <set>
#include <vector>
#include <functional>

using namespace std;

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