MacOS Big Sur x86_64 complier error during R devtool install

Question

I am trying to install an R package with the following command:

devtools::install_github('ococrook/bandle)

However, I keep running into compiler issues. When I run the command I get many, many errors. For example this error related to BH:

clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include    -fPIC  -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c Bessel2ndKind.cpp -o Bessel2ndKind.o
   In file included from Bessel2ndKind.cpp:1:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp.h:59:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/exceptions_impl.h:38:
   In file included from /usr/local/include/execinfo.h:28:
   /usr/local/include/os/base.h:274:37: warning: type nullability specifier '_Nullable' is a Clang extension [-Wnullability-extension]
   typedef void (*os_function_t)(void *_Nullable);
                                       ^
   Bessel2ndKind.cpp:621:55: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
                                              nk, tau, D = D, j + 1, nu).t();
                                                       ~ ^ ~
   Bessel2ndKind.cpp:774:49: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
                                        nk, tau, D = D, j + 1).t();
                                                 ~ ^ ~
   In file included from Bessel2ndKind.cpp:2:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/math/special_functions/bessel.hpp:24:
   /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/math/special_functions/detail/bessel_ik.hpp:97:18: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
       BOOST_ASSERT(abs(x) <= 2);
                    ^
   /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/math/special_functions/detail/bessel_ik.hpp:366:9: note: in instantiation of function template specialization 'boost::math::detail::temme_ik<long double, boost::math::policies::policy<detail::forwarding_arg1, detail::forwarding_arg2>>' requested here
           temme_ik(u, x, &Ku, &Ku1, pol);             // Temme series
           ^
   /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/math/special_functions/bessel.hpp:246:4: note: in instantiation of function template specialization 'boost::math::detail::bessel_ik<long double, boost::math::policies::policy<detail::forwarding_arg1, detail::forwarding_arg2>>' requested here
      bessel_ik(v, x, &I, &K, need_k, pol);
      ^
   /Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include/boost/math/special_functions/bessel.hpp:258:11: note: in instantiation of function template specialization 'boost::math::detail::cyl_bessel_k_imp<long double, boost::math::policies::policy<detail::forwarding_arg1, detail::forwarding_arg2>>' requested here
      return cyl_bessel_k_imp(v, x, bessel_no_int_tag(), pol);
             ^

Or this error related to RcppArmadillo:

clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include    -fPIC  -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c leapfrogGPcpp.cpp -o leapfrogGPcpp.o
   In file included from leapfrogGPcpp.cpp:1:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp.h:59:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/exceptions_impl.h:38:
   In file included from /usr/local/include/execinfo.h:28:
   /usr/local/include/os/base.h:274:37: warning: type nullability specifier '_Nullable' is a Clang extension [-Wnullability-extension]
   typedef void (*os_function_t)(void *_Nullable);
                                       ^
   In file included from leapfrogGPcpp.cpp:1:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:49:
   In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/armadillo:646:
   /Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include/armadillo_bits/op_inv_meat.hpp:200:28: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
       const  T abs_det_val = std::abs(det_val);

So far I have tried this , and this , and this , and this . However, so far, none of these solutions have worked and I am running out of ideas on how to solve this.

Any help would be greatly appreciated, Thanks!

Answer 1

Try following the instructions here and change the default timeout to ensure the relatively large "pRolocdata" package is downloaded completely, ie

options(timeout = 600)
devtools::install_github('ococrook/bandle')

Using this approach, Bandle installed with a bunch of warnings but without error on my system.

sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

loaded via a namespace (and not attached):
[1] compiler_4.1.1 tools_4.1.1  

My ~/.R/Makevars file:

LOC = /usr/local/gfortran
CC=$(LOC)/bin/gcc -fopenmp
CXX=$(LOC)/bin/g++ -fopenmp
CXX11 = $(LOC)/bin/g++ -fopenmp

CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L$(LOC)/lib -Wl,-rpath,$(LOC)/lib
CPPFLAGS=-I$(LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++