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!

I am not a macOS user and cannot help besides mentioning the standard resources that are [the mac.R-Project.org page](https://mac.r-project.org/), the [page by @coatless](https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/), the r-sig-mac mailing list, and the rcpp-devel mailing list. — Dirk Eddelbuettel, Sep 19 '21 at 17:55
Please distinguish warnings from errors. They are not the same. You can often ignore certain warnings. In fact, you have not shown any error in your snippets. Please show where the compilation actually stops. Look for the actual word **"error"**. — Vladimir F Героям слава, Sep 19 '21 at 17:59
there is an active [issue on github](https://github.com/ococrook/bandle/issues/8). In case you didn't notice yet. Maybe you can contribute there. — mnist, Sep 19 '21 at 18:21
Another note: I am also using big sur and can replicate the issue — mnist, Sep 19 '21 at 18:21

score 0 · Answer 1 · answered Oct 17 '21 at 11:45

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

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++

MacOS Big Sur x86_64 complier error during R devtool install

1 Answers1