Problems in installing RcppArmadillo on macOS Monterey

[nikdraka]

Hi. I have an issue when installing RcppArmadillo on my computer (macOS Monterey). I want to install a package from github and it requires installing RcppArmadillo. I did install with install.package("RcppArmadillo") and call its library but when I install the package from github, tonnes of warnings show up. Here are the warnings.

install_github("config-i1/smooth")
Downloading GitHub repo config-i1/smooth@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: nloptr (2.0.0 -> 2.0.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
✔ checking for file ‘/private/var/folders/fh/h16m_j410rjc0vltls1lx7qr0000gn/T/Rtmpf9Q5Zu/remotes23440f1033f/config-i1-smooth-a747588/DESCRIPTION’ ...
─ preparing ‘smooth’:
✔ 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
─ building ‘smooth_3.1.7.41007.tar.gz’

• installing source package ‘smooth’ ...
  ** 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 -I/usr/local/include -Xclang -fopenmp -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
  In file included from RcppExports.cpp:4:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:642:26: error: no template named 'numeric_limits'
  bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:642:60: error: no template named 'numeric_limits'
  bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:643:18: error: no template named 'numeric_limits'
  int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:643:50: error: no template named 'numeric_limits'
  int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:648:17: error: no template named 'numeric_limits'
  static_assert(numeric_limits<_FloatT>::radix == 2, "FloatT has incorrect radix");
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:651:25: error: no template named 'numeric_limits'
  return _FloatBigger ? numeric_limits<_IntT>::max() : (numeric_limits<_IntT>::max() >> _Bits << _Bits);
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:651:58: error: no template named 'numeric_limits'
  return _FloatBigger ? numeric_limits<_IntT>::max() : (numeric_limits<_IntT>::max() >> _Bits << _Bits);
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:645:25: error: no return statement in constexpr function
  _LIBCPP_CONSTEXPR _IntT __max_representable_int_for_float() _NOEXCEPT {
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:661:16: error: no template named 'numeric_limits'
  using _Lim = numeric_limits<_IntT>;
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:664:12: error: use of undeclared identifier '_Lim'
  return _Lim::max();
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:665:21: error: use of undeclared identifier '_Lim'
  } else if (__r <= _Lim::lowest()) {
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:666:12: error: use of undeclared identifier '_Lim'
  return _Lim::min();
  ^
  In file included from RcppExports.cpp:4:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:30:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/unordered_map:437:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__hash_table:16:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/algorithm:653:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/functional:490:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__algorithm/search.h:15:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:14:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:14:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/concepts:134:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__functional_base:22:
  In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/exception:83:
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cstdlib:138:9: error: target of using declaration conflicts with declaration already in scope
  using ::abs _LIBCPP_USING_IF_EXISTS;
  ^
  /usr/local/include/stdlib.h:132:6: note: target of using declaration
  int abs(int) __pure2;
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:338:1: note: conflicting declaration
  using ::abs _LIBCPP_USING_IF_EXISTS;
  ^
  In file included from RcppExports.cpp:4:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:65:
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/complex:853:1: error: declaration conflicts with target of using declaration already in scope
  abs(const complex<_Tp>& __c)
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:338:1: note: target of using declaration
  using ::abs _LIBCPP_USING_IF_EXISTS;
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:338:9: note: using declaration
  using ::abs _LIBCPP_USING_IF_EXISTS;
  ^
  In file included from RcppExports.cpp:4:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:65:
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/complex:910:16: error: reference to unresolved using declaration
  return abs(__c.real());
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
  using ::abs _LIBCPP_USING_IF_EXISTS;
  ^
  In file included from RcppExports.cpp:4:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:65:
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/complex:912:16: error: reference to unresolved using declaration
  return abs(__c.imag());
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
  using ::abs _LIBCPP_USING_IF_EXISTS;
  ^
  In file included from RcppExports.cpp:4:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:65:
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/complex:969:16: error: reference to unresolved using declaration
  __re = abs(__re);
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
  using ::abs _LIBCPP_USING_IF_EXISTS;
  ^
  In file included from RcppExports.cpp:4:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:65:
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/complex:1022:29: error: reference to unresolved using declaration
  return complex<_Tp>(log(abs(__x)), arg(__x));
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
  using ::abs _LIBCPP_USING_IF_EXISTS;
  ^
  In file included from RcppExports.cpp:4:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
  In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:65:
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/complex:1049:23: error: reference to unresolved using declaration
  return polar(sqrt(abs(__x)), arg(__x) / _Tp(2));
  ^
  /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
  using ::abs _LIBCPP_USING_IF_EXISTS;
  ^
  fatal error: too many errors emitted, stopping now [-ferror-limit=]
  20 errors generated.
  make: *** [RcppExports.o] Error 1
  ERROR: compilation failed for package ‘smooth’
• removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/smooth’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/smooth’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/fh/h16m_j410rjc0vltls1lx7qr0000gn/T//Rtmpf9Q5Zu/file234f0c3e68/smooth_3.1.7.41007.tar.gz’ had non-zero exit status

I have tried this suggestion (https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/), but no avail. I installed and reinstalled xcode (IDE or command line tools), and it still didn't work. However, when I execute a simple helloworld.rcpp, it works.

First, I am not sure what are the problems - I do not and cannot understand the warnings, to be honest. So, can you pinpoint the main issue of my problem? Secondly, if you know what is the main problem, could you please let me know how to solve this?

Thank you very much, your help is much appreciated.

[eddelbuettel]

You are attempting to install via install_github("config-i1/smooth") from repo config-i1/smooth

You reported this at repo RcppCore/RcppArmadillo. Not the same thing.

I plane to close unless you can actionally provide a standard, common, reproducible bug report showing an issue in installation or use of RcppArmadillo. We do this as volunteers here, and we cannot debug errors in another project using ours.

I hope you understand.

[eddelbuettel]

Moreover, smooth is a CRAN package so a binary is provided for your convenience as installing from source on macOS can have its challenges as you noticed. I suggest you stick to install.packages("smooth", type="binary").

[nikdraka]

Hi Dirk Apologies for the inconvenience and I will try your suggestion. Thanks Kandrika

…

On Tue, 17 May 2022 at 19:59, Dirk Eddelbuettel ***@***.***> wrote: Moreover, smooth is a CRAN package so a binary is provided for your convenience as installing from source on macOS can have its challenges as you noticed. I suggest you stick to install.packages("smooth", type="binary"). — Reply to this email directly, view it on GitHub <#380 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALF25AZ7X6NYZXAPN22IGLLVKPUCVANCNFSM5WF27CSQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>