Error while installing "RcppArmadillo" package in R - c++

Question

I am using macOS High Sierra version 10.13.4. While installing "RcppArmadillo"package, I get the following two WARNING messages :
checking whether /usr/local/clang6/bin/clang++ -Wall accepts -g... (cached) yes
checking whether g++ version is sufficient... almost
configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++.
checking for macOS... found
checking for macOS Apple compiler... not found
checking for clang compiler... found
checking for OpenMP compatible version of clang... found and suitable
checking LAPACK_LIBS... R-supplied partial LAPACK found
configure: WARNING: Some complex-valued LAPACK functions may not be available
When I type "gcc --version" on my terminal, I get
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 9.1.0 (clang-902.0.39.2)
Target: x86_64-apple-darwin17.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
And my Makevars file in R looks like:
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
F77 = /usr/local/bin/gfortran
FC = $F77
CXX = /usr/local/clang6/bin/clang++ -Wall
LDFLAGS=-L/usr/local/clang6/lib
CC= /usr/local/clang6/bin/clang
SHLIB_CXXLD=ccache /usr/local/clang6/bin/clang++
CXX11 = /usr/local/clang6/bin/clang++
CXX98 = /usr/local/clang6/bin/clang++
CXX14 = /usr/local/clang6/bin/clang++
How can I remove these two WARNING signs?

Answer 1

In short, these are warnings and not errors. Moreover, these warnings do not matter.
Let's talk about what each warning means...
First Warning
configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++.
This is stating that the compiler defined in the Makevars file's CXX variable is identifying as gcc but is not the gcc compiler. In essence, each compiler has its own predefined header, see Section 3.7.2 Common Predefined Macros of The C Preprocessor, and this check is focused on verifying that a modern gcc compiler is selected. However, it's hard to check the presence of a compiler if the compiler is lying about who it is.
For details on the origin, see discussion in the issue Add a check message success in config after g++version check #183 and the commit the default message on the g++ test).
Second Warning
configure: WARNING: Some complex-valued LAPACK functions may not be available
Within this warning, there is a complaint that the underlying Linear Algebra PACKage is the same one that is shipped with R. Unfortunately, the LAPACK that is shipped with R is severely limited and a bit out of date. So, the check here is hoping for an external LAPACK being present via either OpenBLAS, Intel MKL, or ATLAS. Due to the way this check is structured, unless you are compiling R from source -- that is you opt not to use the binary provided by CRAN -- there is no way to avoid the hiccup.
Simply put, the CRAN binary looks for the LAPACK in a specific location. Switching to another LAPACK would require the establishment of a symbolic link to the existing lRlapack location, which is what the check searches for. Though, it isn't advisable doing such a symbolic link. (Sorry vecLib lovers!)
If you are interested in compiling from source, consider viewing Section A.3 Linear algebra of R Installation and Administration, which describes the procedure for using external LAPACKs.