Can't install reticulate in R - r

Question

I'm trying to install reticulate so I can execute some Python code I've written from within R. Unfortunately, I'm having trouble installing the package and haven't had much luck in determining the reason.
I've found that it likely has something to do with compiling the package and possible issues with gcc or different versions of c++ compilers, but I'm a bit out of my depth with those issues and haven't been able to get anything working. I've tried uninstalling and reinstalling xcode command line tools, but that didn't solve the issue. Beyond that, I'm not entirely sure where to start. I'm hoping somebody has experienced this and there's a straightforward answer, I'd really appreciate any help.
> install.packages('reticulate')
There is a binary version available but the source version is later:
binary source needs_compilation
reticulate 1.13 1.14 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y
installing the source package ‘reticulate’
trying URL 'https://cran.rstudio.com/src/contrib/reticulate_1.14.tar.gz'
Content type 'application/x-gzip' length 1504849 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
* installing *source* package ‘reticulate’ ...
** package ‘reticulate’ successfully unpacked and MD5 sums checked
** libs
/usr/local/bin/gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
/usr/local/bin/gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c event_loop.cpp -o event_loop.o
/usr/local/bin/gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c libpython.cpp -o libpython.o
/usr/local/bin/gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c output.cpp -o output.o
/usr/local/bin/gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c python.cpp -o python.o
/usr/local/bin/gcc-8 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c readline.cpp -o readline.o
/usr/local/bin/gcc-8 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o reticulate.so RcppExports.o event_loop.o libpython.o output.o python.o readline.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/reticulate/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘reticulate’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/reticulate/libs/reticulate.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/reticulate/libs/reticulate.so, 6): Symbol not found: __ZNSt15basic_streambufIcSt11char_traitsIcEE5imbueERKSt6locale
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/reticulate/libs/reticulate.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.5/Resources/library/reticulate/libs/reticulate.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/reticulate’
Warning in install.packages :
installation of package ‘reticulate’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/4g/ctbqp07114x4brzp4hr8zfc40000gn/T/RtmpDNvElq/downloaded_packages’
Session Info:
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.15.2
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.3 tools_3.5.3 yaml_2.2.0

Answer 1

Okay, I suggest to use conda to create a new environment and install there R anew. Because then you solve the issues - since only one line conda install -c conda-forge r-reticulate will install you reticulate and r-base solving for you all issues.
However some people (who don't know what conda is) won't be happy with my suggestion. I can't and won't help them.
But for those who know conda, I recommend:
conda create --name R_reticulate
source activate R_reticulate
conda install -c conda-forge r-reticulate
(of course you could determine version numbers when installing into conda environment ...)
if the version of R in your local env now is the same like your global R, you can even overtake most of the library installed in the pre-existing R - thus you don't have to reinstall them all over again. Simply by manipulating the path variable in your conda env's R.
(Just as a hack and if you are lazy to install everything anew, probably because you want just to play around with reticulate first, before you install it into your global R).
For that, in your global R, determine where your R packages are installed by .libPaths() from within your global R console.
Then start R in your R_reticulate conda environment,
and at beginning of session do
my_libPaths <- .libPaths()
# and e.g. add one or some of your global .libPaths() paths
# to here by
my_libPaths <- c(my_libPaths, one_of_global_path)
.libPaths(my_libPaths) # assign new libpaths!
# the order of the paths in the vector is important - decides about where R looks first!
# of course you can change order like you want in the vector!
By that, you don't have to re-install libraries.
However, the version number of global and local (conda) R must be same so that this works.
Otherwise you will get always warnings when loading libraries ...
Simpler is of course to re-install everything into your conda env's R. (conda will help you for this a lot!).