Working with an R package under a conda environment in macOS - r

Question

I am trying to work with an R package that includes Rcpp + OpenMP in a conda environment in macOS. I read the conda environment documentation; however, I could not fix the problem I have in the following reproducible example. Most of the documentation is based on addressing OpenMP issues (clang+llvm) on macOS. I was wondering if there are any resources or documentation for the conda environment. These steps work on a Linux system (with conda) and macOS (without conda) without any problem.
Here is the reproducible example:
In a macOS:
Step 1: Create a conda environment and install R:
conda create -n env r-essentials r-base
Step 2: activate the environment
conda activate env
Step 3: install rstudio
conda install -c r rstudio
Step 4: install some required packages
conda install -c r r-devtools
conda install -c r r-wcorr
conda install -c r r-ranger
conda install -c conda-forge r-rcpparmadillo
conda install -c r r-testthat
conda install -c conda-forge r-superlearner
conda install -c conda-forge r-polycore
conda install -c conda forge r-logger
conda install -c anaconda llvm
conda install -c conda-forge openmp
Step 5: Run rstudio
Step 6: Inside rstudio
library('devtools')
install_github('fasrc/CausalGPS')
I get the following error:
In file included from ColorSpace.cpp:1:
In file included from ./ColorSpace.h:4:
In file included from env/bin/../include/c++/v1/typeinfo:60:
In file included from env/bin/../include/c++/v1/exception:81:
In file included from env/bin/../include/c++/v1/cstdlib:85:
In file included from env/bin/../include/c++/v1/stdlib.h:100:
env/bin/../include/c++/v1/math.h:773:12: error: no member named 'labs' in the global namespace; did you mean 'abs'?
return ::labs(__x);
~~^
~/env/bin/../include/c++/v1/math.h:772:39: note: 'abs' declared here
inline _LIBCPP_INLINE_VISIBILITY long abs(long __x) _NOEXCEPT {
^
~/env/bin/../include/c++/v1/math.h:777:12: error: no member named 'llabs' in the global namespace
return ::llabs(__x);
~~^
~/env/bin/../include/c++/v1/math.h:785:12: error: no member named 'fabsf' in the global namespace
return ::fabsf(__lcpp_x);
~~^
~/env/bin/../include/c++/v1/math.h:789:12: error: no member named 'fabs' in the global namespace; did you mean 'abs'?
return ::fabs(__lcpp_x);
~~^
~/env/bin/../include/c++/v1/math.h:772:39: note: 'abs' declared here
inline _LIBCPP_INLINE_VISIBILITY long abs(long __x) _NOEXCEPT {
^
~/env/bin/../include/c++/v1/math.h:794:12: error: no member named 'fabsl' in the global namespace
return ::fabsl(__lcpp_x);
~~^
I think I need to set some environmental variables; however, I could not find out which variables I should export. Do you have any idea?

Answer 1

Works for me, with some adjustments that I regard as better practice:
don't use RStudio from Conda - it is an abandoned project; see alternatives
only use conda-forge channel - mixing channels can have dynamic library issues
use a YAML for more reliable specification of requirements
explicitly declare R version (r-base)
include everything in the declared Imports (except what is included as dependencies of other packages)
conda-forge::r-cli>=3 builds are broken, so I pin that to newest working version
use mamba because conda is slow
Here is a YAML for creating the environment:
causalgps-env.yaml
name: causalgps
channels:
- conda-forge
dependencies:
- r-base=4.1
- r-tidyverse
- r-devtools
- r-xgboost
- r-superlearner
- r-earth
- r-ranger
- r-gam
- r-kernsmooth
- r-gnm
- r-polycor
- r-wcorr
- r-rlang
- r-glue
- r-logger
- r-cli>=2,<3
And the steps are:
Create env.
## install Mamba if you don't have it
## conda install -n base conda-forge::mamba
mamba env create -n causalgps -f causalgps-env.yaml
Run R session in env.
conda activate causalgps
R
Install package.
library(devtools)
install_github('fasrc/CausalGPS')
Test loading.
library(CausalGPS) ## works