Cannot compile R packages under Conda - r

Question

OK, this is driving me crazy.
I'm attempting to use Conda as a quasi-package manager for R on my Mac (OS 10.15) as I have done (successfully) on other Unix installations.
Repeatedly, the error I get is the following
Before the creation of a new conda environment, we have:
$ gcc -v
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.0 (clang-1100.0.33.8)
Target: x86_64-apple-darwin19.2.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
and
$ which clang
/usr/bin/clang
We create a new empty environment and check again
$ conda create --name r_env
$ conda activate r_env
$ gcc -v
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.0 (clang-1100.0.33.8)
Target: x86_64-apple-darwin19.2.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
$ which clang
/usr/bin/clang
Great. So far so good.
Now we install R and check again.
$ conda install r=3.6
$ gcc -v
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.0 (clang-1100.0.33.8)
Target: x86_64-apple-darwin19.2.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
$ which clang
/Users/dgarfield/miniconda3/envs/r_env/bin/clang
$ clang -v
clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin19.2.0
Thread model: posix
InstalledDir: /Users/dgarfield/miniconda3/envs/r_env/bin
It appears that we have a new clang!
Why is this a problem?
$ R
> install.packages("XML")
trying URL 'https://cran.uni-muenster.de/src/contrib/XML_3.98-1.20.tar.gz'
Content type 'application/x-gzip' length 1600829 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/private/var/folders/dg/hbvl43fn0b7flfk6l__3bwth0000gq/T/Rtmplh4pEL/R.INSTALL12b2d7b634136/XML':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘XML’
* removing ‘/Users/dgarfield/miniconda3/envs/r_env/lib/R/library/XML’
The downloaded source packages are in
‘/private/var/folders/dg/hbvl43fn0b7flfk6l__3bwth0000gq/T/RtmpaiTLe8/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("XML") :
installation of package ‘XML’ had non-zero exit status
This works perfectly fine on a standard (non-Conda) installation. My guess is that the culprit is this new clang.
Following what I have seen elsewhere, I have tried this with
CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
and
CONDA_BUILD_SYSROOT=/opt/MacOSX10.9.sdk
So it doesn't seem to be anything too weird with the headers (??). But I'm out of ideas and could use some guidance.
(and yes, I know that in the case of XML, conda could to the install for me, but that isn't the case for all packages).
Thanks!