Rcpp compilation breaks in R 4.1.0 running on Big Sur 11.4

[jphill1]

Hello!

I've recently updated to R 4.1.0 as well as Xcode 12.5.1 after installing macOS Big Sur 11.4. However, I am unable to run R packages requiring compiled code via Rcpp.

I have both Clang 12.0.5 build 1205 and Command Line Tools 12.5.1.0.1.1623191612 installed.

However, in RStudio, I am continually prompted to install additional build tools and I can't seem to figure out why. I can bypass this with options(buildtools.check = function(action) TRUE), but this doesn't resolve the problem.

When I attempt to build my package I get a number of errors which I found are due to Rcpp not being able to be compiled properly, similar to those found here

Cannot compile R packages with c++ code after updating to macOS Catalina

devtools::build("my_package")
Error: Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.

When I call the above link and click either Yes or No, I receive the exact same error message again.

I've also followed this link for assistance

Release To R 4.0.0 and Beyond! · coatless-mac/r-macos-rtools

but the issue still persists.

Here is my brew config. Note: I did not install R via Homebrew, so no need to run `brew install -- cask r'.

HOMEBREW_VERSION: 3.2.0
ORIGIN: https://github.com/Homebrew/brew
HEAD: 09f7bc27a99469cf947431df4754737dfbadb31d
Last commit: 3 weeks ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: b1c76d0f6e481ae009775f96f89c6cd1c635822d
Core tap last commit: 6 days ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.rMYzzALIlM/org.macosforge.xquartz:0
HOMEBREW_MAKE_JOBS: 4
Homebrew Ruby: 2.6.3 =>     /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: quad-core 64-bit broadwell
Clang: 12.0.5 build 1205
Git: 2.10.1 => /usr/local/bin/git
Curl: 7.64.1 => /usr/bin/curl
macOS: 11.4-x86_64
CLT: 12.5.1.0.1.1623191612

Disclaimer: I posted an issue (#118) on this on GitHub pkgbuild repo. Jim Hester, a fellow macOS user and RStudio aficionado has been helpful, but we've still not been able to arrive at a solution.

So, I thought I'd cast a wider net by asking on this forum.

Any help is warmly welcomed and greatly appreciated

Thanks!

[kbrevoort]

Hi. Were you able to find a solution to your problem?

I seem to be having the same issue. I upgraded to Big Sur v. 11.5.1 and as soon as I did I started getting the same "could not find tools necessary to compile a package" error message. I've tried reinstalling Xcode and Command Line Tools, but haven't been able to really diagnose the problem or figure out how to fix it.

Thanks!

[jphill1]

Same here... no solution. I'm still stuck!

I've tried everything I can think of and managed to find via Googling.

This said, I've noticed my Makevars file in the .R folder still says it using Clang4 even though I have Clang12 installed. I am unable to edit this file because apparently I don't have permission to do so.

I have done everything instructed on

R Compiler Tools for Rcpp on macOS | The Coatless Professor

but I still get the weird pop-up window asking me to install additional tools.

[jphill1]

@kbrevoort I fixed the issue!

Turns out R was pointing to an old clang version in my Makevars.

I just deleted it using

sudo rm ~/.R/Makevars

I hope this helps you out!