I have never considered myself a good developer. Coding activities such as writing some functions in Rcpp for an R package and building my personal website (nianqiaoju.github.io) already makes me proud.
Last night, I had some trouble building a package in RStudio. At the beginning, I thought it was because I accidentally included a test file in the
ProjectDirectory/R folder, but it was not the case. So I had no choice but to read the error messages carefully.
I did not keep a record of this, but important bits of the messages look like:
ld: unknown option: -platform_version
clang: error: linker command failed with exit code 1 (use -v to see invocation)
That’s when I started to realize that this had to do with a recent MacOS update and probably my package was fine. Interestingly, I did not recall authorizing a system update and learned about this only through running
sessionInfo() in console. These are some trouble shooting steps I did in RStudio console:
- check if devtools works:
devtools::load_all()–>> leads to error messages
- check if Rcpp works:
Rcpp::evalCpp("2+2")–>> leads to error messages.
It seemed like the operating system update has ‘disabled’ my R compiler tools for RCpp. Unfortunately, despite the huge amount of information on stack-overflow and github issues, I did not see any error messages matching exactly what I saw and there were some conflicting information. Moreover, I did not want to install the whole XCode app or to cause any irreversible damages. After one hour of trial and errors, below is what I think solved my crisis.
- run in terminal
xcode-select --installand it turns out my command line tools are already installed since the message
xcode-select: error: command line tools are already installed, use "Software Update" to install updates.
- run in terminal
gcc --versionand this is to confirm that the command
gccis recognized by my terminal.
- set the file
~/.R/Makevarsto point to the system headers. I did it with vim: add the following lines to the file and comment out what’s already there.
# clang: start CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk # clang: end
I believe that the last step did the magic for me and I was able to build packages from source without any trouble.
In this process this stack-overflow discussion and this blogpost were the most helpful.