Fail to install R kernel for Jupyter in Mac

0
votes

I use the following lines:

install.packages('devtools')
devtools::install_github('IRkernel/IRkernel')

but get warnings:

  • installing source package ‘IRkernel’ ... Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'default/America/Los_Angeles' ** R ** inst ** tests ** preparing package for lazy loading xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Warning: running command '/usr/bin/otool -L /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pbdZMQ/libs/pbdZMQ.so' had status 1 Error : .onLoad failed in loadNamespace() for 'pbdZMQ', details: call: if (org != fn.libzmq.4.dylib) { error: missing value where TRUE/FALSE needed ERROR: lazy loading failed for package ‘IRkernel’
  • removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRkernel’

I try to solve this problem by

xcode-select --install

but get 

Error: object 'xcode' not found
1
rmacoskerneljupyter
So what version of Xcode do you have (if any)? You do need it to compile packages from github since they are typically not provided as binaries. (It's not something that Apple provides standard.) – IRTFM

1 Answers

0
votes

Late answer, but this just happened to me and I got the

Error: object 'xcode' not found

because I was still running R in Terminal. Make sure you quit R with

quit()

and then run

xcode-select --install

again (using Bash/Terminal, not R from within Terminal).