Dual exceptions for 'IRkernel' and 'pbdzmq'

[shivendra90]

Was writing a sample R script when pyCharm threw these exceptions: java.lang.Throwable: Failed to generate skeleton for 'IRkernel'. The error was:

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: 
/Library/Developer/CommandLineTools/usr/bin/xcrun
Error: package or namespace load failed for ‘IRkernel’:
.onLoad failed in loadNamespace() for 'pbdZMQ', details:
 call: if (id[2] != fn.dylib) {
 error: missing value where TRUE/FALSE needed
In addition: Warning message:
In system(paste(cmd.ot, " -D ", fn.dylib, sep = ""), intern = TRUE) :
running command '/usr/bin/otool -D /Users/Shiv/Library/R/3.5/library/pbdZMQ/libs/libzmq.5.dylib' 
had status 1
Execution halted

If you think this issue with plugin and not your R installation, please file a ticket under 
https://github.com/holgerbrandl/r4intellij/issues

at com.intellij.openapi.diagnostic.Logger.error(Logger.java:123)
at com.r4intellij.packages.RSkeletonGenerator.lambda$updateSkeletons$1(RSkeletonGenerator.java:236)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

Similar exceptions for modules 'pbdZMQ' as well as 'tcltk' that I'm including in the below txt file instead of pasting the whole message.

error.txt

[holgerbrandl]

Thanks for reporting the issue.

[ktisha]

Looks like the problem appears after the OS update and caused by the license agreement in Xcode.

Open the Terminal App and enter:

xcode-select --install

See more information here -- https://apple.stackexchange.com/questions/254380/macos-mojave-invalid-active-developer-path

[shivendra90]

Yes, there is also a similar issue when using the Atom editor interactively and it relates to Xcode's license agreement. Have fixed it on my side, will test on PyCharm and report back.