Hi, I just updated R:
R version 4.0.1 (2020-06-06)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5
trying to install some bioconductor packages (ChIPQC and DiffBind) but they seem to be getting hung up due to the survival package. They won't run with the older binary version, but any package I try to install from source rather than binary produces the following error message.
install.packages('survival')
There is a binary version available but the source version is later:
binary source needs_compilation
survival 3.1-12 3.2-3 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘survival’
trying URL 'https://cran.rstudio.com/src/contrib/survival_3.2-3.tar.gz'
Content type 'application/x-gzip' length 7475152 bytes (7.1 MB)
==================================================
downloaded 7.1 MB
* installing *source* package ‘survival’ ...
** package ‘survival’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘survival’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/survival’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/survival’
Warning in install.packages :
installation of package ‘survival’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/lf/tsvys90s2pnbs0nf08wq9bmr0000gn/T/RtmpwGpyDe/downloaded_packages’