I'm trying to knit an rmarkdown file to a HTML but I keep getting the notification to update rmarkdown and digest packages. I keep trying to update these packages but I end up getting a non-zero exit status and can't knit the file. I keep getting the same codes below:
> install.packages("digest")
There is a binary version available but the source version is later:
binary source needs_compilation
digest 0.6.25 0.6.26 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘digest’
trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.26.tar.gz'
Content type 'application/x-gzip' length 163988 bytes (160 KB)
==================================================
downloaded 160 KB
* installing *source* package ‘digest’ ...
** package ‘digest’ 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 ‘digest’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/digest’
Warning in install.packages :
installation of package ‘digest’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/85/gmsx9yzj2h7bfzlsmz1x_0080000gn/T/Rtmp21PMeJ/downloaded_packages’
> install.packages("rmarkdown")
There is a binary version available but the source version is later:
binary source needs_compilation
rmarkdown 2.3 2.4 FALSE
installing the source package ‘rmarkdown’
trying URL 'https://cran.rstudio.com/src/contrib/rmarkdown_2.4.tar.gz'
Content type 'application/x-gzip' length 3202546 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
* installing *source* package ‘rmarkdown’ ...
** package ‘rmarkdown’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘digest’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘rmarkdown’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rmarkdown’
Warning in install.packages :
installation of package ‘rmarkdown’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/85/gmsx9yzj2h7bfzlsmz1x_0080000gn/T/Rtmp21PMeJ/downloaded_packages’