Error about "file exists" when opening a project

[bioteamMichael]

I just updated R via homebrew, and now when I launch the RStudio IDE on my mac and open an existing project I get

Warning message:
In file.symlink(from, to) :
  cannot symlink '/usr/local/Cellar/r/4.0.2_1/lib/R/library/base' to '/Users/mike/src/work/gRED/packrat/lib-R/x86_64-apple-darwin19.5.0/4.0.2/base', reason 'File exists'

I'm assuming that this is something with the update to R, since the symlink exists but points to the old version of R I had:

$ ls -l /Users/mike/src/work/gRED/packrat/lib-R/x86_64-apple-darwin19.5.0/4.0.2/base
lrwxr-xr-x 1 mike staff 44 Jun 23 21:58 /Users/mike/src/work/gRED/packrat/lib-R/x86_64-apple-darwin19.5.0/4.0.2/base -> /usr/local/Cellar/r/4.0.2/lib/R/library/base

Running packrat::restore() didn't seem to help out any.

[bioteamMichael]

Quitting RStudio, deleting all the symlinks in ~/src/work/gRED/packrat/lib-R/x86_64-apple-darwin19.5.0/4.0.2, and then relaunching caused everything to be relinked correctly, but I'd be curious to know why that happened.

Could it be because homebrew provided an updated build of 4.0.2?

[kevinushey]

That seems possible. Packrat is supposed to be able to refresh those symlinks on demand as required.

packrat/R/library-support.R

Lines 3 to 33 in 5173a3f

	symlinkSystemPackages <- function(project = NULL) {
	project <- getProjectDir(project)
	# skip symlinking if requested by user
	if (identical(opts$symlink.system.packages(), FALSE))
	return(FALSE)
	# Get the path to the base R library installation
	sysLibPath <- normalizePath(R.home("library"), winslash = "/", mustWork = TRUE)
	## Get the system packages
	sysPkgs <- utils::installed.packages(sysLibPath)
	sysPkgsBase <- sysPkgs[!is.na(sysPkgs[, "Priority"]), ]
	sysPkgNames <- rownames(sysPkgsBase)
	## Make a directory where we can symlink these libraries
	libRdir <- libRdir(project = project)
	if (!file.exists(libRdir))
	if (!dir.create(libRdir, recursive = TRUE))
	return(FALSE)
	## Generate symlinks for each package
	for (pkg in sysPkgNames) {
	source <- file.path(sysLibPath, pkg)
	target <- file.path(libRdir, pkg)
	if (!ensurePackageSymlink(source, target))
	return(FALSE)
	}
	TRUE
	}

packrat/R/library-support.R

Lines 72 to 118 in 5173a3f

	ensurePackageSymlink <- function(source, target) {
	cleanRecursivePackageSymlinks(source)
	# If we have a symlink already active in the
	# target location, check that it points to the
	# library corresponding to the current running
	# R session.
	if (file.exists(target)) {
	if (isPathToSamePackage(source, target))
	return(TRUE)
	# Remove the old symlink target (swallowing errors)
	tryCatch(
	unlink(target, recursive = !is.symlink(target)),
	error = identity
	)
	# Check if the file still exists and warn if so
	if (file.exists(target)) {
	# request information on the existing file
	info <- paste(capture.output(print(file.info(target))), collapse = "\n")
	msg <- c(
	sprintf("Packrat failed to remove a pre-existing file at '%s'.", target),
	"Please report this issue at 'https://github.com/rstudio/packrat/issues'.",
	"File info:",
	info
	)
	warning(paste(msg, collapse = "\n"))
	}
	}
	# If, for some reason, the target directory
	# still exists, bail as otherwise symlinking
	# will not work as desired.
	if (file.exists(target))
	stop("Target '", target, "' already exists and is not a symlink")
	# Perform the symlink.
	symlink(source, target)
	# Success if the file now exists
	file.exists(file.path(target, "DESCRIPTION"))
	}

Regardless, the right way to "fix" this is to delete the old symlinks so that Packrat can refresh them, or to simply disable sandboxing altogether (if you don't need to rely on the system library being sandboxed).