Issues using renv in docker image with a volume mount

[ramnathv]

@kevinushey I am running RStudio Server in a docker image with a volume mount. When I log in to RStudio, .libPaths() links to two libaries, a /usr/local/lib/R/site-library which holds the custom packages installed during the docker build and a usr/local/lib/R/library which holds the base+recommended packages that ship with R. In order to have access to the custom packages as well, I initialize renv in my project directory using:

renv::init(settings = list(external.libraries = "/usr/local/lib/R/site-library"))

After initialization, when I try to load packages that are compiled (e.g. rappdirs, yaml etc), I run into the following error, which I believe is because of the cache being in a volume mount with noexec permissions.

Error: package or namespace load failed for ‘rappdirs’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/ramnath/.cache/R/renv/cache/v5/R-4.2/x86_64-pc-linux-gnu/rappdirs/0.3.3/5e3c5dc0b071b21fa128676560dbe94d/rappdirs/libs/rappdirs.so':
  /home/ramnath/.cache/R/renv/cache/v5/R-4.2/x86_64-pc-linux-gnu/rappdirs/0.3.3/5e3c5dc0b071b21fa128676560dbe94d/rappdirs/libs/rappdirs.so: failed to map segment from shared object

If I remove the offending packages from the cache folder, they load correctly, as they now load from the external library.

My question is what is considered best-practice in handling such a situation. Is there a way I can tell renv NOT to copy some packages to the cache? I searched around for mounting a volume with exec permissions, but could not find a reasonable approach to do that. I would love to get some pointers on how to approach this. Thanks in advance.

[kevinushey]

Is there a way I can tell renv NOT to copy some packages to the cache?

Not on that granularity -- the cache is either "on" or "off" for a project. In theory we could add an extension here:

renv/R/records.R

Lines 37 to 52 in d52a544

	renv_record_cacheable <- function(record) {
	# check if the record has been marked as cacheable
	cacheable <- record$Cacheable %||% TRUE
	if (identical(cacheable, FALSE))
	return(FALSE)
	# check for unknown source
	source <- renv_record_source(record)
	if (source == "unknown")
	return(FALSE)
	# record is ok
	TRUE
	}

To disable the cache wholesale, you could use the use.cache = FALSE setting; see https://rstudio.github.io/renv/reference/settings.html for some more details.

[ramnathv]

@kevinushey On further investigation, I realized that I have to nuke compiled packages from the renv project library due to the aforementioned error. Once I do that they are loaded from the site-library. I realize that the issue is because I volume mount my home directory in a docker image, and as a result the project library is on a disk with noexec permissions. Is it possible to volume mount with exec permissions in docker? If not, is there any other workaround here, since it seems to be a big blocker using renv in docker settings, unless one sets up a shared cache.

[kevinushey]

I'm not sure to be honest. The advice I've been able to find online seems roughly:

• Prefer using bind mounts if you need the mount to be exec,
• Maybe it's possible to pass an argument through --volume-opt?

Perhaps worth an ask on StackOverflow or some other Docker-specific forum?