when tempdir() is overridden by the TMPDIR global variable, e.g. with snakemake in its script directive, an expected tmp directory is unavailable for use at some point that it's unconditionally accessed, leading to a rather cryptic hard crash.
my guess is that this is related to the invocation of rmarkdown::render, when its processing directories are instructed to be tempdir(). we'd first need to track down exactly where the code is going down, and then fix it.
when tempdir() is overridden by the TMPDIR global variable, e.g. with snakemake in its script directive, an expected tmp directory is unavailable for use at some point that it's unconditionally accessed, leading to a rather cryptic hard crash.
my guess is that this is related to the invocation of rmarkdown::render, when its processing directories are instructed to be tempdir(). we'd first need to track down exactly where the code is going down, and then fix it.