File paths with drake on a shared drive - r

Question

I am encountering some odd drake behaviour which I just can't figure out. I am trying to add a .rmd to my drake plan. I am working on a remote machine AND on a network drive on that machine. If I try to add an .rmd file to my plan like this:
> library(drake)
> library(rmarkdown)
>
> list.files()
[1] "drake_testing.Rproj" "foo.png" "report.Rmd"
>
> plan <- drake_plan(
+ png("foo.png"),
+ plot(iris$Sepal.Length ~ iris$Sepal.Width),
+ dev.off(),
+ report = render(
+ input = knitr_in("report.Rmd"),
+ output_file = "report.html",
+ quiet = TRUE
+ )
+
+ )
>
> plan
# A tibble: 4 x 2
target command
<chr> <expr>
1 drake_target_1 png("foo.png")
2 drake_target_2 plot(iris$Sepal.Length ~ iris$Sepal.Width)
3 drake_target_3 dev.off()
4 report render(input = knitr_in("report.Rmd"), output_file = "report.html", quiet = TRUE)
>
> ## Turn your plan into a set of instructions
> config <- drake_config(plan)
Error: The specified file is not readable: report.Rmd
>
> traceback()
13: stop(txt, obj, call. = FALSE)
12: .errorhandler("The specified file is not readable: ", object,
mode = errormode)
11: digest::digest(object = file, algo = config$hash_algorithm, file = TRUE,
serialize = FALSE)
10: rehash_file(file, config)
9: rehash_storage(target = target, file = file, config = config)
8: FUN(X[[i]], ...)
7: lapply(X = X, FUN = FUN, ...)
6: weak_mclapply(X = keys, FUN = FUN, mc.cores = jobs, ...)
5: lightly_parallelize_atomic(X = X, FUN = FUN, jobs = jobs, ...)
4: lightly_parallelize(X = knitr_files, FUN = storage_hash, jobs = config$jobs,
config = config)
3: cdl_get_knitr_hash(config)
2: create_drake_layout(plan = plan, envir = envir, verbose = verbose,
jobs = jobs_preprocess, console_log_file = console_log_file,
trigger = trigger, cache = cache)
1: drake_config(plan)
I have tried the following permutations to make this work:
Move the .rmd to the local drive and call it with the full path to there
Add in file.path inside and outside of knitr_in to complete a full path.
Try using file_in for each of the scenarios above.
I have also tried debugging but I get a little lost when drake turns the file name into a hash then turns it back into the basename of the file (i.e. report.Rmd). The error ultimately happens when digest::digest is called.
Does anyone have experience attempting to figure out something like this?

Answer 1

I think the answer depends on whether you get the same error when you call digest("report.Rmd", file = TRUE) on its own outside drake_config(plan). If it errors (which I am betting it does) there may be something strange about your file system that clashes with R. If that is the case, then there is unfortunately nothing drake can do.
I also suggest some changes to your plan:
plan <- drake_plan(
plot_step = {
png(file_out("foo.png")),
plot(iris$Sepal.Length ~ iris$Sepal.Width),
dev.off()
},
report = render(
input = knitr_in("report.Rmd"),
output_file = "report.html",
quiet = TRUE
)
)
Or better yet, compartmentalize your work in reusable functions:
plot_foo = function(filename) {
png(filename),
plot(iris$Sepal.Length ~ iris$Sepal.Width),
dev.off()
}
plan <- drake_plan(
foo = plot_foo(file_out("foo.png")),
report = render(
input = knitr_in("report.Rmd"),
output_file = "report.html",
quiet = TRUE
)
)
A target is a skippable workflow step with a meaningful return value and/or output file(s). png() and dev.off() are part of the plotting step, and file_out() tells drake to watch foo.png for changes. Also, it is good practice to name your targets. Usually, the return values of targets are meaningful, just like variables in R.