Is there a known problem with downloading files in examples?

[dankelley]

Summary: I wonder how to debug a problem with build_site() and downloading to a tempdir().

I'm working on a package that downloads oceanographic data. As I understand it, that's a problem for a package that might have hopes of getting on CRAN.

Some of the functions have a parameter that I call destdir, which is where to save the downloaded files. In my work, that will be ~/data/, for example. But, in my example code, I use tempdir() to get a temporary directory in which to save the files.

This scheme works in practice. And it works within examples, when I run those examples locally, or when I run the "check" action in RStudio.

However, when I try building the package docs with pkgdown::build_site(), I get that a download occurs, but then that gzfile cannot find the file. An example is below.

Warning message:
In gzfile(file, mode) :
  cannot open compressed file '/var/folders/8b/l4h64m1j22v5pb7vj049ff140000gn/T//RtmpNry5AV/downlit/base', probable reason 'No such file or directory'

This is odd, because I'm calling it with

destdir <- tempdir("amsr")
file <- dod.amsr(destdir = destdir)

where I'm stating that the text "amsr" ought to be part of the directory name.

I don't really know how to debug this sort of problem. My code (https://github.com/dankelley/dod/) is quite long. Should I try to boil it down and post that, or is there a known problem that can occur with downloads to temporary directories?

[jayhesselberth]

AKAIK there's nothing intrinsic to pkgodwn that should prevent this, but as you surmised CRAN will not allow it.

tempdir() doesn't take a pattern as an argument. tempfile() does though. See ?tempdir.

And yes I suggest that you make a minimal package that recapitulates the problem. There are some instructrions for that here.

[dankelley]

Thanks, you're right on the mistake about supplying a parameter to tempdir(). That wasn't the problem though. Based on your advice, I made a small project (at https://github.com/dankelley/downloadtest) and found as follows. (Please note that I do not absolutely need this to work, but I really do like making a website with pkgdown because if there are examples that are run, users can see the results. Lots of users prefer that to using the ? mechanism and clicking on the run-code phrase.)

1. it builds OK, and it runs OK when I copy-paste to the console and also when I click the run-examples phrase in the docs shown in RStudio
2. it checks OK with the RStudio 'check' button
3. when I try pkgdown::build_site() (version 2.1.0 of pkgdown) and I get as follows, which is the same sort of thing I had in my actual project.

Reading man/linesInRemoteFile.Rd
trying URL 'https://raw.githubusercontent.com/dankelley/dod/main/NEWS.md'
Content type 'text/plain; charset=utf-8' length 1613 bytes
==================================================
downloaded 1613 bytes

Warning message:
In gzfile(file, mode) :
  cannot open compressed file '/var/folders/8b/l4h64m1j22v5pb7vj049ff140000gn/T//RtmptPkNky/downlit/base', probable reason 'No such file or directory'
Error: 
! in callr subprocess.
Caused by error in `build_reference()`:
! Failed to parse Rd in linesInRemoteFile.Rd
Caused by error in `gzfile()`:
! cannot open the connection
ℹ See `$stdout` and `$stderr` for standard output and error.
Type .Last.error to see the more details.

[jayhesselberth]

I can't see your test repo: https://github.com/dankelley/downloadtest

Is it in private status?

[dankelley]

Oh, I'm so sorry about that. I didn't make it in my usual way. It's public now. My apologies for being such a bother.

[dankelley]

FYI, my session info is as follows.

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS 15.0

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Halifax
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

loaded via a namespace (and not attached):
[1] compiler_4.4.1 tools_4.4.1