[R-pkg-devel] Do you run R on Fedora or Debian?

[Roy Mendelssohn - NOAA Federal]

Thanks.  Yes,  that is what I figured out last night.  I believe the problem is actually coming from rerddap,  not rerddapXtracto - which as I said creates a tempdir on first call.  I am submitting a new version of rerddap today,  as well as a new version of rerddapXtracto in the next few days.  I will look at hoardr and see if I can take it over.  I know hoardr uses R6 methods,  of which I know nothing,  maintaining it may be over my capabilities,  but I will give it a look.

I really appreciate the help several people have given me.  This is the best of what help-lists are suppose to be about.

-Roy

PS - If a do take over hoardr,  what is the process for becoming the new maintainer of a CRAN package



> On Dec 11, 2022, at 3:45 AM, Ivan Krylov <krylov.r00t using gmail.com> wrote:
> 
> On Sat, 10 Dec 2022 14:00:22 -0800
> Roy Mendelssohn - NOAA Federal via R-package-devel
> <r-package-devel using r-project.org> wrote:
> 
>> CRAN has sent me a notice about the following:
>> 
>> https://www.stats.ox.ac.uk/pub/bdr/donttest/rerddapXtracto.out
>> 
>> I can not reproduce it.  I test on my Mac,  the cache space is
>> properly handled  (by a package outside mine).  Same with Debian on
>> r-hub.  I installed Fedora on a virtual machine, no problem  (it is
>> assigned a space in /tmp).
> 
> I've trace()d rerddap:::gen_key to notify me when a file with the cache
> key of 4f8f83808465a7f7619285e9871747af is being downloaded. Since
> digest::digest defaults to serialize = TRUE, this should only work with
> R-to-be-4.3.0 (I compiled R-devel r83400, same as in the failed check):
> 
> library(rerddapXtracto)
> trace(
> rerddap:::gen_key,
> quote({
>  if(digest::digest(ky) == '4f8f83808465a7f7619285e9871747af') {
>   cat('\n\nFound a match\n\n')
>   str(url); str(args); print(ky); str(digest::digest(ky))
>   message('\n\nFound a match\n\n')
>  }
> }),
> at = 3
> )
> example(rxtracto)
> example(rxtracto_3D)
> example(rxtractogon)
> 
> Surprisingly, there were no hits. I also tried copying and pasting all
> code from the vignette and even uncommenting the code marked as
> \dontrun{}, also with no results.
> 
> The code that actually creates these files lives in the rerddap
> package. The page at
> <https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-gcc>
> says that packages are checked in parallel. What if an unlucky reverse
> dependency of rerddap was being checked at the same time as your
> package, making rerddapXtracto get its NOTE?
> 
> I cleaned ~/.cache/R, put the rerddap source package in a directory and
> ran:
> 
> (res <- tools::check_packages_in_dir(
> '.', check_args = '--run-donttest', reverse = list(recursive = TRUE),
> check_env = c(
>  "_R_CHECK_DONTTEST_EXAMPLES_=true",
>  "_R_CHECK_THINGS_IN_OTHER_DIRS_=true"
> )
> ))
> 
> I got a NOTE for plotdap!
> 
> * checking for new files in some other directories ... NOTE
> Found the following files/directories:
>  ‘~/.cache/R’ ‘~/.cache/R/rerddap’
>  ‘~/.cache/R/rerddap/1b43b4335f06b318b914ba2cc2f88872.nc’
>  ‘~/.cache/R/rerddap/4f8f83808465a7f7619285e9871747af.nc’
>  ‘~/.cache/R/rerddap/8cb244e059b86865b7933a3d9b72fe16.csv’
> 
> Looking at the examples for plotdap::add_griddap and
> plotdap::add_tabledap, I think that they may be responsible for the
> NOTE, because there's no pre-example cache setup and teardown. I also
> finally got a match from my tracing code by running
> example(add_griddap).
> 
> There's more than one way to do it right; my favourite would be to wrap
> the pre-example code and post-example code in \dontshow{}, changing the
> cache settings in the first block and restoring them in the second one.
> Everywhere else I would use on.exit(), but examples are special in
> their relationship with autoprinting and crashing there being
> disallowed, making this approach feasible.
> 
> -- 
> Best regards,
> Ivan

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn using noaa.gov www: https://www.pfeg.noaa.gov/

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"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.