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

Roy Mendelssohn - NOAA Federal roy@mende|@@ohn @end|ng |rom no@@@gov
Sun Dec 11 00:02:06 CET 2022 

Thanks for the effort.  Yep that is what I see when I run in my virtual machine. I will play with it some more,  and hopefully someone from CRAN will see this and chime in.  I am more than willing to try to fix this,  I just can not reproduce the error.

-Roy

> On Dec 10, 2022, at 2:53 PM, Dirk Eddelbuettel <edd using debian.org> wrote:
> 
> 
> On 10 December 2022 at 14:27, Roy Mendelssohn - NOAA Federal wrote:
> | Perfect.  Thanks.  That is what I am seeing and that is what is expected.  I have even gotten into a debugger,  and looked at to where the file was downloaded,  right after the download,  and it is in a proper temporary space.
> | 
> | Dirk if you really want to be a glutton for punishment,  could you try this:
> | 
> | install.packages("rerddapXtracto",  dependencies = TRUE)
> | library(rerddapXtracto)
> | xcoord <- mbnms$Longitude
> | ycoord <- mbnms$Latitude
> | dataInfo <- rerddap::info('etopo180')
> | parameter = 'altitude'
> | xName <- 'longitude'
> | yName <- 'latitude'
> | bathy <- rxtractogon (dataInfo, parameter = parameter, xcoord = xcoord,
> |                       ycoord = ycoord)
> | 
> | What you would be looking for is any sign that this has left a file in cache in the user's space.  I don't find any in my virtual machine
> 
> As luck would have it [1] I still had that container session open in a tab
> from byobu [2] so continuing (and another 102 (!!!!!!!) packages as binaries
> installed in three or four seconds, gotta bless #r2u) 
> 
>> install.packages("rerddapXtracto",  dependencies = TRUE) # argument is > redundant, btw
> Install system packages as root...
> Reading package lists... Done
> Building dependency tree... Done
> Reading state information... Done
> Ign https://r2u.stat.illinois.edu/ubuntu jammy InRelease
> Hit https://r2u.stat.illinois.edu/ubuntu jammy Release
> [ ... many lines from r2u & bspm processing omitted ... ]
> Setting up r-cran-plotdap (1.0.0-1.ca2204.1) ...
> Setting up r-cran-rerddapxtracto (1.1.3-1.ca2204.1) ...
> Processing triggers for libc-bin (2.35-0ubuntu3.1) ...
>> library(rerddapXtracto)
>> xcoord <- mbnms$Longitude
>> ycoord <- mbnms$Latitude
>> dataInfo <- rerddap::info('etopo180')
>> parameter = 'altitude'
>> xName <- 'longitude'
>> yName <- 'latitude'
>> bathy <- rxtractogon (dataInfo, parameter = parameter, xcoord = xcoord, ycoord = ycoord)
>> 
>> getwd()                                                                     
> [1] "/"
>> 
> 
> Nothing spewn to stdout. Jumping into the same Docker session via the
> much-underappreciated backdoor trick:
> 
> edd using rob:~/git/digest(master)$ docker ps
> CONTAINER ID   IMAGE                    COMMAND   CREATED          STATUS          PORTS     NAMES
> 18f6bf0e3bb1   eddelbuettel/r2u:jammy   "bash"    39 minutes ago   Up 39 minutes             nervous_black
> edd using rob:~/git/digest(master)$ docker exec -ti nervous_black bash
> root using 18f6bf0e3bb1:/# ls
> bin  boot  dev  etc  home  lib  lib32  lib64  libx32  media  mnt  opt  proc  root  run  sbin  srv  sys tmp  usr  var
> root using 18f6bf0e3bb1:/# cd ~
> root using 18f6bf0e3bb1:~# ls
> root using 18f6bf0e3bb1:~#
> 
> we see no files in / (where we started) or $HOME.
> 
> | Assuming that pans out,  now my question is how to respond to CRAN.  I can give you one guess who from CRAN sent me the notice,  As I said,  I don't know how to fix something when everything I am have available to behaves properly.
> 
> I have no idea. But I would trust Ivan's advice as he is essentially always
> spot on and minimize / control interaction.  If CRAN reports this to you,
> they see it. You should have access to `tempdir()` and friends to make things
> per-session, or else you need to ask the user (once) and then store in
> user-supplied location.  I think that was discussed here recently.
> 
> Good luck,  Dirk
> 
> [1] Also commonly called 'attention deficit disorder'
> [2] A more user-friendly variant of tmux
> 
> 
> | Thanks,
> | 
> | -Roy
> | 
> | > On Dec 10, 2022, at 2:16 PM, Dirk Eddelbuettel <edd using debian.org> wrote:
> | > 
> | > 
> | > On 10 December 2022 at 14:00, Roy Mendelssohn - NOAA Federal via R-package-devel 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 would really appreciate it if someone who runs Debian or Fedora could test the following:
> | > | 
> | > | install.packages("rerddap",  dependencies = TRUE)
> | > | library(rerddap)
> | > | cache_setup(temp_dir = TRUE)
> | > | 
> | > | The last line should print where the cache is setup.  That is called at the start of all of my functions that do downloads.  If you could run that and send me the result I would appreciate it (snd privately no need to spam the list with that).  I am at a loss as to how to respond to CRAN because I can't reproduce that error on anything I can test.  The cacheing is actually done by the package 'crul'.  
> | > 
> | > I used r2u [1] here to install the thirty-six (!!) required dependencies in a
> | > five or so seconds [2], for convenience in Docker with the Ubuntu 22.04
> | > image.  So from
> | > 
> | >  docker run --rm -ti eddelbuettel/r2u:jammy bash
> | > 
> | > to
> | > 
> | >  apt update -qq 
> | >  install.r rerddap
> | > 
> | > and then as you requested
> | > 
> | >> library(rerddap)
> | >> cache_setup(temp_dir = TRUE)
> | >  [1] "/tmp/Rtmp3sVsk1/R/rerddap"
> | >> 
> | > 
> | > which seems correct: within the per-R-session temp directory.
> | > 
> | > Hth, Dirk
> | > 
> | > [1] See https://eddelbuettel.github.io/r2u/
> | > [2] That's the point of r2u. See [1].
> | > 
> | > -- 
> | > dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
> | 
> | **********************
> | "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/
> | 
> | "Old age and treachery will overcome youth and skill."
> | "From those who have been given much, much will be expected" 
> | "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
> | 
> 
> -- 
> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org

**********************
"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/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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