Re: [R-pkg-devel] Do you run R on Fedora or Debian?
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 wrote:
>
> On Sat, 10 Dec 2022 14:00:22 -0800
> 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'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
>
> 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.mendelss...@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.
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
On Sat, 10 Dec 2022 14:00:22 -0800
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'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
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
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
I'm not sure I'm looking at the right versions, but it appears your
package uses hoardr::hoard() for caching. I looked for the source for
hoardr::hoard, and found it at
https://github.com/ropensci-archive/hoardr
It says the package has been "abandoned", with a version number slightly
higher than the one on CRAN.
So conceivably your problem is caused by a bug in the hoardr package,
and it looks like the authors of that package aren't going to deal with it.
Duncan Murdoch
On 10/12/2022 5:00 p.m., 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'.
Thanks,
-Roy
**
"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.mendelss...@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.
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
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 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@rob:~/git/digest(master)$ docker ps
> CONTAINER ID IMAGECOMMAND CREATED STATUS
> PORTS NAMES
> 18f6bf0e3bb1 eddelbuettel/r2u:jammy "bash"39 minutes ago Up 39
> minutes nervous_black
> edd@rob:~/git/digest(master)$ docker exec -ti nervous_black bash
> root@18f6bf0e3bb1:/# ls
> bin boot dev etc home lib lib32 lib64 libx32 media mnt opt proc
> root run sbin srv sys tmp usr var
> root@18f6bf0e3bb1:/# cd ~
> root@18f6bf0e3bb1:~# ls
> root@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 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
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
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$Latitude
> dataInfo <- rerddap::info('etopo180')
> parameter = 'altitude'
> xName <- 'longitude'
> yName <- 'latitude'
> bathy <- rxtractogon (dataInfo, parameter = parameter, xcoord = xcoord,
> ycoord = ycoord)
>
> getwd()
[1] "/"
>
Nothing spewn to stdout. Jumping into the same Docker session via the
much-underappreciated backdoor trick:
edd@rob:~/git/digest(master)$ docker ps
CONTAINER ID IMAGECOMMAND CREATED STATUS
PORTS NAMES
18f6bf0e3bb1 eddelbuettel/r2u:jammy "bash"39 minutes ago Up 39
minutes nervous_black
edd@rob:~/git/digest(master)$ docker exec -ti nervous_black bash
root@18f6bf0e3bb1:/# ls
bin boot dev etc home lib lib32 lib64 libx32 media mnt opt proc
root run sbin srv sys tmp usr var
root@18f6bf0e3bb1:/# cd ~
root@18f6bf0e3bb1:~# ls
root@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 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
| >
| >>
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
On Sat, 10 Dec 2022 14:00:22 -0800
Roy Mendelssohn - NOAA Federal via R-package-devel
wrote:
> cache_setup(temp_dir = TRUE)
Unfortunately, it prints a path under tempdir() for me on my Debian
oldstable machine.
I see that the error came from the "donttest" check from an extra test
that's not on by default with --as-cran. Unfortunately, not even
running _R_CHECK_DONTTEST_EXAMPLES_=true \
_R_CHECK_THINGS_IN_OTHER_DIRS_=TRUE R CMD check --as-cran \
--run-donttest rerddapXtracto_1.1.3.tar.gz reproduces the issue for me.
As a measure of last resort, could it help to manually go over
rerddapXtracto examples and see if any are wrapped in \donttest{} and
may be missing a cache setting?
--
Best regards,
Ivan
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
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
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.
Thanks,
-Roy
> On Dec 10, 2022, at 2:16 PM, Dirk Eddelbuettel 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 | e...@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.mendelss...@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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Re: [R-pkg-devel] Do you run R on Fedora or Debian?
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 | e...@debian.org
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[R-pkg-devel] Do you run R on Fedora or Debian?
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'.
Thanks,
-Roy
**
"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.mendelss...@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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