Re: [R-pkg-devel] CRAN submission struggle

[Roy Mendelssohn - NOAA Federal via R-package-devel]

And a second good starting place would be:

https://r-pkgs.org

HTH,

-Roy

> On Dec 16, 2023, at 9:48 AM, Roy Mendelssohn - NOAA Federal 
>  wrote:
> 
> 
> 
>> On Dec 16, 2023, at 9:41 AM, Christiaan Pieterse  
>> wrote:
>> 
>> I checked the tar file using *R CMD check --as-cran
>>  "iopspackage_2.1.0.tar.gz". *This yielded errors, warnings and notes
>>  which I don't know how to solve and suspect are due to me setting the file
>>  up wrong.
> 
> A good start might be to provide the "errors, warnings and notes"
> 
> 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.
> 

**
"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] CRAN submission struggle

[Roy Mendelssohn - NOAA Federal via R-package-devel]

> On Dec 16, 2023, at 9:41 AM, Christiaan Pieterse  
> wrote:
> 
>  I checked the tar file using *R CMD check --as-cran
>   "iopspackage_2.1.0.tar.gz". *This yielded errors, warnings and notes
>   which I don't know how to solve and suspect are due to me setting the file
>   up wrong.

A good start might be to provide the "errors, warnings and notes"

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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Re: [R-pkg-devel] winbuilder

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Not too long after I sent the message it came back up. 

Thanks!  

-Roy

> On Oct 18, 2023, at 8:39 AM, Michael Dewey  wrote:
> 
> Dear Roy
> 
> When I just checked using the winbuilder_queue function from the foghorn 
> package it seemed to respond and had one package in the queue. Not sure that 
> is definitive evicence.
> 
> Michael
> 
> On 18/10/2023 16:16, Roy Mendelssohn - NOAA Federal via R-package-devel wrote:
>> I am not sure who is the appropriate person to contact,  but thought I would 
>> try here since WInbuilder is a big help in package testing.  Winbuilder 
>> appears to be down at the moment.
>> 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
> 
> -- 
> Michael

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[R-pkg-devel] winbuilder

[Roy Mendelssohn - NOAA Federal via R-package-devel]

I am not sure who is the appropriate person to contact,  but thought I would 
try here since WInbuilder is a big help in package testing.  Winbuilder appears 
to be down at the moment.

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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Re: [R-pkg-devel] CRAN test complaints about package that passes most platforms

[Roy Mendelssohn - NOAA Federal via R-package-devel]

> On Aug 11, 2023, at 1:41 PM, J C Nash  wrote:
> 
> - Is there an M1Mac test platform to which packages can be submitted? Brian
> Ripley did have one, but trying the link I used before seems not to present
> a submission dialog.

Perhaps:

https://mac.r-project.org/macbuilder/submit.html

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

[Roy Mendelssohn - NOAA Federal via R-package-devel]

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
> <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.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?

[Roy Mendelssohn - NOAA Federal via R-package-devel]

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). 

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

[Roy Mendelssohn - NOAA Federal via R-package-devel]

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

[Roy Mendelssohn - NOAA Federal via R-package-devel]

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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Re: [R-pkg-devel] Cannot submit package due to false-positive rejection

[Roy Mendelssohn - NOAA Federal via R-package-devel]

I run into this all the time.  The trick is to find a minimal example that the 
package will work with that shows how to make a call,  and allows for CRAN, 
especially on new submissions,  to test to some extent that the function works. 
 For more real-life examples,  write a good vignette that uses the larger 
dataset,  but remember that the build of the vignette also has a time limit, I 
think it is 10 minutes but don't quote me on that.

I may mis-state this a little,  but I believe CRAN does a nightly build of the 
entire environment.  If things take too long,  the build would never finish.  I 
am certain there are several reasons for doing this,  but one reason is to 
attempt to insure that all packages work together so that they will work when 
you install them into your environment.  As compared to another,  unnamed 
language where even using the package manager I have had to trash the entire 
environment due to inconsistencies, so packages wouldn't load. Once even after 
a clean install and an "update all",  several major packages wouldn't load due 
to inconsistencies.  If that ever has happened in R I don't remember it,  and 
why I go to the trouble to get my packages into CRAN,  because a lot of users 
just want things to work when they install the package,  and CRAN helps with 
that.

HTH,

-Roy



> On Oct 28, 2022, at 3:02 PM, Jeff Newmiller  wrote:
> 
> This is definitely not a false positive. Find a way to not run long calcs 
> during the CRAN build. There is no alternative.
> 
> One way this can be done is by only running your examples when an environment 
> variable of your choosing exists. Since CRAN machines won't configure that 
> variable, you can get around this hard requirement.
> 
> On October 28, 2022 12:48:44 PM PDT, Ying Li via R-package-devel 
>  wrote:
>> Hello all,
>> 
>> Our package did not pass the automagical checks when submitted to CRAN. We 
>> think the rejection is a false positive, so we �reply-all to that message 
>> and explain� as following the official instruction. We provided explanation 
>> for all notes in that email (replied to 
>> cran-submissi...@r-project.org) but 
>> did not receive any message after 9 days.
>> 
>> I am looking for suggestions on what to do in this case: should we continue 
>> waiting for CRAN team�s reply? Or is it necessary to eliminate those notes 
>> and then submit the package again?
>> 
>> Below are the notes from CRAN teams' auto-check service and our explanation 
>> send to CRAN team:
>> 
>>> Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
>>> Check: CRAN incoming feasibility, Result: NOTE
>>> Maintainer: 'Arindam RoyChoudhury 
>>> mailto:arr2...@med.cornell.edu>>'
>> 
>>> New submission
>> 
>>> Possibly misspelled words in DESCRIPTION:
>>>   Peng (17:5)
>>>   Phylogenetics (17:32)
>>>  al (17:13)
>>>   et (17:10)
>> 
>>> Size of tarball: 14208488 bytes
>> 
>> Explain:  This is a new submission. These words are not misspelled.
>> 
>>> Flavor: r-devel-windows-x86_64
>>> Check: examples, Result: NOTE
>>> Examples with CPU (user + system) or elapsed time > 10s
>>>  user system elapsed
>>> RDM 40.05   0.89   40.94
>> 
>> Explain:  This is because a large dataset is used in the example. An example 
>> with large dataset is necessary, as this package is meant for analyzing 
>> large datasets.
>> 
>> 
>>> Flavor: r-devel-linux-x86_64-debian-gcc
>>> Check: examples, Result: NOTE
>>> Examples with CPU (user + system) or elapsed time > 5s
>>> user system elapsed
>>> RDM 24.399  0.888  25.289
>> 
>> Explain:  This is because a large dataset is used in the example. An example 
>> with large dataset is necessary, as this package is meant for analyzing 
>> large datasets.
>> 
>> Any suggestions or comments would be appreciated. Thank you in advance!
>> 
>> Best,
>> Ying
>> 
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
> 
> -- 
> Sent from my phone. Please excuse my brevity.
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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] R Package AQLSchemes

[Roy Mendelssohn - NOAA Federal via R-package-devel]

https://cran.r-project.org/web//packages/AQLSchemes/index.html

-Roy

> On Oct 25, 2022, at 2:01 PM, John Lawson  wrote:
> 
> AQLSChemes

**
"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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[R-pkg-devel] failing CRAN nightly builds

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

About a week ago I received a notice that my package 'rerddapXtracto' was 
failing nightly builds and i needed to fix it or face being archived.  Fair 
enough.  The next day I submitted a fix.  My package has one example that 
always comes in just above the time that is checked for.  That this is so is in 
the CRAN notes.

After I got the note that the new package failed the automated test for this 
reason,  I responded with this fact and asked it to be reconsidered, as it has 
been in the past.  Since then,  I have sent two more reminders with no 
response.  I realize CRAN folks are pretty busy,  but I really don't want the 
package removed from CRAN,  so am mainly hoping this email will give a little 
nudge,  or if people have other suggestions.

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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Re: [R-pkg-devel] Found the following (possibly) invalid URLs:

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks!.  It tried it again,  got a 404,  then tried it again,  got the site.  
I will take it up with the people in charge.

-Roy

> On Sep 29, 2022, at 1:55 PM, Ben Bolker  wrote:
> 
>  I get a 404.
> 
> On 2022-09-29 4:50 p.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
> wrote:
>> In testing a new version of one of my package on win builder,   I get the 
>> following:
>> Found the following (possibly) invalid URLs:
>> .
>> .
>> .
>>   URL: 
>> https://www.integratedecosystemassessment.noaa.gov/regions/california-current-region/index.html
>> From: inst/doc/Using_rerddap.html
>> Status: 404
>> Message: Not Found
>> It is only in the vignette as a place to look up more about a project,  it 
>> is never actually accessed,  moreover at least from my home computer it is 
>> valid URL that I reach. I know I can include something about this in 
>> cran-comments,  but I would prefer not generating any notes so human 
>> intervention isn't needed.  Any suggestions?  Can others test the URL to see 
>> if they have problems reaching it.
>> 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
> 
> -- 
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> (Acting) Graduate chair, Mathematics & Statistics
> > E-mail is sent at my convenience; I don't expect replies outside of working 
> > hours.
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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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[R-pkg-devel] Found the following (possibly) invalid URLs:

[Roy Mendelssohn - NOAA Federal via R-package-devel]

In testing a new version of one of my package on win builder,   I get the 
following:

Found the following (possibly) invalid URLs:
.
.
.
  URL: 
https://www.integratedecosystemassessment.noaa.gov/regions/california-current-region/index.html
From: inst/doc/Using_rerddap.html
Status: 404
Message: Not Found

It is only in the vignette as a place to look up more about a project,  it is 
never actually accessed,  moreover at least from my home computer it is valid 
URL that I reach. I know I can include something about this in cran-comments,  
but I would prefer not generating any notes so human intervention isn't needed. 
 Any suggestions?  Can others test the URL to see if they have problems 
reaching it.

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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Re: [R-pkg-devel] Internet resources and Errors

[Roy Mendelssohn - NOAA Federal via R-package-devel]

try/stop is in the operational code.  But it is easy enough to make it so that 
the code always returns something, even when there is an internet access 
problem.

As I said,  if  "failing gracefully" and ever actually been defined with 
examples life would have been much easier for a number of packages developers.

-Roy


> On Sep 24, 2021, at 10:55 AM, Greg Minshall  wrote:
> 
> Roy,
> 
>> All internet calls are wrapped in 'try()'.  If that shows an error, I
>> write a message to the screen about the error, and call stop(),
>> perhaps with a further message in that call.
> 
> out of ignorance, i ask ...
> 
> in your package's operational code ("its API", or whatever), when a
> required internet access fails, i would think a message and a stop(),
> might be the reasonable thing to do.
> 
> in examples or tests, either doing the access itself, or calling your
> operational code, one might try() and not stop(), but, rather, go on to
> the next example/test.
> 
> in your comment above, is the try()/stop() in your operational code or
> in your tests/examples?
> 
> cheers, Greg

**
"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] Internet resources and Errors

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Not off-hand.  it is weird that the only error is on Solaris.  I do test on the 
r-hub Solaris before submission.  But at the same time,  given some of the 
responses that I have received (which I thank) I probably don't meet the CRAN 
idea of "graceful".  Easy enough for me to change as I am catching these so 
just need to change what I do.

I have seen other posts where people comment that the Solaris test machine 
appears to have an internet connection a good bit slower or less reliable than 
other test machines,  so timeouts occur,  but I can't discern that with what I 
have.

-Roy



> On Sep 24, 2021, at 9:29 AM, Bill Dunlap  wrote:
> 
> Can you tell if the failure to download was due to a Solaris-specific issue 
> or due to the Solaris test machine not being fully connected to the internet?
> 
> -Bill
> 
> On Fri, Sep 24, 2021 at 7:50 AM Roy Mendelssohn - NOAA Federal via 
> R-package-devel  wrote:
> Hi All:
> 
> I am getting dinged again on CRAN  (just Solaris for some reason),  and the 
> problem is how to exit if there is a failure of accessing the resource,  I 
> know it has been discussed here before,  but I just am not understanding what 
> is desired to end properly. As I have been reminded:
> 
> 'Packages which use Internet resources should fail gracefully with an 
> informative message
> if the resource is not available or has changed (and not give a check warning 
> nor error).'
> 
> All internet calls are wrapped in 'try()'.  If that shows an error,  I  write 
> a message to the screen about the error,  and call stop(), perhaps with a 
> further message in that call.   Somehow this does not appear to meet the 
> standard.Can someone then please tell me what I should do instead.  The 
> point is I have checked that the access to the internet resources has worked, 
>  i have seen that it hasn't,  now what should be the steps to take to exit 
> gracefully.
> 
> I also want to add to what others have said about the frustrations of dealing 
> with Solaris.  I have spent a fair amount of time getting things to  work 
> with Solaris which no one uses.  In this instance the package test is only 
> failing on Solaris.   Not a good use of limited time IMO.
> 
> Thanks for any advice.
> 
> -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

**
"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] Internet resources and Errors

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks to all who replied.  I want to especially point out Maelle's response 
because as I said I am not the first person to raise this question in terms of 
accessing internet resources.  Yes,  graceful is in the eye of the beholder,  
which i why such guidelines are really helpful.

-Roy

> On Sep 24, 2021, at 8:59 AM, Duncan Murdoch  wrote:
> 
> On 24/09/2021 11:27 a.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
> wrote:
>> Just so I am clear,  I should not call stop(),  but instead call a return() 
>> and return something or other  (there is nothing to skip to - it is doing a 
>> data download and either it works or it failed).  Is there a preferred 
>> something to return?  And it is okay to write a message to the screen?
> 
> I don't think it matters what you return, as long as the caller understands 
> that it didn't get any data.  If this is a function you export, make sure to 
> describe that possibility in its help page.
> 
> As far as I know it's okay to use message() (or cat() or print(), but 
> message() is preferred) to give your message, just not stop() or warning() -- 
> those will signal a problem to CRAN that you should fix.
> 
> Duncan Murdoch
> 
>> I should add that when I first ran into this awhile back I asked what 
>> "failed gracefully" means,  and never received a response.  To me,  writing 
>> out a message to the user and stopping is graceful exit, but obviously it is 
>> not.  What would help then, since this problem has been cited by others, is 
>> more explicit guidelines as to what constitutes a graceful exit with 
>> examples.  My $0.02
>> -Roy
>>> On Sep 24, 2021, at 8:03 AM, Ben Bolker  wrote:
>>> 
>>>  I think you're not supposed to stop().
>>> 
>>>  You should just proceed with the other tests (skipping any tests/examples 
>>> that depend on access to the inaccessible internet resources, or values 
>>> derived from the failing call, to work)
>>> 
>>>  Does that help?
>>> 
>>> On 9/24/21 10:49 AM, Roy Mendelssohn - NOAA Federal via R-package-devel 
>>> wrote:
>>>> Hi All:
>>>> I am getting dinged again on CRAN  (just Solaris for some reason),  and 
>>>> the problem is how to exit if there is a failure of accessing the 
>>>> resource,  I know it has been discussed here before,  but I just am not 
>>>> understanding what is desired to end properly. As I have been reminded:
>>>> 'Packages which use Internet resources should fail gracefully with an 
>>>> informative message
>>>> if the resource is not available or has changed (and not give a check 
>>>> warning nor error).'
>>>> All internet calls are wrapped in 'try()'.  If that shows an error,  I  
>>>> write a message to the screen about the error,  and call stop(), perhaps 
>>>> with a further message in that call.   Somehow this does not appear to 
>>>> meet the standard.Can someone then please tell me what I should do 
>>>> instead.  The point is I have checked that the access to the internet 
>>>> resources has worked,  i have seen that it hasn't,  now what should be the 
>>>> steps to take to exit gracefully.
>>>> I also want to add to what others have said about the frustrations of 
>>>> dealing with Solaris.  I have spent a fair amount of time getting things 
>>>> to  work with Solaris which no one uses.  In this instance the package 
>>>> test is only failing on Solaris.   Not a good use of limited time IMO.
>>>> Thanks for any advice.
>>>> -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-p

Re: [R-pkg-devel] Internet resources and Errors

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Just so I am clear,  I should not call stop(),  but instead call a return() and 
return something or other  (there is nothing to skip to - it is doing a data 
download and either it works or it failed).  Is there a preferred something to 
return?  And it is okay to write a message to the screen?  

I should add that when I first ran into this awhile back I asked what "failed 
gracefully" means,  and never received a response.  To me,  writing out a 
message to the user and stopping is graceful exit, but obviously it is not.  
What would help then, since this problem has been cited by others, is more 
explicit guidelines as to what constitutes a graceful exit with examples.  My 
$0.02

-Roy



> On Sep 24, 2021, at 8:03 AM, Ben Bolker  wrote:
> 
>  I think you're not supposed to stop().
> 
>  You should just proceed with the other tests (skipping any tests/examples 
> that depend on access to the inaccessible internet resources, or values 
> derived from the failing call, to work)
> 
>  Does that help?
> 
> On 9/24/21 10:49 AM, Roy Mendelssohn - NOAA Federal via R-package-devel wrote:
>> Hi All:
>> I am getting dinged again on CRAN  (just Solaris for some reason),  and the 
>> problem is how to exit if there is a failure of accessing the resource,  I 
>> know it has been discussed here before,  but I just am not understanding 
>> what is desired to end properly. As I have been reminded:
>> 'Packages which use Internet resources should fail gracefully with an 
>> informative message
>> if the resource is not available or has changed (and not give a check 
>> warning nor error).'
>> All internet calls are wrapped in 'try()'.  If that shows an error,  I  
>> write a message to the screen about the error,  and call stop(), perhaps 
>> with a further message in that call.   Somehow this does not appear to meet 
>> the standard.Can someone then please tell me what I should do instead.  
>> The point is I have checked that the access to the internet resources has 
>> worked,  i have seen that it hasn't,  now what should be the steps to take 
>> to exit gracefully.
>> I also want to add to what others have said about the frustrations of 
>> dealing with Solaris.  I have spent a fair amount of time getting things to  
>> work with Solaris which no one uses.  In this instance the package test is 
>> only failing on Solaris.   Not a good use of limited time IMO.
>> Thanks for any advice.
>> -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
> 
> -- 
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> Graduate chair, Mathematics & Statistics
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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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[R-pkg-devel] Internet resources and Errors

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

I am getting dinged again on CRAN  (just Solaris for some reason),  and the 
problem is how to exit if there is a failure of accessing the resource,  I know 
it has been discussed here before,  but I just am not understanding what is 
desired to end properly. As I have been reminded:

'Packages which use Internet resources should fail gracefully with an 
informative message
if the resource is not available or has changed (and not give a check warning 
nor error).'

All internet calls are wrapped in 'try()'.  If that shows an error,  I  write a 
message to the screen about the error,  and call stop(), perhaps with a further 
message in that call.   Somehow this does not appear to meet the standard.
Can someone then please tell me what I should do instead.  The point is I have 
checked that the access to the internet resources has worked,  i have seen that 
it hasn't,  now what should be the steps to take to exit gracefully.

I also want to add to what others have said about the frustrations of dealing 
with Solaris.  I have spent a fair amount of time getting things to  work with 
Solaris which no one uses.  In this instance the package test is only failing 
on Solaris.   Not a good use of limited time IMO.

Thanks for any advice.

-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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Re: [R-pkg-devel] Change package maintainer

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi Uwe:

Is what you described the preferred way to change maintainers  (I have just 
taken over another package),  or would you prefer receiving an email from the 
old maintainer before the submission?

Thanks,

-Roy

> On Jul 1, 2021, at 8:38 AM, Uwe Ligges  
> wrote:
> 
> 
> 
> On 01.07.2021 16:10, Javier García Chamorro wrote:
>> Hi there, I have recently uploaded the first version of my R package to
>> CRAN. As it is part of my final degree project, I need to change the
>> maintainer to my supervisor, now that I have finished the project.
>> I changed in the DESCRIPTION file the proper data to do so, but when
>> receiving back the email from CRAN the only NOTE I have is this one:
>> * checking CRAN incoming feasibility ... NOTE
>> Maintainer: 'Fernando Carazo Developer '
>> New maintainer:
>>   Fernando Carazo Developer 
>> Old maintainer(s):
>>   Javier Garcia Developer 
> 
> 1. Correct the name of the new maintainer whose family name is probably not 
> "Developer". Apparently nobody spotted this in your initial submission.
> 
> 2. After successful submission to CRAN, the old maintainer will receive a 
> confirmation request which you have to respond to.
> 
> Best,
> Uwe Ligges
> 
> 
> 
>> What do I need to do here?
>> Thank you
>> Javier
>>  [[alternative HTML version deleted]]
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> 
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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] Question about preventing CRAN package archival

[Roy Mendelssohn - NOAA Federal via R-package-devel]

After looking up matrixcalc on CRAN,  I would recommend contacting the 
maintainer,  who is listed as:

> Frederick Novomestky 


The reason I say this is what is blowing up the package in the nightly builds 
is a careless error in one Example:

>   > x <- matrix( c( 2, 4, 2, 1, 3, 1, 5, 2, 1, 2, 3, 3 ), nrow=4, ncol=4, 
> byrow=TRUE )
> Error in matrix(c(2, 4, 2, 1, 3, 1, 5, 2, 1, 2, 3, 3), nrow = 4, ncol = 
> 4, : 
>  data length differs from size of matrix: [12 != 4 x 4]
> 

That should be pretty easy for the maintainer to fix and to resubmit.

-Roy


> On Jun 2, 2021, at 10:36 AM, Ben Staton  wrote:
> 
> My package uses the MIT license, so would that not meet the compatibility
> requirements?
> 
> I will attempt to reach out to the package author - thanks for your help!
> 
> On Wed, Jun 2, 2021 at 10:31 AM Ben Bolker  wrote:
> 
>>That all sounds exactly right.
>>   GPL >= 2 allows you to use the material without asking permission as
>> long as your package is compatibly licensed (e.g. also GPL).
>>   Under normal circumstances it would be polite to ask permission, but
>> if the reason for doing this is that the maintainer is unreachable in
>> the first place ...
>> 
>>  If you want to try a little harder, it seems quite possible that you
>> can reach the matrixcalc maintainer at the (personal) e-mail address
>> shown in this page:
>> 
>> https://www.facebook.com/photo/?fbid=10208324530363130=ecnf.1000413042
>> 
>>   (Possibly an identity confusion, but I rate that as unlikely based on
>> other facebook snooping)
>> 
>>   I don't think a short, polite e-mail request would be out of bounds,
>> they can always ignore it or tell you to go away.
>> 
>>   cheers
>>Ben Bolker
>> 
>> On 6/2/21 1:15 PM, Ben Staton wrote:
>>> Hello,
>>> 
>>> Thank you for your detailed list of solutions.
>>> 
>>> I was initially tempted to go with option 1 (move matrixcalc to suggests
>>> and check for its existence before using functions that rely on it), but
>> as
>>> mentioned, this is not a long term fix.
>>> 
>>> I unfortunately can't take on the responsibilities of option 2 (becoming
>>> the package maintainer) -- there is much that this package does that I do
>>> not understand, and do not wish to feign authority!
>>> 
>>> I plan to take option 3 (copy the needed functions into my package).
>> There
>>> are only three functions I need from matrixcalc, and all three are fairly
>>> simple (is.square.matrix
>>> ,
>>> is.symmetric.matrix
>>> , and
>>> is.positive.definite
>>> ) and
>> there
>>> is only one function in postpack that needs them. I plan to define them
>>> within the postpack function. matrixcalc is licensed under GPL >= 2 and
>>> based on my scan of the license text, this is allowed. Is that correct?
>>> 
>>> Regarding option 4 (contacting the matrixcalc maintainer), the original
>>> email from CRAN mentioned that they have attempted to contact the package
>>> author with no response.
>>> 
>>> Thank you!
>>> 
>>> On Wed, Jun 2, 2021 at 9:52 AM J C Nash  wrote:
>>> 
 I just downloaded the source matrixcalc package to see what it
>> contained.
 The functions
 I looked at seem fairly straightforward and the OP could likely develop
 equivalent features
 in his own code, possibly avoiding a function call. Avoiding the
>> function
 call means NAMESPACE etc. are not involved, so fewer places for getting
 into
 trouble, assuming the inline code works properly.
 
 JN
 
 
 On 2021-06-02 12:37 p.m., Duncan Murdoch wrote:
> On 02/06/2021 12:13 p.m., Ben Staton wrote:
>> Hello,
>> 
>> I received an email notice from CRAN indicating that my R package
>> ('postpack') will be archived soon if I do not take any action and I
 want
>> to avoid that outcome. The issue is not caused by my package, but
 instead a
>> package that my package depends on:
>> 
>> "... package 'matrixcalc' is now scheduled for archival on 2021-06-09,
>> and archiving this will necessitate also archiving its strong reverse
>> dependencies."
>> 
>> Evidently, xyz has been returning errors on new R builds prompting
>> CRAN
 to
>> list it as a package to be archived. My package, 'postpack' has
>> 'matrixcalc' listed in the Imports field, which I assume is why I
 received
>> this email.
>> 
>> I want to keep 'postpack' active and don't want it to be archived. I
 still
>> need package 'matrixcalc' for my package, but not for most functions.
 Could
>> I simply move package 'matrixcalc' to the Suggests list and submit the
 new
>> version to CRAN to remove the "Strong Reverse Dependency" issue that
>> triggered this email to avoid CRAN from archiving my package?
> 
> That's part of one solution, 

Re: [R-pkg-devel] CRAN nightly tests

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks.Will do so,

-Roy

> On Apr 9, 2021, at 4:23 PM, Uwe Ligges  
> wrote:
> 
> 
> 
> On 09.04.2021 21:02, Roy Mendelssohn - NOAA Federal via R-package-devel wrote:
>> Just trying to get some information about the CRAN nightly tests.  Are all 
>> the tests for a particular package run a the same time?  
> 
> No.
> 
>> If not,  is there any way to determine when a particular test was last run 
>> (there is a time at the top of the page,  but it may or may not apply to all 
>> of the OSes).  
> 
> No.
> 
> 
> Also can I get the IP address of the the machine that runs the Solaris test?  
> I am befuddled that the Solaris test can not access our server at all.  We 
> did have to block a number of IP addresses recently,  my concerned is that th 
> Solaris test machine may hav been blocked.
> 
> 
> The list does not know. Even the CRAN team does not know the IP address. 
> Professor Ripley runs that machine, so you may ask him via c...@r-project.org.
> 
> Best,
> Uwe Ligges
> 
>> 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

**
"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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[R-pkg-devel] CRAN nightly tests

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Just trying to get some information about the CRAN nightly tests.  Are all the 
tests for a particular package run a the same time?  If not,  is there any way 
to determine when a particular test was last run (there is a time at the top of 
the page,  but it may or may not apply to all of the OSes).  Also can I get the 
IP address of the the machine that runs the Solaris test?  I am befuddled that 
the Solaris test can not access our server at all.  We did have to block a 
number of IP addresses recently,  my concerned is that th Solaris test machine 
may hav been blocked.

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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Re: [R-pkg-devel] Checking on Debian on RHub

[Roy Mendelssohn - NOAA Federal via R-package-devel]

My apologies, it is the Fedora instance.  Short version summary:

Warning messages:
5558#> 1: In i.p(...) : installation of package ‘rgdal’ had non-zero exit status
5559#> 2: In i.p(...) : installation of package ‘sf’ had non-zero exit status
5560#> 3: In i.p(...) :
5561#> installation of package ‘plotdap’ had non-zero exit status

'plotdap' depends on sf which is why it fails.  Long version is at 
https://builder.r-hub.io/status/rerddapXtracto_1.1.0.tar.gz-f3facfb7e282436c98dce8b5014de474

Thanks,

-Roy

> On Apr 8, 2021, at 7:35 AM, Roy Mendelssohn - NOAA Federal 
>  wrote:
> 
> Thanks Gabor.  I will post more information later today when I get a chance.  
> I actually put something on issue tracker a year or two ago,  after posting 
> here and having suggested that I raise an issue.
> 
> I really appreciate the work going into RHub - the reason I am having this 
> problem is I use RHub to check my submissions.  I just keep failing in my 
> CRAN submissions on Debian while passing on Windows and Mac, sort of 
> frustrating.
> 
> -Roy
> 
>> On Apr 8, 2021, at 12:22 AM, Gábor Csárdi  wrote:
>> 
>> Hi,
>> 
>> Which one is your package? Which spatial package fails? Can you link
>> to an issue in the issue tracker, if there is one?
>> 
>> As for an alternative, you can run a Docker container. This works on
>> Linux, Windows and macOS, on any recent enough machine. You can run
>> one of the R-hub containers, e.g.
>> https://hub.docker.com/repository/docker/rhub/debian-gcc-devel and
>> then try to fix the installation issue. Or you can try a bigger
>> container that tries to mirror CRAN exactly:
>> https://hub.docker.com/r/cran/debian
>> 
>> Gabor
>> 
>> On Thu, Apr 8, 2021 at 6:49 AM Roy Mendelssohn - NOAA Federal via
>> R-package-devel  wrote:
>>> 
>>> Hi All:
>>> 
>>> I still have problems with checking one of my packages on RHub running 
>>> Debian,  as the Preprocessing fails in building in some of the needed 
>>> spatial packages.  This problem was reported quite awhile ago,  and never 
>>> appears to have been completely fixed.  Is there an alternate place I can 
>>> test a package under Debian that is consistent with CRAN.
>>> 
>>> 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
> 
> **
> "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.
> 

**
"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] Checking on Debian on RHub

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks Gabor.  I will post more information later today when I get a chance.  I 
actually put something on issue tracker a year or two ago,  after posting here 
and having suggested that I raise an issue.

I really appreciate the work going into RHub - the reason I am having this 
problem is I use RHub to check my submissions.  I just keep failing in my CRAN 
submissions on Debian while passing on Windows and Mac, sort of frustrating.

-Roy

> On Apr 8, 2021, at 12:22 AM, Gábor Csárdi  wrote:
> 
> Hi,
> 
> Which one is your package? Which spatial package fails? Can you link
> to an issue in the issue tracker, if there is one?
> 
> As for an alternative, you can run a Docker container. This works on
> Linux, Windows and macOS, on any recent enough machine. You can run
> one of the R-hub containers, e.g.
> https://hub.docker.com/repository/docker/rhub/debian-gcc-devel and
> then try to fix the installation issue. Or you can try a bigger
> container that tries to mirror CRAN exactly:
> https://hub.docker.com/r/cran/debian
> 
> Gabor
> 
> On Thu, Apr 8, 2021 at 6:49 AM Roy Mendelssohn - NOAA Federal via
> R-package-devel  wrote:
>> 
>> Hi All:
>> 
>> I still have problems with checking one of my packages on RHub running 
>> Debian,  as the Preprocessing fails in building in some of the needed 
>> spatial packages.  This problem was reported quite awhile ago,  and never 
>> appears to have been completely fixed.  Is there an alternate place I can 
>> test a package under Debian that is consistent with CRAN.
>> 
>> 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

**
"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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[R-pkg-devel] Checking on Debian on RHub

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

I still have problems with checking one of my packages on RHub running Debian,  
as the Preprocessing fails in building in some of the needed spatial packages.  
This problem was reported quite awhile ago,  and never appears to have been 
completely fixed.  Is there an alternate place I can test a package under 
Debian that is consistent with CRAN.

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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Re: [R-pkg-devel] Note: checking CRAN incoming feasibility but the package did not pass

[Roy Mendelssohn - NOAA Federal via R-package-devel]

To the best of my knowledge,  new submissions always get that note,  and new 
submissions are handled differently, as they are given closer inspection by a 
human, and since this is all-volunteer the amount of time that can take for the 
code review can vary greatly.  If you are greatly concerned there is something 
more than that.  you can respond to the email querying if the only problem is 
the new submission and you should just sit tight,  or if there is something 
else.  Again,  since it is a few individuals it may take a couple of days to 
receive a response.  You can also check the status of your submission both at:

https://itsalocke.com/cransays/articles/dashboard

and

 ftp://cran.r-project.org/incoming/.

If all is going correctly your package should be in the "inspect" folding 
pending review.

HTH,

-Roy


> On Feb 13, 2021, at 3:06 PM, Elysée Aristide  wrote:
> 
> Greetings,
> 
> I submitted my package CDatanet.
> There was no error from Windows and Debian but just this note : "checking
> CRAN incoming feasibility"
> However, the package did not pass the incoming checks. My understanding was
> that this note is normal and does not matter.
> Here is the message I got from CRAN.
> 
> package CDatanet_0.0.1.tar.gz does not pass the incoming checks
> automatically, please see the following pre-tests:
> Windows: <
> https://win-builder.r-project.org/incoming_pretest/CDatanet_0.0.1_20210212_184621/Windows/00check.log
>> 
> Status: 1 NOTE
> Debian: <
> https://win-builder.r-project.org/incoming_pretest/CDatanet_0.0.1_20210212_184621/Debian/00check.log
>> 
> Status: 1 NOTE
> 
> 
> 
> Please fix all problems and resubmit a fixed version via the webform.
> 
> 
> Please, could you help me to solve this issue?
> 
> 
> Best,
> 
> *-*
> 
> *Aristide Elysée HOUNDETOUNGAN*
> *Ph.D. Candidate in Economics at Université Laval*
> *Personal website : *www.ahoundetoungan.com
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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] help interpreting a response from CRAN

[Roy Mendelssohn - NOAA Federal via R-package-devel]

I have found win-builder timings come close,  but only close.  My experience is 
that the CRAN timings were uniformly slower than those on win-builder.  But I 
also find that I can get quite significant differences between 
win-builder-release and win-builder-devel.  So I also take the slowest that I 
can find as a basis,  and assume the actual times will be slower than that.

HTH,

-Roy

> On Nov 22, 2020, at 5:15 PM, Ben Bolker  wrote:
> 
>  And one more (last for a while): presumably there is no way to check CRAN 
> windows timing without submitting to CRAN ... ?  (I will obviously do my best 
> by doing arithmetic on the tests that I set to be skipped, but it would be 
> nice to be able to double-check without wasting everyone's time ... I guess 
> if I knew that CRAN submissions would *always automatically* be rejected with 
> Windows test times>10 min, I could use CRAN submission itself as my test ... 
> but maybe that's a bad idea?)
> 
> On 11/22/20 4:06 PM, Uwe Ligges wrote:
>> Thanks Dirk. Yes, for lme4 the tests for each archiecture take longer than 5 
>> min, so the overall check time exceeds 10 min.
>> So one can follow Dirk's advise.
>> As a general remark for others who will read this in the future:
>> tests should test the software, but it is generally not important to have 
>> real world examples. Small data and few iterations are typically sufficient 
>> for tests.
>> It is also possible to run less important tests only conditionally if some 
>> environment variable is set that you only define on your machine.
>> Best,
>> Uwe Ligges
>> On 22.11.2020 20:36, Dirk Eddelbuettel wrote:
>>> 
>>> On 22 November 2020 at 13:44, Ben Bolker wrote:
>>> |My current guess is that the problem is with the too-long check time 
>>> on Windows (NOTE: "Overall checktime 18 min > 10 min")
>>> 
>>> Yes.
>>> |   I guess I have to get busy setting more tests and examples to 
>>> skip-on-CRAN (kind of a pain as there's no low-hanging fruit - other than 
>>> the 'testthat' tests, none of the individual test files take longer than 
>>> 15sec, although this is doubled because they have to be run on 386 and x64 
>>> ...)
>>> 
>>> It's under your control. You can detect 'are we on Windows' and branch or, 
>>> as
>>> I do with test runner I use, exit_file("...") based on such conditions.
>>> 
>>> |   An alternative is that this is a confusingly worded message indicating 
>>> that there are strong rev dependencies so the package needs to be further 
>>> checked? (That seems unlikely as it explicitly asks me to resubmit)
>>> 
>>> No. If there were any (even false positive ones) they'd be listed there.
>>> 
>>> Hth, Dirk
>>> 
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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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[R-pkg-devel] Number of days since last submission

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

A few days ago I put on CRAN a new version of a package.  Since then it has 
thrown some errors,  all do to the fact that sometimes on CRAN the rebuild of 
the Vignette fails. I received a notice about this from CRAN.  Now however,  
when I test on winbuilder,  I get a Note because of the last time since a 
re-submissio.  Should I just submit the new version and not worry about the 
note?

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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Re: [R-pkg-devel] pretest order

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks.  I had a feeling that was the case from looking at the queue.  Does the 
clearing make them run or do they need to be resubmitted?

-Roy


> On Oct 23, 2020, at 2:43 PM, Uwe Ligges  
> wrote:
> 
> Generally by submission time, but there is a series of packages unprocessed 
> stuck in the queue, will clear that up shortly.
> 
> 
> Best,
> Uwe
> 
> On 23.10.2020 19:17, Roy Mendelssohn - NOAA Federal via R-package-devel wrote:
>> Just out of curiousity,  how is pretest order determined?  I have a package 
>> that was submitted yesterday that is still waiting pretest,  while one I 
>> submitted today was just pretested.   Both are just bug fixes of existing 
>> packages,  not new packages.
>> Thanks for the info and the work on CRAN,  Having to deal recently with 
>> package hell in Python, I appreciate these efforts.
>> -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

**
"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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[R-pkg-devel] pretest order

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Just out of curiousity,  how is pretest order determined?  I have a package 
that was submitted yesterday that is still waiting pretest,  while one I 
submitted today was just pretested.   Both are just bug fixes of existing 
packages,  not new packages. 

Thanks for the info and the work on CRAN,  Having to deal recently with package 
hell in Python, I appreciate these efforts.

-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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Re: [R-pkg-devel] Pre-test failure

[Roy Mendelssohn - NOAA Federal via R-package-devel]

https://win-builder.r-project.org/incoming_pretest/plotdap_0.0.8_20201023_155845/Windows/00check.log

my problem is I don't have Windows myself.  So I assume if I can pass both 
winbuilders I should be good.  Here is the link to winbuilder_release I just 
ran:

https://win-builder.r-project.org/exQtKk9TKIeP

As you can see,  that is ok and rebuilt the vignette just fine.  

Thanks,

-Roy


> On Oct 23, 2020, at 8:22 AM, Ben Bolker  wrote:
> 
>   Can you share the links to the CRAN pre-test logs? Someone here might be 
> able to guess what went wrong ...
> 
>   (FWIW I always *think* I'm testing very carefully, and I almost always get 
> something wrong ...)
> 
> On 10/23/20 11:18 AM, Roy Mendelssohn - NOAA Federal via R-package-devel 
> wrote:
>> I test my packages very carefully before submission.  Earlier today I 
>> submitted a package that passed this morning on both winbuilder_release and 
>> winbuilder_devel.  The pre-test submission failed on rebuilding the 
>> vignette.  I just tried again on winbuilder_release and winbuilder_devel,  
>> no problems.  There are no problems either on my Mac or a Fedora image. 
>> Moreover I tested the specific lines that were flagged,  and they work fine
>> So my questions are:
>> 1.  Should I just resubmit assuming it was some kind of quirk?
>> 2. Do I need to bump up the version to resubmit?
>> 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

**
"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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[R-pkg-devel] Pre-test failure

[Roy Mendelssohn - NOAA Federal via R-package-devel]

I test my packages very carefully before submission.  Earlier today I submitted 
a package that passed this morning on both winbuilder_release and 
winbuilder_devel.  The pre-test submission failed on rebuilding the vignette.  
I just tried again on winbuilder_release and winbuilder_devel,  no problems.  
There are no problems either on my Mac or a Fedora image. Moreover I tested the 
specific lines that were flagged,  and they work fine

So my questions are:

1.  Should I just resubmit assuming it was some kind of quirk?

2. Do I need to bump up the version to resubmit?

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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Re: [R-pkg-devel] URL Note

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks.  I had checked for that but at first didn't find the one instance where 
this occurred.  Got it.

-Roy

> On Oct 22, 2020, at 2:18 PM, Uwe Ligges  
> wrote:
> 
> 
> 
> On 22.10.2020 23:15, Roy Mendelssohn - NOAA Federal via R-package-devel wrote:
>> Hi All:
>> I am working on a small bug fix in a package,  and on winbuilder_devel  (not 
>> on release) I get the following Note:
>>> Found the following (possibly) invalid URLs:
>>>   URL: https://erddap.marine.ie/erddap (moved to 
>>> https://erddap.marine.ie/erddap/)
>>> From: inst/doc/UsingrerddapXtracto.html
>>> Status: 200
>>> Message: OK
>>> 
>> The problem is https://erddap.marine.ie/erddap  is a valid URL, and is the 
>> proper one.  I know I can put something in my cran_comments,  but I would 
>> rather submit with no Notes.  Any suggestions for a fix that I can take?
> 
> The server reported a permament move to the other URL given above, hence you 
> simply need a trailinmg slash.
> 
> Best,
> Uwe Ligges
>> 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

**
"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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[R-pkg-devel] URL Note

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

I am working on a small bug fix in a package,  and on winbuilder_devel  (not on 
release) I get the following Note:

> Found the following (possibly) invalid URLs:
>   URL: https://erddap.marine.ie/erddap (moved to 
> https://erddap.marine.ie/erddap/)
> From: inst/doc/UsingrerddapXtracto.html
> Status: 200
> Message: OK
> 
The problem is https://erddap.marine.ie/erddap  is a valid URL, and is the 
proper one.  I know I can put something in my cran_comments,  but I would 
rather submit with no Notes.  Any suggestions for a fix that I can take?

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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Re: [R-pkg-devel] Warnings from gdal

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks.  What has made it really difficult is that devtools::check() runs fine 
on my Mac,  I installed Fedora on a virtual machine on my Mac,  
devtools::check() also runs fine,  so it makes it really difficult to pin down 
things because I can't get into a debugger to see why CRAN is throwing errors, 
or more importantly if steps I have taken to correct the errors are working.  
When I can't reproduce the warning it makes it very difficult.

-Roy


> On Jul 27, 2020, at 10:20 AM, Trent McDonald  wrote:
> 
> Hope this helps.  I had a similar issue with my package.  Prior to the
> recent change, GDAL did not throw a warning for empty (NA) CRS
> strings. After change, it does.  projectRaster is throwing the warning
> because it thinks input and output crs are the same (perhaps CRS is
> missing?).  The purpose of projectRaster is to change crs's, so
> identical crs's make little sense. I suggest making sure the input CRS
> is valid (not NA) and that output CRS is different than the input.
> 
> Trent McDonald
> Principal Statistician
> 
> Western EcoSystems Technology, Inc.
> Environmental & Statistical Consultants
> 1610 Reynolds Street
> Laramie, WY 82072
> 307-760-4721
> www.west-inc.com
> 
> Trent McDonald
> Principal Statistician
> 
> Western EcoSystems Technology, Inc.
> Environmental & Statistical Consultants
> 1610 Reynolds Street
> Laramie, WY 82072
> 307-760-4721
> www.west-inc.com
> 
> 
> On Sun, Jul 26, 2020 at 8:12 AM Roy Mendelssohn - NOAA Federal via
> R-package-devel  wrote:
>> 
>> I have a package on CRAN that  has a graphics component that calls a package 
>> that ultimately calls 'rgdal that CRAN is unhappy about.  'rgdal' now throws 
>> a warning if 'crs' is used,  and unless I am misreading the problems (see 
>> https://cran.r-project.org/web/checks/check_results_rerddapXtracto.html) 
>> that is what is causing the problems.  I am not certain that I can suppress 
>> warnings because it is from a package that calls a package (in this case 
>> raster) that calls rgdal.
>> 
>> Any advice appreciated, in particular if I am mis-reading the warning.
>> 
>> 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

**
"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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[R-pkg-devel] Warnings from gdal

[Roy Mendelssohn - NOAA Federal via R-package-devel]

I have a package on CRAN that  has a graphics component that calls a package 
that ultimately calls 'rgdal that CRAN is unhappy about.  'rgdal' now throws a 
warning if 'crs' is used,  and unless I am misreading the problems (see 
https://cran.r-project.org/web/checks/check_results_rerddapXtracto.html) that 
is what is causing the problems.  I am not certain that I can suppress warnings 
because it is from a package that calls a package (in this case raster) that 
calls rgdal.

Any advice appreciated, in particular if I am mis-reading the warning.

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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Re: [R-pkg-devel] Winbuilder queues jammed again?

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Download the 'rhub' package.  Then submission to 'rhub' is one easy command.

HTH,

-Roy

> On Mar 5, 2020, at 3:33 PM, Rolf Turner  wrote:
> 
> 
> On 6/03/20 11:14 am, Ben Bolker wrote:
> 
> 
> 
>> It's probably been suggested already in this thread, but perhaps
>> rhub would work for you as an alternative?
> 
> 
> 
> Quite possibly, but I have no real idea what "rhub" is.  I've seen it 
> referred to many times but the references always assume that you know all 
> about it already.
> 
> I'll try to investigate.  Thanks for the suggestion.
> 
> cheers,
> 
> Rolf
> 
> 
> -- 
> Honorary Research Fellow
> Department of Statistics
> University of Auckland
> Phone: +64-9-373-7599 ext. 88276
> 
> __
> R-package-devel@r-project.org mailing list
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**
"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] Suggests in a Package

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks.  And thanks for the tip.

-Roy

> On Feb 4, 2020, at 10:20 AM, Duncan Murdoch  wrote:
> 
> On 04/02/2020 1:13 p.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
> wrote:
>> Hi All:
>> I still get a little confused on what it means if a package is listed in 
>> "Suggest" in my package.  I have been working to try and keep dependencies 
>> down.  One of my packages produces maps with data, and I have been asked if 
>> the maps can be made interactive.  It turns out this can be done very easily 
>> using "plotly" and I want to include something about that in the vignette. 
>> What my question is if I Suggest "plotly" in the package,  does a user have 
>> to have "plotly" installed in order to install and run the package?  My 
>> understanding is not,  so someone who doesn't want to do this doesn't need 
>> to install "plotly" but I wanted to double-check.
> 
> Your understanding is correct:  someone who doesn't have plotly installed 
> should still be able to install and run your package.
> 
> You should make sure that any functions that need plotly check for it first.  
> The recommended way to do that is to use a requireNamespace("plotly") test, 
> e.g. something like
> 
>  if (requireNamespace("plotly")) {
> plotly::plotly(...)
>  } else
> stop("This function requires the 'plotly' package")
> 
> Your tests that use such a function should only be run if 
> requireNamespace("plotly") returns TRUE.
> 
> Duncan Murdoch

**
"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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[R-pkg-devel] Suggests in a Package

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

I still get a little confused on what it means if a package is listed in 
"Suggest" in my package.  I have been working to try and keep dependencies 
down.  One of my packages produces maps with data, and I have been asked if the 
maps can be made interactive.  It turns out this can be done very easily using 
"plotly" and I want to include something about that in the vignette. What my 
question is if I Suggest "plotly" in the package,  does a user have to have 
"plotly" installed in order to install and run the package?  My understanding 
is not,  so someone who doesn't want to do this doesn't need to install 
"plotly" but I wanted to double-check.

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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Re: [R-pkg-devel] new package processing time

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Did you check on https://itsalocke.com/cransays/articles/dashboard?  If it is a 
first time submission,  there is a code review and that can take some time.

-Roy

> On Feb 3, 2020, at 3:56 PM, Marcelo Araya Salas  wrote:
> 
> Hi all
> 
> I submitted a new package to CRAN a couple of weeks ago. Does anyone know
> how long does it take for the package to be processed? New package versions
> are usually processed in a few hours so that's why I am wondering if
> everything is fine.
> 
> thanks
> 
> Marcelo
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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] CRAN rules re. web scraping?

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi Spencer:

I think that message means what it says,  and I read it as pretty 
straightforward and business like.  The issue is not web scraping.  There are 
two errors here:

1.  You can not write to the user's space without first explicitly asking 
permission of the user.   The suggested policy is to write to a temp directory, 
 R has tempdir() and related commands for how to do this.

2.  When accessing something over the internet,  failure of the access must be 
checked for and the program exiting gracefully.  The second error appears to be 
that at times on the builds the .csv file is not downloaded,  but there is no 
check,  just an error is thrown.  There are a number of ways to catch such 
errors,  such as "try...catch"  which will solve this problem

HTH,

-Roy


> On Jan 22, 2020, at 5:48 PM, Spencer Graves 
>  wrote:
> 
> Hello, All:
> 
> 
> GOOD NEWS AND BAD NEWS:
> 
> 
>   * First the good news:  I heard from Brian Ripley;  see below.  
> His web site says, "He retired in August 2014 on grounds of ill health." 
> (http://www.stats.ox.ac.uk/~ripley/)  I was pleased to see that he seems 
> to be well enough to send me the email below.
> 
> 
>   * BAD NEWS:  My Ecfun package is violating current CRAN rules 
> regarding "not writing anywhere in the file space".  (See below.)
> 
> 
> QUESTION:
> 
> 
>   How do you suggest I respond to this?
> 
> 
>   It's hard for me to fix, because I cannot replicate the error and 
> I don't understand the rules Prof. Ripley is trying to enforce. The 
> "CRAN Package Check Results for" this package show an error on 1 
> platform (r-devel-linux-x86_64-fedora-gcc), NOTEs on 3 platforms 
> (Fedora-clang and Debian), and "OK" on 9 others.  I can program selected 
> tests not to run on CRAN, e.g., with (!fda::CRAN()).
> 
> 
>   However, I suspect I should be able to do better than that.
> 
> 
>   Suggestions?
> 
> 
>   Thanks,
>   Spencer Graves
> 
> 
> p.s.  The development version of this package is available at 
> "https://github.com/sbgraves237/Ecfun;.
> 
> 
> https://cloud.r-project.org/web/checks/check_results_Ecfun.html
> 
> 
>  Forwarded Message 
> Subject:  CRAN package Ecfun
> Date: Tue, 21 Jan 2020 21:26:02 +
> From: Prof Brian Ripley 
> Reply-To: CRAN 
> To:   Spencer Graves 
> CC:   CRAN 
> 
> 
> 
> This has been intermittently failing its checks for a week: different 
> check runs failed (in the 24h prior to) the 14th, 15th, 17th and today. 
> The current failure is
> 
> Check: examples
> Result: ERROR
> Running examples in ‘Ecfun-Ex.R’ failed
> The error most likely occurred in:
> 
>> ### Name: read.testURLs
>> ### Title: Read a file produced by testURLs
>> ### Aliases: read.testURLs
>> ### Keywords: IO
>> 
>> ### ** Examples
>> 
>> # Test only 2 web sites, not the default 4,
>> # and test only twice, not the default 10 times:
>> tst <- testURLs(c(
> + PVI="http://en.wikipedia.org/wiki/Cook_Partisan_Voting_Index;,
> + house="http://house.gov/representatives;),
> + n=2, maxFail=2)
> 1
> 1579634784, PVI, TRUE 0.828
> 1579634785, house, FALSE 0.051
> 1579634785, house, FALSE 0.048
> 2
> 1579634785, PVI, TRUE 0.043
> 1579634785, house, FALSE 0.11
> 1579634785, house, FALSE 0.035
>> 
>> # The above should have created a file 'testURLresults.csv'
>> # in the working directory. Read it.
>> 
>> dat <- read.testURLs()
> Error in read.table(file = file, header = header, sep = sep, quote = 
> quote, :
> more columns than column names
> Calls: read.testURLs -> read.csv -> read.table
> 
> That does not conform to the policy on Internet access, not least as no 
> attempt is made to check if the file was created, let alone that it has 
> the expected layout. Nor does it conform to the policy on not writing 
> anywhere in the file space (and that shows on its CRAN results page too).
> 
> Please correct ASAP and before Feb 4 to safely retain the package on CRAN.
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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-pkg-devel] netcdf question

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

I am wondering if it is possible to find out when packages that use the netcdf 
libraries are built on the CRAN machines (such as ncdf4) what versions of the 
netcdf library are being used on at least Mac and Windows?

If this is the wrong place to ask,  please point me to where I should ask.

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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Re: [R-pkg-devel] Tarball can't be unpacked

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks!

Yes,  have had to do more than one download because unfortunately was still 
getting Notes,  which based on rHub I think I have cleared up.  But I find I 
don't always get the same results from win-builder as rHub  (the former closer 
to what I get from CRAN submission).  And just for the record,  and I have 
previously reported this directly to rHub,  many of the rHub Linux machines can 
not properly build and load any package using rgdal-rgeos, because they can't 
properly access the underlying libraries.

-Roy


> On Oct 14, 2019, at 12:26 PM, Uwe Ligges  
> wrote:
> 
> 
> 
> On 14.10.2019 20:43, Roy Mendelssohn - NOAA Federal wrote:
>> I have tried the upload page several times.  it gives the following error
>> ERROR: Access to the path 
>> 'C:\Inetpub\ftproot\R-release\plotdap_0.0.4.tar.gz' is denied.
> 
> Ah, reason is that there is already a version that you uploaded before. 
> Nobody reported this so far. Apparently my cron service died and no on demand 
> checks have been performed since saturday.
> I restarted cron now, but it will take a while to process the queues.
> 
> 
> Best,
> Uwe Ligges
> 
> 
> 
>> Same for R-devel. Permission problems?
>> Thanks,
>> -Roy
>>> On Oct 14, 2019, at 11:41 AM, Duncan Murdoch  
>>> wrote:
>>> 
>>> On 14/10/2019 10:26 a.m., Roy Mendelssohn - NOAA Federal via 
>>> R-package-devel wrote:
>>>> I am seeing the same problems still.  I am using devtools,  and am failing 
>>>> on the ftp,  with both win_release() and win_devel().
>>> 
>>> Have you tried submitting using the instructions on the CRAN page 
>>> https://cloud.r-project.org/web/packages/policies.html?  It's possible that 
>>> devtools is sending your file to the wrong place.
>>> 
>>> Duncan Murdoch
>>> 
>>>> Thanks,
>>>> -Roy
>>>>> On Oct 14, 2019, at 2:00 AM, Uwe Ligges  
>>>>> wrote:
>>>>> 
>>>>> Please resubmit, we had a space problem oin the check machine.
>>>>> 
>>>>> Best,
>>>>> Uwe Ligges
>>>>> 
>>>>> On 13.10.2019 07:00, Dalgleish, James (NIH/NCI) [V] via R-package-devel 
>>>>> wrote:
>>>>>> * using log directory 'd:/RCompile/CRANincoming/R-devel/CNVScope.Rcheck'
>>>>>> * using R Under development (unstable) (2019-10-10 r77275)
>>>>>> * using platform: x86_64-w64-mingw32 (64-bit)
>>>>>> * using session charset: ISO8859-1
>>>>>> * checking whether tarball can be unpacked ... ERROR
>>>>>> cannot unpack 'CNVScope_2.7.6.tar.gz'
>>>>>> * DONE
>>>>>> Status: 1 ERROR
>>>>>> I've submitted my package to win-builder, but just can't get it to check 
>>>>>> it. I've checked it locally and it passes with flying colors (no notes 
>>>>>> of any kind). I have used the package on my own machine to build from 
>>>>>> source. Is win-builder down? How can my tarball be broken? It works on 
>>>>>> my machine, so I can't imagine it's a broken tarball. Is there some 
>>>>>> compression flag I should change when building the package?
>>>>>> __
>>>>>> 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
>>>> **
>>>> "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 
>&

Re: [R-pkg-devel] Tarball can't be unpacked

[Roy Mendelssohn - NOAA Federal via R-package-devel]

I have tried the upload page several times.  it gives the following error

ERROR: Access to the path 'C:\Inetpub\ftproot\R-release\plotdap_0.0.4.tar.gz' 
is denied.

Same for R-devel. Permission problems?

Thanks,

-Roy


> On Oct 14, 2019, at 11:41 AM, Duncan Murdoch  wrote:
> 
> On 14/10/2019 10:26 a.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
> wrote:
>> I am seeing the same problems still.  I am using devtools,  and am failing 
>> on the ftp,  with both win_release() and win_devel().
> 
> Have you tried submitting using the instructions on the CRAN page 
> https://cloud.r-project.org/web/packages/policies.html?  It's possible that 
> devtools is sending your file to the wrong place.
> 
> Duncan Murdoch
> 
>> Thanks,
>> -Roy
>>> On Oct 14, 2019, at 2:00 AM, Uwe Ligges  
>>> wrote:
>>> 
>>> Please resubmit, we had a space problem oin the check machine.
>>> 
>>> Best,
>>> Uwe Ligges
>>> 
>>> On 13.10.2019 07:00, Dalgleish, James (NIH/NCI) [V] via R-package-devel 
>>> wrote:
>>>> * using log directory 'd:/RCompile/CRANincoming/R-devel/CNVScope.Rcheck'
>>>> * using R Under development (unstable) (2019-10-10 r77275)
>>>> * using platform: x86_64-w64-mingw32 (64-bit)
>>>> * using session charset: ISO8859-1
>>>> * checking whether tarball can be unpacked ... ERROR
>>>> cannot unpack 'CNVScope_2.7.6.tar.gz'
>>>> * DONE
>>>> Status: 1 ERROR
>>>> I've submitted my package to win-builder, but just can't get it to check 
>>>> it. I've checked it locally and it passes with flying colors (no notes of 
>>>> any kind). I have used the package on my own machine to build from source. 
>>>> Is win-builder down? How can my tarball be broken? It works on my machine, 
>>>> so I can't imagine it's a broken tarball. Is there some compression flag I 
>>>> should change when building the package?
>>>> __
>>>> 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
>> **
>> "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

**
"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] Tarball can't be unpacked

[Roy Mendelssohn - NOAA Federal via R-package-devel]

I am seeing the same problems still.  I am using devtools,  and am failing on 
the ftp,  with both win_release() and win_devel().

Thanks,

-Roy

> On Oct 14, 2019, at 2:00 AM, Uwe Ligges  
> wrote:
> 
> Please resubmit, we had a space problem oin the check machine.
> 
> Best,
> Uwe Ligges
> 
> On 13.10.2019 07:00, Dalgleish, James (NIH/NCI) [V] via R-package-devel wrote:
>> * using log directory 'd:/RCompile/CRANincoming/R-devel/CNVScope.Rcheck'
>> * using R Under development (unstable) (2019-10-10 r77275)
>> * using platform: x86_64-w64-mingw32 (64-bit)
>> * using session charset: ISO8859-1
>> * checking whether tarball can be unpacked ... ERROR
>> cannot unpack 'CNVScope_2.7.6.tar.gz'
>> * DONE
>> Status: 1 ERROR
>> I've submitted my package to win-builder, but just can't get it to check it. 
>> I've checked it locally and it passes with flying colors (no notes of any 
>> kind). I have used the package on my own machine to build from source. Is 
>> win-builder down? How can my tarball be broken? It works on my machine, so I 
>> can't imagine it's a broken tarball. Is there some compression flag I should 
>> change when building the package?
>> __
>> 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

**
"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] checking CRAN incoming feasibility NOTE

[Roy Mendelssohn - NOAA Federal via R-package-devel]

use this::use_cran_comments()

There is a place to put that it is a new submission

I would recommend also testing using:

devtools::check_win_release()
devtools::check_win_devel()

You should only have the one note that it is a new  submission.  When you 
submit,  you may or may not get a note that it was rejected by the automatic 
checker. Sit tight, someone from CRAN will see that it is a new submission.  A 
new submission is given a much more thorough review,  so it can take a coupe 
days or more for CRAN to get back to you.  You can check the status of CRAN 
submissions at:

https://cransays.itsalocke.com/articles/dashboard.html

HTH,

-Roy


> On Oct 5, 2019, at 2:52 PM, R. Mark Sharp  wrote:
> 
> I getting ready to submit a package to CRAN for the first time. I have run 
> cran_prep <- check_for_cran() using the rhub package. I understand that as a 
> new package it will generate a NOTE. As a novice, I do not know what is to be 
> expected within that NOTE and want to make sure the NOTEs I have received are 
> satisfactory. I have not found an example of a minimal first submission NOTE. 
> Below is what I am getting from the above test on rhub. I have three test 
> environments but only two NOTEs. Do these results indicate a problem to be 
> addressed?
> 
>> cran_prep$cran_summary()
> For a CRAN submission we recommend that you fix all NOTEs, WARNINGs and 
> ERRORs.
> ## Test environments
> - R-hub windows-x86_64-devel (r-devel)
> - R-hub ubuntu-gcc-release (r-release)
> - R-hub fedora-clang-devel (r-devel)
> 
> ## R CMD check results
> ❯ On windows-x86_64-devel (r-devel), ubuntu-gcc-release (r-release)
>  checking CRAN incoming feasibility ... NOTE
>  Maintainer: 'R. Mark Sharp '
> 
>  New submission
> 
>  License components with restrictions and base license permitting such:
>MIT + file LICENSE
>  File 'LICENSE':
>Copyright 2017-2019 R. Mark Sharp
> 
>Permission is hereby granted, free of charge, to any person obtaining a 
> copy of this software and associated documentation files (the "Software"), to 
> deal in the Software without restriction, including without limitation the 
> rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
> sell copies of the Software, and to permit persons to whom the Software is 
> furnished to do so, subject to the following conditions:
> 
>The above copyright notice and this permission notice shall be included in 
> all copies or substantial portions of the Software.
> 
>THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 
> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 
> SOFTWARE.
> 
> ❯ On fedora-clang-devel (r-devel)
>  checking CRAN incoming feasibility ...NB: need Internet access to use CRAN 
> incoming checks
>   NOTE
>  Maintainer: ‘R. Mark Sharp ’
> 
>  License components with restrictions and base license permitting such:
>MIT + file LICENSE
>  File 'LICENSE':
>Copyright 2017-2019 R. Mark Sharp
> 
>Permission is hereby granted, free of charge, to any person obtaining a 
> copy of this software and associated documentation files (the "Software"), to 
> deal in the Software without restriction, including without limitation the 
> rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
> sell copies of the Software, and to permit persons to whom the Software is 
> furnished to do so, subject to the following conditions:
> 
>The above copyright notice and this permission notice shall be included in 
> all copies or substantial portions of the Software.
> 
>THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 
> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 
> SOFTWARE.
> 
> 0 errors ✔ | 0 warnings ✔ | 2 notes ✖
>> 
> R. Mark Sharp, Ph.D.
> Data Scientist and Biomedical Statistical Consultant
> 7526 Meadow Green St.
> San Antonio, TX 78251
> mobile: 210-218-2868
> rmsh...@me.com
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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

Re: [R-pkg-devel] Resubmitting after a few days

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks all.  I asked because I don't want to unnecessarily overburden the CRAN 
maintainers.  In this case,  it wasn't a minor bug.

-Roy

> On Sep 25, 2019, at 4:36 AM, Dirk Eddelbuettel  wrote:
> 
> 
> On 24 September 2019 at 11:43, Roy Mendelssohn - NOAA Federal via 
> R-package-devel wrote:
> | A few days ago I  had to resubmit because an external URL I was using in my 
> vignette changed and the nightly builds were issuing warnings.  This morning 
> a user reported a bug.  I have the fix and a new version,  but the test 
> machines,  and I suppose it will also be true of CRAN,  are unhappy about the 
> interval since last submit.  Should I just submit the new version anyway with 
> a note in cram-comments that this is a bug fix.
> 
> Yes: AFAICT these are recommendations to not overburden CRAN.
> 
> And I have hit two distinct types:
> 
> - more than six uploads in six months (which happened when an upstream
>   package was hyperactive) which lead me to space uploads out a little more
>   as "one a month should be plenty" indeed
> 
> - less than seven days since the last upload (which lead me to just wait two
>   days on a very recent "better bug fix to a bug fix" upload I made, and
>   then got me the very automated processing)
> 
> You can look in the R sources for what the cutoffs are (which is how I
> confirmed it was 7) and act accordingly.  So yes, in sum, explain what you do
> to CRAN -- and some human will generally do the Right Thing.
> 
> (And big thanks and kudos to CRAN for the increased automation documented in
> the short update at the end of the most recent R Journal issue. Very
> impressive, and very well done.)
> 
> Dirk
> 
> -- 
> http://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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[R-pkg-devel] Resubmitting after a few days

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

A few days ago I  had to resubmit because an external URL I was using in my 
vignette changed and the nightly builds were issuing warnings.  This morning a 
user reported a bug.  I have the fix and a new version,  but the test machines, 
 and I suppose it will also be true of CRAN,  are unhappy about the interval 
since last submit.  Should I just submit the new version anyway with a note in 
cram-comments that this is a bug fix.

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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Re: [R-pkg-devel] Finding UTF character in .RData file

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Okay I found it.  I looked at the code for  tools:::.check_package_datasets(),  
took out the core part,  ran every string  I had in every dataset,  it came 
out.  A degree symbol.

Thanks for telling me about the function.  Still surprised that the test 
machines don't flag it.  Or is this a new test on CRAN?

-Roy


> On Aug 5, 2019, at 10:48 AM, Roy Mendelssohn - NOAA Federal 
>  wrote:
> 
> Using tools:::.check_package_datasets() produces the error,  but doesn't give 
> out any more information.  I don't know enough about some fo the write() 
> function.  If I write to csv of some sort,  will this information be 
> preserved?
> 
> Thanks,
> 
> -Roy
> 
> 
>> On Aug 5, 2019, at 8:57 AM, Roy Mendelssohn - NOAA Federal 
>>  wrote:
>> 
>> Thanks.  What is surprising me is I can't reproduce the error either 
>> directly on my Mac or on rhub::windows and I am waiting for the result of 
>> win-builder  (I can't check most rhub::linux  because it fails to correctly 
>> build a number of required packages,  something I have reported but still 
>> persists - like rgdal,  rerddap, crul,  ncdf4).
>> 
>> -Roy
>> - 
>>> On Aug 5, 2019, at 8:50 AM, Duncan Murdoch  wrote:
>>> 
>>> On 05/08/2019 10:51 a.m., Roy Mendelssohn - NOAA Federal via 
>>> R-package-devel wrote:
>>>> Hi All:
>>>> The recent nighty CRAN checks on one of my packages reports:
>>>> Check: data for non-ASCII characters
>>>> Result: NOTE
>>>>Note: found 1 marked UTF-8 string
>>>> When  originally submitted this was not the case.  All my data files are 
>>>> .RData files,  and even more so most are binary data.  If they were text 
>>>> files I could readily scan for UTF,  is there a way once I read the data 
>>>> into R to do a similar scan from within R.  I just ran the most recent  
>>>> (Github) version of devtools::check() and it doesn't report an error.  Or 
>>>> is there a way I can get more specific information from the CRAN nightly 
>>>> build or Rhub or the like?
>>> 
>>> That message comes when the tools:::.check_package_datasets function 
>>> detects a string containing a UTF-8 encoding.  You can run it directly and 
>>> you might get a more informative message.  If not, I suppose you could 
>>> fix() it and add some extra debugging messages
>>> 
>>> It's argument is "pkgDir"; I think that is the directory holding the files 
>>> after untarring the .tar.gz file.
>>> 
>>> Duncan Murdoch
>> 
>> **
>> "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: http://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.
>> 
> 
> **
> "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: http://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.
> 

**
"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: http://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] Finding UTF character in .RData file

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Using tools:::.check_package_datasets() produces the error,  but doesn't give 
out any more information.  I don't know enough about some fo the write() 
function.  If I write to csv of some sort,  will this information be preserved?

Thanks,

-Roy


> On Aug 5, 2019, at 8:57 AM, Roy Mendelssohn - NOAA Federal 
>  wrote:
> 
> Thanks.  What is surprising me is I can't reproduce the error either directly 
> on my Mac or on rhub::windows and I am waiting for the result of win-builder  
> (I can't check most rhub::linux  because it fails to correctly build a number 
> of required packages,  something I have reported but still persists - like 
> rgdal,  rerddap, crul,  ncdf4).
> 
> -Roy
> - 
>> On Aug 5, 2019, at 8:50 AM, Duncan Murdoch  wrote:
>> 
>> On 05/08/2019 10:51 a.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
>> wrote:
>>> Hi All:
>>> The recent nighty CRAN checks on one of my packages reports:
>>> Check: data for non-ASCII characters
>>> Result: NOTE
>>> Note: found 1 marked UTF-8 string
>>> When  originally submitted this was not the case.  All my data files are 
>>> .RData files,  and even more so most are binary data.  If they were text 
>>> files I could readily scan for UTF,  is there a way once I read the data 
>>> into R to do a similar scan from within R.  I just ran the most recent  
>>> (Github) version of devtools::check() and it doesn't report an error.  Or 
>>> is there a way I can get more specific information from the CRAN nightly 
>>> build or Rhub or the like?
>> 
>> That message comes when the tools:::.check_package_datasets function detects 
>> a string containing a UTF-8 encoding.  You can run it directly and you might 
>> get a more informative message.  If not, I suppose you could fix() it and 
>> add some extra debugging messages
>> 
>> It's argument is "pkgDir"; I think that is the directory holding the files 
>> after untarring the .tar.gz file.
>> 
>> Duncan Murdoch
> 
> **
> "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: http://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.
> 

**
"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: http://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] Finding UTF character in .RData file

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks.  What is surprising me is I can't reproduce the error either directly 
on my Mac or on rhub::windows and I am waiting for the result of win-builder  
(I can't check most rhub::linux  because it fails to correctly build a number 
of required packages,  something I have reported but still persists - like 
rgdal,  rerddap, crul,  ncdf4).

-Roy
 - 
> On Aug 5, 2019, at 8:50 AM, Duncan Murdoch  wrote:
> 
> On 05/08/2019 10:51 a.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
> wrote:
>> Hi All:
>> The recent nighty CRAN checks on one of my packages reports:
>> Check: data for non-ASCII characters
>> Result: NOTE
>>  Note: found 1 marked UTF-8 string
>> When  originally submitted this was not the case.  All my data files are 
>> .RData files,  and even more so most are binary data.  If they were text 
>> files I could readily scan for UTF,  is there a way once I read the data 
>> into R to do a similar scan from within R.  I just ran the most recent  
>> (Github) version of devtools::check() and it doesn't report an error.  Or is 
>> there a way I can get more specific information from the CRAN nightly build 
>> or Rhub or the like?
> 
> That message comes when the tools:::.check_package_datasets function detects 
> a string containing a UTF-8 encoding.  You can run it directly and you might 
> get a more informative message.  If not, I suppose you could fix() it and add 
> some extra debugging messages
> 
> It's argument is "pkgDir"; I think that is the directory holding the files 
> after untarring the .tar.gz file.
> 
> Duncan Murdoch

**
"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: http://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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[R-pkg-devel] Finding UTF character in .RData file

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

The recent nighty CRAN checks on one of my packages reports:

Check: data for non-ASCII characters 
Result: NOTE 
 Note: found 1 marked UTF-8 string 

When  originally submitted this was not the case.  All my data files are .RData 
files,  and even more so most are binary data.  If they were text files I could 
readily scan for UTF,  is there a way once I read the data into R to do a 
similar scan from within R.  I just ran the most recent  (Github) version of 
devtools::check() and it doesn't report an error.  Or is there a way I can get 
more specific information from the CRAN nightly build or Rhub or the like?

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: http://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] Needing rgeos from sf

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks,  actually have similar code for some other packages that must have been 
causing similar problems  (that part was from the original author,  I am now 
the maintainer).  Now I understand why he had something similar in the code.  
There is a comment about Namespaces not being handled properly in those 
packages.

Will try that.  I actually have rgdal and rgeos in Imports,  they were getting 
flagged in the CRAN nightly builds.  If I have them in that one statement,  
that should take care of both issues I believe.

But it would be nice to figure out why this is happening,  and only on Windows. 
 Sort of frustrating when you follow the guidelines but get failures,  but what 
also what is good about things like CRAN,  for whatever reason this will insure 
I work across platforms.

-Roy


> On Jul 25, 2019, at 12:56 PM, Duncan Murdoch  wrote:
> 
> On 25/07/2019 3:47 p.m., Roy Mendelssohn - NOAA Federal wrote:
>> Okay I added rgeos but now it can't find rgdal.  as in:
>>> Error: processing vignette 'using_plotdap.Rmd' failed with diagnostics:
>>> package 'rgdal' is not available
>>> --- failed re-building 'using_plotdap.Rmd'
>>> 
>> A question I asked before is if there is anyway to check that 'rgdal' and 
>> 'rgeos' are properly installed on the winbuider servers, as well as 'sf' and 
>> 'sp'?  'devtools::check()' on my mac produces no errors,  same with  'rhub' 
>> using Fedora,  but I get the same errors on 'rhub' using Windows.So it 
>> appears to be a problem with Windows,  and again I am not calling these 
>> packages directly so I should not need to Import them.
> 
> You're right, you shouldn't need to import them if you don't call them 
> directly.  However, if some package that you do need requires them, then your 
> build or checks will fail without them.
> 
> It's probably getting tedious, but you could work around this as well, by 
> figuring out what part of using_plotdap.Rmd needs rgdal, and wrapping that 
> code in something like
> 
> if (requireNamespace("rgdal")) {
>  # code that needs it
> }
> 
> I think this will mean you need to add rgdal to the Suggests list for your 
> package to avoid other warnings.
> 
> Duncan Murdoch
> 
>> Thanks,
>> -Roy
>>> On Jul 25, 2019, at 12:38 PM, Duncan Murdoch  
>>> wrote:
>>> 
>>> On 25/07/2019 3:21 p.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
>>> wrote:
>>>> I have been testing a package for resubmission with bug fixes.  On the 
>>>> present CRAN builds I get:
>>>>> Result: NOTE
>>>>> Namespaces in Imports field not imported from:
>>>>>  ‘mapdata’ ‘maptools’ ‘plot3D’ ‘rgdal’ ‘rgeos’
>>>>>  All declared Imports should be used.
>>>> However,  if I remove rgeos from the imports I get from win builder:
>>>>> Error in st_as_sfc.SpatialPolygons(sp::geometry(x), ...) :
>>>>>  package rgeos required for finding out which hole belongs to which 
>>>>> exterior ring
>>>> Note that I am not calling 'rgeos',  either 'sf' or 'sp' is,  but does not 
>>>> appear to be properly importing all the need namespaces.
>>>> Best way  to proceed?  Include rgeos in Import and get the Note,  or 
>>> 
>>> A simple workaround would be to add a function that calls something from 
>>> rgeos just to satisfy the check, e.g.
>>> 
>>> # Just to satisfy the checks...
>>> dummy <- function() rgeos::getScale()
>>> 
>>> I don't think there are warnings if dummy is never used or exported, but if 
>>> there are, I think that's a pretty harmless call to make.
>>> 
>>> Duncan Murdoch
>> **
>> "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: http://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.
> 

**
"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: http://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] Needing rgeos from sf

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Okay I added rgeos but now it can't find rgdal.  as in:

> Error: processing vignette 'using_plotdap.Rmd' failed with diagnostics:
> package 'rgdal' is not available
> --- failed re-building 'using_plotdap.Rmd'
> 

A question I asked before is if there is anyway to check that 'rgdal' and 
'rgeos' are properly installed on the winbuider servers, as well as 'sf' and 
'sp'?  'devtools::check()' on my mac produces no errors,  same with  'rhub' 
using Fedora,  but I get the same errors on 'rhub' using Windows.So it 
appears to be a problem with Windows,  and again I am not calling these 
packages directly so I should not need to Import them.

Thanks,

-Roy


> On Jul 25, 2019, at 12:38 PM, Duncan Murdoch  wrote:
> 
> On 25/07/2019 3:21 p.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
> wrote:
>> I have been testing a package for resubmission with bug fixes.  On the 
>> present CRAN builds I get:
>>> Result: NOTE
>>> Namespaces in Imports field not imported from:
>>>  ‘mapdata’ ‘maptools’ ‘plot3D’ ‘rgdal’ ‘rgeos’
>>>  All declared Imports should be used.
>> However,  if I remove rgeos from the imports I get from win builder:
>>> Error in st_as_sfc.SpatialPolygons(sp::geometry(x), ...) :
>>>  package rgeos required for finding out which hole belongs to which 
>>> exterior ring
>> Note that I am not calling 'rgeos',  either 'sf' or 'sp' is,  but does not 
>> appear to be properly importing all the need namespaces.
>> Best way  to proceed?  Include rgeos in Import and get the Note,  or 
> 
> A simple workaround would be to add a function that calls something from 
> rgeos just to satisfy the check, e.g.
> 
> # Just to satisfy the checks...
> dummy <- function() rgeos::getScale()
> 
> I don't think there are warnings if dummy is never used or exported, but if 
> there are, I think that's a pretty harmless call to make.
> 
> Duncan Murdoch

**
"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: http://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] Cran check on Solaris

[Roy Mendelssohn - NOAA Federal via R-package-devel]

I have been having similar problems with win-builder release for the last 
several days.  It appears that some of the needed DLLs are not there.  I have 
been reporting them to Uwe, and he is working through resolving the issues.  
Part of it is the test fails on one DLL,  and then when that is repaired fails 
on another.

This is mostly a PSA as others may run into this.  If you do run into it,  it 
is probably worth at least reporting the specific error so it can be checked,  
Besides Rcpp,  I have had issues with a number of the packages used by ggplot2, 
 as well as rlang and glue

-Roy

> On May 28, 2019, at 11:50 AM, Iñaki Ucar  wrote:
> 
> On Tue, 28 May 2019 at 20:12, Τόλης Χαλκής  wrote:
>> 
>> Dear all,
>> 
>> we have submitted the package volesti to CRAN and it is temporarily
>> accepted, because the check in solaris and
>> windows r-release-windows-ix86+x86_64 failed as you can see here
>> https://cran.r-project.org/web/checks/check_results_volesti.html
>> 
>> The check in solaris fails when the lpsolve library is linked with
>> volesti.so and the error is the following:
>> "ld: fatal: dlopen() of support library (-lstdc++) failed with error:
>> ld.so.1: ld: fatal: -lstdc++: open failed: No such file or directory"
>> I tried to fix the bug by using some flags in the makefile of lpsolve
>> library but nothing worked (I check it in rhub).
>> 
>> In windows the error is the following:
>> "Error: package or namespace load failed for 'Rcpp' in library.dynam(lib,
>> package, package.lib):
>> 
>> DLL 'Rcpp' not found: maybe not installed for this architecture?"
>> 
>> But the check in rhub is successful for the same version of windows os.
> 
> Don't worry about this second one. It's probably a temporal problem,
> but surely not related to your package.
> 
> Iñaki
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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: http://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] WInbuilder and rHub updating

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks for the info.  No special requests.  Just no point in sending in a test 
until the package gets there.

-Roy

> On May 21, 2019, at 4:47 AM, Uwe Ligges  
> wrote:
> 
> For winbuilder and general incoming check services:
> 
> New packages on CRAN should be directly available for incoming checks, 
> perhaps with some short technical delays of less than one hour.
> 
> 
> For winbuilder on demand checks, there may be a lag of 2 days. Requests may 
> be considered.
> 
> Best,
> Uwe Ligges
> 
> 
> On 19.05.2019 20:09, Roy Mendelssohn - NOAA Federal via R-package-devel wrote:
>> Subject:
>> WInbuilder and rHub updating
>> From:
>> Roy Mendelssohn - NOAA Federal 
>> Date:
>> 19.05.2019, 20:09
>> To:
>> Roy Mendelssohn - NOAA Federal via R-package-devel 
>> 
>> To:
>> Roy Mendelssohn - NOAA Federal via R-package-devel 
>> 
>> HI All:
>> I have a package I am developing that depends on a package that was just 
>> accepted and appears on CRAN.  Do Winbuilder and rHub update daily,  or if 
>> not,  what is the usual lag for new packages to appear on the test machines. 
>>  Or may generally,  is there a way to query what packages are available on 
>> either or both of these?  That would be the biggest help.
>> 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: http://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

**
"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: http://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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[R-pkg-devel] WInbuilder and rHub updating

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
HI All:

I have a package I am developing that depends on a package that was just 
accepted and appears on CRAN.  Do Winbuilder and rHub update daily,  or if not, 
 what is the usual lag for new packages to appear on the test machines.  Or may 
generally,  is there a way to query what packages are available on either or 
both of these?  That would be the biggest help.

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: http://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.

--- End Message ---
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Re: [R-pkg-devel] R3.6.0 suppressing S3 overwrite messages

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
Thanks again.  I use httr explicitly,  I believe hoardr is used by another 
package that I use.  I don't think the conflict will cause problems given how I 
am using them,  but your explanation clarifies what is going on for me to check 
on.

-Roy


> On May 18, 2019, at 1:23 PM, Duncan Murdoch  wrote:
> 
> On 18/05/2019 4:03 p.m., Duncan Murdoch wrote:
>> On 18/05/2019 3:42 p.m., Roy Mendelssohn - NOAA Federal via
>> R-package-devel wrote:
>>> 
>>> My memory is that this was discussed here,  but i can't find the emails, 
>>> including in the archives ( i did find a similar query from Yihui on 
>>> r-dev.).  Probably there,  I am just not seeing it.  In the package I am 
>>> working on for submission,  when I load the package i get:
>> There was a thread about this on R-help, started by Rolf Turner on April
>> 29, subject "Message produced under R 3.6.0.".
>> Users can suppress those messages, but I don't think package writers
>> can:  they indicate true bugs, and the packages mentioned (ggplot2,
>> crul, hoardr in your case) need to be fixed to get rid of them.
> 
> Sorry, that claim isn't correct.  For example, hoardr has a conflict with 
> httr, but it's really a weakness of S3 that is causing this:  they both 
> define things with class "cache_info", and the warning you're seeing is 
> because both have print.cache_info methods.  However, the classes are 
> unrelated.  I think the problem is that R can only have one print.cache_info 
> method active, and you somehow got both hoardr and httr loaded at the same 
> time.
> 
> Either one of them could work around this S3 limitation by changing the name 
> of the class (e.g. to "hoardr_cache_info" or "httr_cache_info"), but I don't 
> think it was fair of me to suggest some flaw in either of those packages for 
> the collision.
> 
> Duncan Murdoch

**
"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: http://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] R3.6.0 suppressing S3 overwrite messages

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
Thanks.  I thought I remembered seeing this discussed.  I was looking in the 
archives for this list,  not r-help.

-Roy


> On May 18, 2019, at 1:03 PM, Duncan Murdoch  wrote:
> 
> On 18/05/2019 3:42 p.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
> wrote:
>> My memory is that this was discussed here,  but i can't find the emails, 
>> including in the archives ( i did find a similar query from Yihui on 
>> r-dev.).  Probably there,  I am just not seeing it.  In the package I am 
>> working on for submission,  when I load the package i get:
> 
> 
> There was a thread about this on R-help, started by Rolf Turner on April 29, 
> subject "Message produced under R 3.6.0.".
> 
> Users can suppress those messages, but I don't think package writers can:  
> they indicate true bugs, and the packages mentioned (ggplot2, crul, hoardr in 
> your case) need to be fixed to get rid of them.
> 
> Duncan Murdoch
> 

**
"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: http://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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[R-pkg-devel] R3.6.0 suppressing S3 overwrite messages

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
Hi All:

My memory is that this was discussed here,  but i can't find the emails, 
including in the archives ( i did find a similar query from Yihui on r-dev.).  
Probably there,  I am just not seeing it.  In the package I am working on for 
submission,  when I load the package i get:

> Registered S3 methods overwritten by 'ggplot2':
>   method from 
>   [.quosures rlang
>   c.quosures rlang
>   print.quosures rlang
> Registered S3 method overwritten by 'crul':
>   method from
>   as.character.form_file httr
> Registered S3 method overwritten by 'hoardr':
>   method   from
>   print.cache_info httr

Can these be suppressed?

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: http://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] Linux Errors on RHub

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
HI:

Though you appear to have found the problem.  it is a package called plotdap,  
the Ubuntu results are here:

https://builder.r-hub.io/status/plotdap_0.0.1.tar.gz-5e8cf0d2b8304290820438dde5593e27

The complete build attempt was:

> #> * installing *source* package ‘rgdal’ ...
> 2626#> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> 2627#> configure: R_HOME: /usr/lib/R
> 2628#> configure: CC: gcc -std=gnu99
> 2629#> configure: CXX: g++
> 2630#> configure: C++11 support available
> 2631#> configure: rgdal: 1.4-3
> 2632#> checking for /usr/bin/svnversion... yes
> 2633#> configure: svn revision: 828
> 2634#> checking for gdal-config... /usr/bin/gdal-config
> 2635#> checking gdal-config usability... yes
> 2636#> configure: GDAL: 1.11.3
> 2637#> checking GDAL version >= 1.11.4... no
> 2638#> configure: error: upgrade GDAL to 1.11.4 or later
> 2639#> ERROR: configuration failed for package ‘rgdal’


I wrote here rather than RHub first because I was unaware of the link  (thanks) 
and my issue was more if I could just go ahead and submit to CRAN despite this, 
 because the problem is not with my package.

Thanks for your response.

-Roy


> 
> On Apr 24, 2019, at 3:06 AM, Gábor Csárdi  wrote:
> 
> 
> FYI,

**
"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: http://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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[R-pkg-devel] Linux Errors on RHub

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
Hi All:

I am checking a package I am hoping to submit to CRAN on RHub.  The Windows and 
Fedora runs worked but the Ubuntu test ended because of the following:

> #> Warning messages:
> 3203#> 1: In i.p(...) : installation of package ‘rgdal’ had non-zero exit 
> status
> 3204#> 2: In i.p(...) : installation of package ‘sf’ had non-zero exit status
> 3205#> 3: In i.p(...) :

I have a few details to work out on Mac and Windows tests (capitalization, a 
note to CRAN that a spelling is correct, reduce times of examples),  but given 
that rgdal and sf are packages on CRAN if I can clean up the other items is it 
appropriate to go ahead and submit?

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: http://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] Vignette timing out on test server

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
Thanks muchly.  That looks like I what I was after.  otherwise I was going to 
have to put tictoc on each chunk.

-Roy

> On Apr 17, 2019, at 2:21 AM, Iñaki Ucar  wrote:
> 
> On Wed, 17 Apr 2019 at 02:41, Roy Mendelssohn - NOAA Federal via
> R-package-devel  wrote:
>> -- Forwarded message ------
>> From: Roy Mendelssohn - NOAA Federal 
>> To: "Maëlle SALMON via R-package-devel" 
>> Cc:
>> Bcc:
>> Date: Tue, 16 Apr 2019 17:41:21 -0700
>> Subject: Vignette timing out on test server
>> Hi All:
>> 
>> The package I am trying to get ready for submission has a Vignette that does 
>> a number of data downloads and some complicate maps with satellite images.  
>> While it knits on my computer,  on checks it times out.  I am looking for 
>> ways to speed it up,  but my question is, is  there a command or a way to 
>> profile a vignette as it knits to  have a record to see which chunks are 
>> using up how much time?
>> 
>> I realize CRAN only runs the vignette code to check that it runs, but it 
>> must have a time limit because I am consistently hitting time outs on test 
>> machines.  So ti would help me if I can identify where all the time is.
> 
> There you go:
> 
> https://stackoverflow.com/questions/24595280/timing-for-chunks
> https://stackoverflow.com/questions/30530008/hook-to-time-knitr-chunks
> 
> -- 
> Iñaki Úcar

**
"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: http://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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[R-pkg-devel] Vignette timing out on test server

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
Hi All:

The package I am trying to get ready for submission has a Vignette that does a 
number of data downloads and some complicate maps with satellite images.  While 
it knits on my computer,  on checks it times out.  I am looking for ways to 
speed it up,  but my question is, is  there a command or a way to profile a 
vignette as it knits to  have a record to see which chunks are using up how 
much time?

I realize CRAN only runs the vignette code to check that it runs, but it must 
have a time limit because I am consistently hitting time outs on test machines. 
 So ti would help me if I can identify where all the time is.

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: http://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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[R-pkg-devel] Splitting maintainer from creator

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
Hi All;

In defining the roles in Description file of a package,  has there been any 
thought of adding a role of maintainer separate from creator  (cre).  While the 
definition given says:

> cre: the creator or maintainer, the person you should bother if you have 
> problems.

that "or" separates two really distinct roles.  To me the sense of the word 
"creator' is the person or persons who originally created the package.  A 
present maintainer may well have only added patches to the present package,  
but would need to be defined as "cre" to be the one to receive emails.

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: http://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] Graphics in examples

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
Thanks muchly.  I wanted to check on that to be certain.

-Roy


> On Mar 19, 2019, at 11:14 AM, Uwe Ligges  
> wrote:
> 
> Yes, graphics goes top the default device, e.g. X11() in an interactve Linux 
> session or pdf() in non interactive usage, e.g. for running examples during 
> an 'R CMD check' run.
> 
> Best,
> Uwe Ligges
> 
> On 19.03.2019 19:03, Roy Mendelssohn - NOAA Federal via R-package-devel wrote:
>> Subject:
>> Graphics in examples
>> From:
>> Roy Mendelssohn - NOAA Federal 
>> Date:
>> 19.03.2019, 19:03
>> To:
>> R Package Development 
>> To:
>> R Package Development 
>> Hi All:
>> I am working on preparing a package for submission.  All the package does is 
>> makes it easy to map data that were downloaded using a different package. 
>> Can graphics be in examples?  Or should I assign the graphics to an object 
>> and leave it at that. Or any other advice.
>> Basically, if graphics can't be handled in some form,  it wouldn't be 
>> possible to create examples that test the program.  In reading over the 
>> different sources for guidelines for submission,  I don't see this 
>> possibility discussed anywhere.
>> 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: http://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

**
"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: http://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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[R-pkg-devel] Graphics in examples

[Roy Mendelssohn - NOAA Federal via R-package-devel]

--- Begin Message ---
Hi All:

I am working on preparing a package for submission.  All the package does is 
makes it easy to map data that were downloaded using a different package. Can 
graphics be in examples?  Or should I assign the graphics to an object and 
leave it at that. Or any other advice.

Basically, if graphics can't be handled in some form,  it wouldn't be possible 
to create examples that test the program.  In reading over the different 
sources for guidelines for submission,  I don't see this possibility discussed 
anywhere.

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: http://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] Cannot submit package due to misspell note

[Roy Mendelssohn - NOAA Federal]

I don't think your DESCRIPTION file is properly formed.  See 
http://r-pkgs.had.co.nz/description.html for more information.  Author fields 
in particular are done in a particular way.

HTH,

-Roy




> On Apr 5, 2018, at 1:17 PM, Dudek Andrzej  wrote:
> 
> CRAN maintainers rejected the package two times already due to this note 
> 
> But for previous version I've been asked to add the references in description 
> field:
> 
>> Package Information:
>> Package: mdsOpt
>> Version: 0.1-4
>> Title: Searching for Optimal MDS Procedure for Metric Data
>> Author(s): Marek Walesiak   Andrzej Dudek
>>   
>> Maintainer: Andrzej Dudek 
>> Depends: smacof, clusterSim
>> Suggests: testthat
>> Description: Searching for optimal multidimensional scaling procedure for
>>   metric data.
> 
> Thanks, can you please extend your description text.
> 
> Can you provide some references in the form authors (year)  or 
>  (no space after 'doi:' and 'arXiv:')?
> 
> Best,
> Swetlana Herbrandt
> 
> 
> 
> So at this point is some kind of vicious circle for me :-)  Maybe adding 
> quotation mark is best idea (?)
> 
> Best ,- 
> 
> Andrzej
> 
> -Original Message-
> From: Ben Bolker [mailto:bbol...@gmail.com] 
> Sent: Thursday, April 5, 2018 9:51 PM
> To: Dudek Andrzej 
> Cc: r-package-devel@r-project.org
> Subject: Re: [R-pkg-devel] Cannot submit package due to misspell note
> 
> Can you clarify what "which cause the rejection at submission process"
> means, i.e. have the CRAN maintainers already rejected your package because 
> of this note, or are you afraid they will?
> 
> Looking at 
> https://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file
> , I agree that there's not much useful guidance. The entry on the Description 
> field is:
> 
>> The mandatory ‘Description’ field should give a comprehensive description of 
>> what the package does. One can use several (complete) sentences, but only 
>> one paragraph. It should be intelligible to all the intended readership 
>> (e.g. for a CRAN package to all CRAN users). It is good practice not to 
>> start with the package name, ‘This package’ or similar. As with the ‘Title’ 
>> field, double quotes should be used for quotations (including titles of 
>> books and articles), and single quotes for non-English usage, including 
>> names of other packages and external software. This field should also be 
>> used for explaining the package name if necessary. URLs should be enclosed 
>> in angle brackets, e.g. ‘’: see also Specifying 
>> URLs.
> 
>  You could protect the names in single quotation marks, but that seems 
> awkward.
> 
>  My best guess (I don't know if the CRAN maintainers would go for this or 
> not) would be to add a References: field, put your references therein, and 
> refer to that field within your Description: field (from TFM, "There is no 
> restriction on the use of other fields not mentioned here ...")  (I don't 
> know if additional fields are spell-checked or not ...)
> 
> 
> 
> On Thu, Apr 5, 2018 at 3:13 PM, Dudek Andrzej  
> wrote:
>> Hello,
>> 
>> I've stuck in submitting new version of package(mdsOpt), due to the 
>> following note,
>> 
>> Possibly mis-spelled words in DESCRIPTION:
>>  De (13:2)
>>  Diday (14:48)
>>  Groenen (12:13, 14:2)
>>  Leeuw (13:5)
>>  Mair (12:30, 13:16)
>>  Walesiak (15:2, 16:2)
>>  Winsberg (14:19)
>> 
>> which cause the rejection at submission process.
>> 
>> The description file / section looks like this:
>> 
>> Description: Selecting the optimal multidimensional scaling (MDS) procedure 
>> for metric data via metric MDS (ratio, interval, mspline) and nonmetric MDS 
>> (ordinal). Selecting the optimal multidimensional scaling (MDS) procedure 
>> for interval-valued symbolic data via metric MDS (ratio, interval, mspline). 
>> Selecting the optimal MDS procedure for statistical data referring to the 
>> evaluation of tourist attractiveness of Lower Silesian counties.
>> (Borg, I., Groenen, P.J.F., Mair, P. (2013) 
>> ,  De Leeuw, J., Mair, P. (2015) 
>> ,
>> Groenen, P.J.F., Winsberg, S., Rodriguez, O., Diday, E. (2006) 
>> , Walesiak, M. (2016) 
>> ,  Walesiak, M. (2017) 
>> ).
>> 
>> I've tried to check  the documentation but found nothing about including 
>> references in description files (which AFAIK is now required).
>> 
>> Thank in advance for any help!
>> 
>> Andrzej
>> 
>> -
>> Andrzej Dudek
>> Professor of Wroclaw University of Economics Department of 
>> Econometrics and Computer Science, Nowowiejska 3, 58-506 Jelenia Góra, 
>> Poland
>> mail: andrzej.du...@ue.wroc.pl
>> 
>> 
>> 
>>[[alternative HTML version deleted]]
>> 
>> 
>> __
>> 

Re: [R-pkg-devel] Cannot submit package due to misspell note

[Roy Mendelssohn - NOAA Federal]

I may be wrong,  but I have "mis-spelled" words in my submissions.  When you 
submit to CRAN,  I am pretty certain the spell-check is automated by a 
spell-checker,  adn if those words aren't recognized they will throw the note.

Try creating a cran-comments.md file, and put into that everything you have 
done to check your submission,  and  every note that you receive.  If those 
words correctly spelled correctly,  put that in the file.  See 
http://r-pkgs.had.co.nz/release.html  for more information on making a good 
submission.  

Even with that,  likely on the automatic check you will get the same response, 
respond to that that  the information is contained in the cran-comments.md 
file,  and then give the maintainers a few days to respond.  I have found the 
amount of time till I get a response is highly variable,  as I am certain the 
maintainers are very busy,  mainly just saying don't panic if you don't hear 
back right away.

HTH,

-Roy


> On Apr 5, 2018, at 12:13 PM, Dudek Andrzej  wrote:
> 
> Hello,
> 
> I've stuck in submitting new version of package(mdsOpt), due to the following 
> note,
> 
> Possibly mis-spelled words in DESCRIPTION:
>  De (13:2)
>  Diday (14:48)
>  Groenen (12:13, 14:2)
>  Leeuw (13:5)
>  Mair (12:30, 13:16)
>  Walesiak (15:2, 16:2)
>  Winsberg (14:19)
> 
> which cause the rejection at submission process.
> 
> The description file / section looks like this:
> 
> Description: Selecting the optimal multidimensional scaling (MDS) procedure 
> for metric data via metric MDS (ratio, interval, mspline) and nonmetric MDS 
> (ordinal). Selecting the optimal multidimensional scaling (MDS) procedure for 
> interval-valued symbolic data via metric MDS (ratio, interval, mspline). 
> Selecting the optimal MDS procedure for statistical data referring to the 
> evaluation of tourist attractiveness of Lower Silesian counties.
> (Borg, I., Groenen, P.J.F., Mair, P. (2013) ,
> De Leeuw, J., Mair, P. (2015) ,
> Groenen, P.J.F., Winsberg, S., Rodriguez, O., Diday, E. (2006) 
> ,
> Walesiak, M. (2016) ,
> Walesiak, M. (2017) ).
> 
> I've tried to check  the documentation but found nothing about including 
> references in description files (which AFAIK is now required).
> 
> Thank in advance for any help!
> 
> Andrzej
> 
> -
> Andrzej Dudek
> Professor of Wroclaw University of Economics
> Department of Econometrics and Computer Science,
> Nowowiejska 3, 58-506 Jelenia G�ra, Poland
> mail: andrzej.du...@ue.wroc.pl
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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: http://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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[R-pkg-devel] Dealing with not so temporary files

[Roy Mendelssohn - NOAA Federal]

Hi All:

Recently there was a proper admonishment to a developer that it is bad 
etiquette writing to a user's home directory,  and for temporary files use the 
functions tempdir() and tempfile().  I am working on a new package (presently 
on Github) that downloads data from a remote server,  reads the data into R,  
but I would like to save that file for the user to access later if they so 
desire.  Saving to the "temp directory" is not a good option for that,  want to 
put it somewhere where the user can easily find it.  What is the proper 
etiquette for this?  Even if I provide an argument for the user to specify the 
location to save the file,  I should provide a default location.  

Any suggestions appreciated.

-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: http://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] Help with CRAN error

[Roy Mendelssohn - NOAA Federal]

Glad you found the solution.  I would add as an aside,  I have found a good 
vignette is worth the effort.  R docs tend to be like Unix docs,  relatively 
short and terse and can be hard for someone not familiar with the package what 
all the options might do.  A good vignette allows you to lay out in detail how 
to use the package,  and to do so in context. 

-Roy

> On Feb 4, 2018, at 11:32 AM, Dev Chakraborty <dpc10s...@gmail.com> wrote:
> 
> Roy,
> 
> I don't use a knitR file, but my DESCRIPTION file had a field:
> 
> VignetteBuilder: knitr
> 
> Deleting this field solved the problem (i.e., got rid of that message in my 
> original email)
> 
> Thanks for all your help.
> 
> Dev
> 
>  
> 
> On Sun, Feb 4, 2018 at 2:05 PM, Roy Mendelssohn - NOAA Federal 
> <roy.mendelss...@noaa.gov> wrote:
> If you can't find the solution yourself,  posting the top matter of your 
> vignette file would also help.
> 
> -Roy
> 
> > On Feb 4, 2018, at 10:54 AM, Joshua Ulrich <josh.m.ulr...@gmail.com> wrote:
> >
> > On Sun, Feb 4, 2018 at 12:47 PM, Dev Chakraborty <dpc10s...@gmail.com> 
> > wrote:
> >> Dear All,
> >>
> >> I get the following message on running R CMD check -- as - cran:
> >>
> >> Package has a VignetteBuilder field but no prebuilt vignette index.
> >>
> >> I do not know how to fix this. Any help will be appreciated.
> >>
> > I don't know how to fix it either.  That said, often a great first
> > step is to search for the error.  A Google search for, "Package has a
> > VignetteBuilder field but no prebuilt vignette index.", which points
> > to: https://stackoverflow.com/q/30976308.
> >
> > And a Google search "VignetteBuilder" has several promising "how to"
> > results, and there is a "Non-Sweave Vignettes" section of Writing R
> > Extensions:
> > https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dSweave-vignettes.
> >
> > It will be easier for others to help you if you can do some
> > investigation on your own and come back with more specifics.
> >
> >> Sincerely,
> >>
> >> Dev
> >>
> >>
> >> --
> >> Dev Chakraborty, PhD
> >> Professor of Radiology retired
> >>
> >>[[alternative HTML version deleted]]
> >>
> >> __
> >> R-package-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
> >
> >
> > --
> > Joshua Ulrich  |  about.me/joshuaulrich
> > FOSS Trading  |  www.fosstrading.com
> > R/Finance 2018 | www.rinfinance.com
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> **
> "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: http://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.
> 
> 
> 
> 
> -- 
> Dev Chakraborty, PhD
> Professor of Radiology retired
> CEO, ExpertCAD Analytics LLC
> 412-480-7318 (cell)
> ‭(412) 427-5085‬ (alt. cell)
> 412-349-5305 (land line)
> 
> Book website:
> https://www.crcpress.com/9781482214840
> Online supplementary material website:
> https://bitbucket.org/dpc10ster/onlinebookk21778
> CAD Project website:
> www.expertcadanalytics.com
> JAFROC website
> www.devchakraborty.com

**
"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: http://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] Help with CRAN error

[Roy Mendelssohn - NOAA Federal]

If you can't find the solution yourself,  posting the top matter of your 
vignette file would also help.

-Roy

> On Feb 4, 2018, at 10:54 AM, Joshua Ulrich  wrote:
> 
> On Sun, Feb 4, 2018 at 12:47 PM, Dev Chakraborty  wrote:
>> Dear All,
>> 
>> I get the following message on running R CMD check -- as - cran:
>> 
>> Package has a VignetteBuilder field but no prebuilt vignette index.
>> 
>> I do not know how to fix this. Any help will be appreciated.
>> 
> I don't know how to fix it either.  That said, often a great first
> step is to search for the error.  A Google search for, "Package has a
> VignetteBuilder field but no prebuilt vignette index.", which points
> to: https://stackoverflow.com/q/30976308.
> 
> And a Google search "VignetteBuilder" has several promising "how to"
> results, and there is a "Non-Sweave Vignettes" section of Writing R
> Extensions:
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dSweave-vignettes.
> 
> It will be easier for others to help you if you can do some
> investigation on your own and come back with more specifics.
> 
>> Sincerely,
>> 
>> Dev
>> 
>> 
>> --
>> Dev Chakraborty, PhD
>> Professor of Radiology retired
>> 
>>[[alternative HTML version deleted]]
>> 
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 
> 
> 
> -- 
> Joshua Ulrich  |  about.me/joshuaulrich
> FOSS Trading  |  www.fosstrading.com
> R/Finance 2018 | www.rinfinance.com
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

**
"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: http://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] R-package did not pass the incoming checks automatically

[Roy Mendelssohn - NOAA Federal]

Hi Márcio:

I do not have solutions to your specific problems, but the errors do appear to 
be coming from the development version of R.  When you run 
devtools::build_win(), run it twice,  once as:

devtools::build_win(version = "R-release")

and once with 

devtools::build_win(version = "R-devel")

which is then more likely to produce the CRAN results before you submit.  Also, 
 as Henrik Bengtsson explained on this list a few weeks ago:

> As far as I understand it, the new R-devel tests basically tests your
> package with the minimal setup of packages (a "sandboxed" .libPaths())
> inferred from you DESCRIPTION (by excluding Suggests of the packages
> you depend on, which is where I think 'webshot' lives).

So R-devel can give different results,  and you need to make certain that your 
Imports and Suggests includes anything that might not be loaded.

Hope this helps some.

-Roy

> On Jan 20, 2018, at 9:47 AM, Márcio Augusto Diniz  
> wrote:
> 
> Hello all,
> 
> I submitted my package (
> https://cran.r-project.org/web/packages/ewoc/index.html) to CRAN and it did
> not pass the automatic checks of win_builder. However,  I did not have the
> same error or warning messages when I ran devtools::win_builder() and
> devtools::run_examples() before. I had the same notes, though.
> 
> See message from win_builder() CRAN:
> 
> * using log directory 'd:/RCompile/CRANincoming/R-devel/ewoc.Rcheck'
> * using R Under development (unstable) (2018-01-19 r74138)
> * using platform: x86_64-w64-mingw32 (64-bit)
> * using session charset: ISO8859-1
> * checking for file 'ewoc/DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'ewoc' version '0.1.1'
> * checking CRAN incoming feasibility ... NOTE
> Maintainer: 'Marcio A. Diniz '
> 
> Found the following (possibly) invalid URLs:
>  URL: https://cran.rstudio.com/web/packages/ewoc/index.html
>From: README.md
>Status: 200
>Message: OK
>CRAN URL not in canonical form
>  Canonical CRAN.R-project.org URLs use https.
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for hidden files and directories ... OK
> * checking for portable file names ... OK
> * checking serialized R objects in the sources ... OK
> * checking whether package 'ewoc' can be installed ... OK
> * checking installed package size ... OK
> * checking package directory ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking for left-over files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * loading checks for arch 'i386'
> ** checking whether the package can be loaded ... OK
> ** checking whether the package can be loaded with stated dependencies ...
> OK
> ** checking whether the package can be unloaded cleanly ... OK
> ** checking whether the namespace can be loaded with stated dependencies
> ... OK
> ** checking whether the namespace can be unloaded cleanly ... OK
> ** checking loading without being on the library search path ... OK
> ** checking use of S3 registration ... OK
> * loading checks for arch 'x64'
> ** checking whether the package can be loaded ... OK
> ** checking whether the package can be loaded with stated dependencies ...
> OK
> ** checking whether the package can be unloaded cleanly ... OK
> ** checking whether the namespace can be loaded with stated dependencies
> ... OK
> ** checking whether the namespace can be unloaded cleanly ... OK
> ** checking loading without being on the library search path ... WARNING
> Error: package or namespace load failed for 'ewoc' in namespaceExport(ns,
> exports):
> undefined exports: iter, nextElem, isplit, irnorm, irunif, irbinom,
> irnbinom, irpois, icount, idiv, ireadLines, iread.table, icountn, iapply
> In addition: Warning message:
> S3 methods 'iter.default', 'iter.iter', 'iter.matrix', 'iter.data.frame',
> 'iter.function', 'nextElem.containeriter', 'nextElem.matrixiter',
> 'nextElem.dataframeiter', 'nextElem.funiter', 'nextElem.abstractiter',
> 'as.list.iter', 'isplit.default', 'isplit.data.frame' were declared in
> NAMESPACE but not found
> Execution halted
> 
> It looks like this package has a loading problem when not on .libPaths:
> see the messages for details.
> ** checking use of S3 registration ... OK
> * checking dependencies in R code ... OK
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... [15s] OK
> * checking Rd files ... OK
> * checking Rd metadata ... OK
> * checking Rd line widths ... OK
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... OK
> * 

Re: [R-pkg-devel] Fixed for messages

[Roy Mendelssohn - NOAA Federal]

Just to complete the record,  the suggested fixes did indeed fix things, and as 
I said Henrik provided a clear explanation of why the results are different in 
R-devel.

Thanks again,

-Roy



> On Jan 8, 2018, at 9:28 AM, Roy Mendelssohn - NOAA Federal 
> <roy.mendelss...@noaa.gov> wrote:
> 
> Thanks.  What I have at the top of my Vignette is:
> 
>> output: 
>> rmarkdown::html_vignette: default
>> 
>> vignette: >
>>  %\VignetteIndexEntry{Usingxtractomatic}
>>  %\VignetteEngine{knitr::rmarkdown}
>>  \usepackage[utf8]{inputenc}
>> ---
>> 
> 
> It is based on the template in RStudio when you choose a vignette as the 
> file.  I have added rmarkdown as well as webshot to my suggests,  and sent to 
> win-builder-devel,  will see what happens.
> 
> Thanks,
> 
> -Roy
> 
> 
> 
>> On Jan 8, 2018, at 9:17 AM, Thierry Onkelinx <thierry.onkel...@inbo.be> 
>> wrote:
>> 
>> Dear Roy,
>> 
>> Make sure that in DESCRIPTION you have at least
>> 
>> Suggests: knitr, rmarkdown
>> VignetteBuilder: knitr
>> 
>> The vignette requires
>> 
>> %\VignetteEngine{knitr::rmarkdown}
>> 
>> webshot is used by rmarkdown or knitr to convert dynamic HTML output
>> to a static image when the output is not HTML. Are you using pdf as
>> output format for the vignette? Consider using
>> rmarkdown::html_vignette.
>> 
>> Best regards,
>> 
>> ir. Thierry Onkelinx
>> Statisticus / Statistician
>> 
>> Vlaamse Overheid / Government of Flanders
>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>> AND FOREST
>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>> thierry.onkel...@inbo.be
>> Havenlaan 88 bus 73, 1000 Brussel
>> www.inbo.be
>> 
>> ///
>> To call in the statistician after the experiment is done may be no
>> more than asking him to perform a post-mortem examination: he may be
>> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
>> The plural of anecdote is not data. ~ Roger Brinner
>> The combination of some data and an aching desire for an answer does
>> not ensure that a reasonable answer can be extracted from a given body
>> of data. ~ John Tukey
>> ///
>> 
>> 
>> 
>> 
>> 2018-01-08 17:40 GMT+01:00 Roy Mendelssohn - NOAA Federal
>> <roy.mendelss...@noaa.gov>:
>>> Thanks Henrik:
>>> 
>>> I am a little slow,  I want to make certain I do this correctly.  I already 
>>> have knitr in my Suggests,  and the message is:
>>> 
>>>>>> knitr::rmarkdown
>>> 
>>> So do I put in my Suggests list  rmarkdown or knitr::rmarkdown
>>> 
>>> And most importantly,  thanks for the explanation about what is happening 
>>> with R-devel.  Of the responses I have seen,  it is the first one (at least 
>>> to me) that is clear what is going on to cause the errors,  and how to 
>>> approach correcting them.
>>> 
>>> -Roy
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> On Jan 8, 2018, at 8:32 AM, Henrik Bengtsson <henrik.bengts...@gmail.com> 
>>>> wrote:
>>>> 
>>>> On Mon, Jan 8, 2018 at 7:31 AM, Roy Mendelssohn - NOAA Federal
>>>> <roy.mendelss...@noaa.gov> wrote:
>>>>> Hi All:
>>>>> 
>>>>> In tesitng a package on winbuild-devel (but not on release)  I get the 
>>>>> following errors or warnings:
>>>>> 
>>>>>> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>>>>>> The vignette engine knitr::rmarkdown is not available, because the 
>>>>>> rmarkdown package is not installed. Please install it.
>>>>>> 
>>>>> 
>>>>> There was an email about this a few days ago,  but then,  as now,  it is 
>>>>> not clear to me specifically what I need to do where so that I don't get 
>>>>> this warning.  Do I need to include rmarkdown in the Suggests,
>>>> 
>>>> Yes, add it to Suggests.
>>>> 
>>>> or do I need to do something specific in the Vignette.  Or is this
>>>> just a question that winbuild hasn't installed it yet in the
>>>> development version and I can ignore it for now?
>>>>> 
>>>&

Re: [R-pkg-devel] Fixed for messages

[Roy Mendelssohn - NOAA Federal]

Thanks.  What I have at the top of my Vignette is:

> output: 
> rmarkdown::html_vignette: default
> 
> vignette: >
>   %\VignetteIndexEntry{Usingxtractomatic}
>   %\VignetteEngine{knitr::rmarkdown}
>   \usepackage[utf8]{inputenc}
> ---
> 

It is based on the template in RStudio when you choose a vignette as the file.  
I have added rmarkdown as well as webshot to my suggests,  and sent to 
win-builder-devel,  will see what happens.

Thanks,

-Roy



> On Jan 8, 2018, at 9:17 AM, Thierry Onkelinx <thierry.onkel...@inbo.be> wrote:
> 
> Dear Roy,
> 
> Make sure that in DESCRIPTION you have at least
> 
> Suggests: knitr, rmarkdown
> VignetteBuilder: knitr
> 
> The vignette requires
> 
> %\VignetteEngine{knitr::rmarkdown}
> 
> webshot is used by rmarkdown or knitr to convert dynamic HTML output
> to a static image when the output is not HTML. Are you using pdf as
> output format for the vignette? Consider using
> rmarkdown::html_vignette.
> 
> Best regards,
> 
> ir. Thierry Onkelinx
> Statisticus / Statistician
> 
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
> AND FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkel...@inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be
> 
> ///
> To call in the statistician after the experiment is done may be no
> more than asking him to perform a post-mortem examination: he may be
> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does
> not ensure that a reasonable answer can be extracted from a given body
> of data. ~ John Tukey
> ///
> 
> 
> 
> 
> 2018-01-08 17:40 GMT+01:00 Roy Mendelssohn - NOAA Federal
> <roy.mendelss...@noaa.gov>:
>> Thanks Henrik:
>> 
>> I am a little slow,  I want to make certain I do this correctly.  I already 
>> have knitr in my Suggests,  and the message is:
>> 
>>>>> knitr::rmarkdown
>> 
>> So do I put in my Suggests list  rmarkdown or knitr::rmarkdown
>> 
>> And most importantly,  thanks for the explanation about what is happening 
>> with R-devel.  Of the responses I have seen,  it is the first one (at least 
>> to me) that is clear what is going on to cause the errors,  and how to 
>> approach correcting them.
>> 
>> -Roy
>> 
>> 
>> 
>> 
>> 
>>> On Jan 8, 2018, at 8:32 AM, Henrik Bengtsson <henrik.bengts...@gmail.com> 
>>> wrote:
>>> 
>>> On Mon, Jan 8, 2018 at 7:31 AM, Roy Mendelssohn - NOAA Federal
>>> <roy.mendelss...@noaa.gov> wrote:
>>>> Hi All:
>>>> 
>>>> In tesitng a package on winbuild-devel (but not on release)  I get the 
>>>> following errors or warnings:
>>>> 
>>>>> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>>>>> The vignette engine knitr::rmarkdown is not available, because the 
>>>>> rmarkdown package is not installed. Please install it.
>>>>> 
>>>> 
>>>> There was an email about this a few days ago,  but then,  as now,  it is 
>>>> not clear to me specifically what I need to do where so that I don't get 
>>>> this warning.  Do I need to include rmarkdown in the Suggests,
>>> 
>>> Yes, add it to Suggests.
>>> 
>>> or do I need to do something specific in the Vignette.  Or is this
>>> just a question that winbuild hasn't installed it yet in the
>>> development version and I can ignore it for now?
>>>> 
>>>> Also I am getting this error (again only in the development version):
>>>> 
>>>>> Error: processing vignette 'Usingxtractomatic.Rmd' failed with 
>>>>> diagnostics:
>>>>> there is no package called 'webshot'
>>>>> 
>>>> 
>>>> 
>>>> 
>>>> Now I don't explicitly use a package called 'webshot',  but the lines 
>>>> referenced in the error message are:
>>>> 
>>>>> require("DT")
>>>>> DT::datatable(searchResult)
>>>>> 
>>>> 
>>>> where "searchResult" is just a list.   DT itself does not explicitly 
>>>> import "webshot" e

[R-pkg-devel] Compiling packages from source on Mac OS X that require "-f openmp" - A solution

[Roy Mendelssohn - NOAA Federal]

Hi All:

I wasn't quite certain the appropriate list for this,  but hopefully this will 
be found as needed. I know I have seen for several packages where building from 
source has failed on the Mac because of an error from using "-f openmp" in the 
compile options,  because the clang on the Mac didn't have openmp.

Now there is an R compatible version of clang with  openmp,  see:

http://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/#after-3-4-0

I just ran into this in trying to compile the latest version of the package 
"bssm".  Installing that version of clang solved the compilation errors.

-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: http://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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[R-pkg-devel] Storing Data Used in an Example

[Roy Mendelssohn - NOAA Federal]

Hi All:

I have a package whose main function is to download environmental data using a 
service.  I have added some plot routines,  As it is, my examples of just the 
downloads push the CRAN limits on time,  so I want the plot examples to use 
data that has already been downloaded and stored as part of the package.

Questions:

1.  Most appropriate place to store the example data (they will be .RData 
files).

2.  What size of data set is considered to be getting too large to be 
appropriate to include in a package.

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: http://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] In Description file, how far removed should the depends go?

[Roy Mendelssohn - NOAA Federal]

Thanks I meant Imports,  just wasn't thinking.  The main issue was how deep to 
recurse.

-Roy

> On Aug 29, 2017, at 9:50 AM, Uwe Ligges <lig...@statistik.tu-dortmund.de> 
> wrote:
> 
> 
> 
> On 29.08.2017 18:24, Roy Mendelssohn - NOAA Federal wrote:
>> HI All:
>> What is best practice for the "depends" in the Description file,  in terms 
>> of how of how many layers down do I list depends?  For example,  if my 
>> package depends on the rerddap package,  is it best practice  to just list 
>> rerddap in the depends,  or should I also list all the packages rerddap 
>> depends on  - which can go many layers deep.  What is best practice for this?
> 
> Only rerddap, and ideally in Imports rather than Depends.
> 
> Best,
> Uwe Ligges
> 
> 
>> 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: http://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

**
"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: http://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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[R-pkg-devel] In Description file, how far removed should the depends go?

[Roy Mendelssohn - NOAA Federal]

HI All:

What is best practice for the "depends" in the Description file,  in terms of 
how of how many layers down do I list depends?  For example,  if my package 
depends on the rerddap package,  is it best practice  to just list rerddap in 
the depends,  or should I also list all the packages rerddap depends on  - 
which can go many layers deep.  What is best practice for this?

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: http://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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[R-pkg-devel] Referring to data in R/sysdata.rda

[Roy Mendelssohn - NOAA Federal]

In my package I have a dataframe that I use but want to hide from the user.  In 
Hadley's book on R Packages,  he says:

>   • If you want to store parsed data, but not make it available to the 
> user, put it in R/sysdata.rda. This is the best place to put data that your 
> functions need.
> 

I have done that,  and sure enough when the package is loaded, the structure is 
there.  However,  when I am working on debugging code, and I refer to the  
structure in a function,  RStudio gives a warning that the structure is out of 
scope, say the data frame is myDF:

myFunc  <-  function(myIndex) {
 junk  <-  myDF[index]
return(junk)
}

RStudio will warn that myDF is out of scope.  My question is if there is a 
proper way to refer to myDF so as not to get the warning,  or just ignore it.  
Basically before submission I try to remove all warnings from the editor,  even 
style ones,  just to have things cleaner.

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: http://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] Fwd: R-package-devel@R-project.org: RANDR

[Roy Mendelssohn - NOAA Federal]

Hi Cathy:
> On Jan 24, 2017, at 2:41 PM, Cathy Lee Gierke  wrote:
> 
> Which I likely do have wrong, because I'm not sure how to make a data file
> available to the example. but that may be a different issue.

See:

http://r-pkgs.had.co.nz/data.html

In fact read through the entire thing.  it will make you like much easier if 
and when you go to submit your package.

-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: http://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] warning from win_build

[Roy Mendelssohn - NOAA Federal]

Thanks to all.  

I will give it several days to work it's way through.  In my case,  I need for 
it to be on build_win.

Happy new year,

-Roy


> On Dec 30, 2016, at 1:49 PM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
> 
> On 29/12/2016 6:50 PM, Duncan Murdoch wrote:
>> On 29/12/2016 2:58 PM, Roy Mendelssohn - NOAA Federal wrote:
>>> HI All:
>>> 
>>> If any cares,  the offending line is in the  ggplot2  file utilities.r 
>>> where it has:
>>> 
>>>> #' A waiver object.
>>>> #'
>>>> #' A waiver is a "flag" object, similar to \code{NULL}, that indicates the
>>>> #' calling function should just use the default value.  It is used in 
>>>> certain
>>>> #' functions to distinguish between displaying nothing (\code{NULL}) and
>>>> #' displaying a default value calculated elsewhere (\code{waiver()})
>>>> #'
>>>> #' @export
>>>> #' @keywords internal
>>>> waiver <- function() structure(NULL, class = "waiver")
>>>> 
>>>> is.waive <- function(x) inherits(x, "waiver")
>>> 
>>> If you then do a multi-file search on "waive" you find that it is used all 
>>> throughout the code base, so anytime waiver() is called, so is the NULL 
>>> structure.
>> 
>> That usage will work:  though waiver() tries to put a class on NULL,
>> structure() puts it on a length-zero list instead.  R-devel's complaint
>> is unnecessary here, but could be avoided with the code change
>> 
>> waiver <- function() structure(list(), class = "waiver")
>> 
>> I've cc'd Hadley to let him know.
> 
> Hadley submitted a patch, which is on CRAN now (version 2.2.1).  It will take 
> a little while to propagate to the mirrors, but things should be fine in your 
> package once you update ggplot2.
> 
> Duncan Murdoch
> 
>> 
>> Duncan Murdoch
>> 
>> 
>>> 
>>> -Roy
>>> 
>>> 
>>> 
>>> 
>>>> 
>>>> On Dec 29, 2016, at 11:44 AM, Roy Mendelssohn - NOAA Federal 
>>>> <roy.mendelss...@noaa.gov> wrote:
>>>> 
>>>> Thanks.  I can wait.  I will also see if I can figure out a work around in 
>>>> the meantime.  Is the submission to winbuild automated?  That is really 
>>>> the only way I have to check, but I don't want to keep on checking if 
>>>> someone's time is being wasted by that.  If automated,  the I don't mind 
>>>> making repeated submissions.
>>>> 
>>>> Thanks again,
>>>> 
>>>> -Roy
>>>> 
>>>> 
>>>> 
>>>>> On Dec 29, 2016, at 11:40 AM, Duncan Murdoch <murdoch.dun...@gmail.com> 
>>>>> wrote:
>>>>> 
>>>>> On 29/12/2016 1:44 PM, Roy Mendelssohn - NOAA Federal wrote:
>>>>>> Thanks,  but as I said,  my next question is how best to proceed with 
>>>>>> CRAN.  I do not want to waste peoples' time with a submission that I 
>>>>>> know before hand will be rejected.   Can I submit with this warning?
>>>>> 
>>>>> I'd recommend waiting a few days.  If you really want to submit soon, you 
>>>>> can figure out which is the offending command, and wrap it in something 
>>>>> that suppresses the warning (e.g. suppressWarnings(), assuming the 
>>>>> conversion to an error happens later).
>>>>> 
>>>>> I don't think your package would be accepted if the vignette won't build 
>>>>> on R-devel.
>>>>> 
>>>>> Duncan Murdoch
>>>>> 
>>>>>> -Roy
>>>>>> 
>>>>>> 
>>>>>>> On Dec 29, 2016, at 10:38 AM, Duncan Murdoch <murdoch.dun...@gmail.com> 
>>>>>>> wrote:
>>>>>>> 
>>>>>>> On 29/12/2016 1:24 PM, Ben Bolker wrote:
>>>>>>>> Sorry, correction/clarification to my last post: it's *not* a bug in
>>>>>>>> ggplot2, rather apparently (?) it's something in base R that has broken
>>>>>>>> tests in both data.table and ggplot2. (Since your code calls ggplot,
>>>>>>>> though, it's presumably in there somewhere, and (?) not your problem.)
>>>>>>> 
>>>>>>> The NEWS item is here:
>>>>>>> 
>>>>>>> http://developer.r-project.org/blosxom.cgi/R-devel/

Re: [R-pkg-devel] warning from win_build

[Roy Mendelssohn - NOAA Federal]

HI All:

If any cares,  the offending line is in the  ggplot2  file utilities.r where it 
has:

> #' A waiver object.
> #'
> #' A waiver is a "flag" object, similar to \code{NULL}, that indicates the
> #' calling function should just use the default value.  It is used in certain
> #' functions to distinguish between displaying nothing (\code{NULL}) and
> #' displaying a default value calculated elsewhere (\code{waiver()})
> #'
> #' @export
> #' @keywords internal
> waiver <- function() structure(NULL, class = "waiver")
> 
> is.waive <- function(x) inherits(x, "waiver")

If you then do a multi-file search on "waive" you find that it is used all 
throughout the code base, so anytime waiver() is called, so is the NULL 
structure.

-Roy




> 
> On Dec 29, 2016, at 11:44 AM, Roy Mendelssohn - NOAA Federal 
> <roy.mendelss...@noaa.gov> wrote:
> 
> Thanks.  I can wait.  I will also see if I can figure out a work around in 
> the meantime.  Is the submission to winbuild automated?  That is really the 
> only way I have to check, but I don't want to keep on checking if someone's 
> time is being wasted by that.  If automated,  the I don't mind making 
> repeated submissions.
> 
> Thanks again,
> 
> -Roy
> 
> 
> 
>> On Dec 29, 2016, at 11:40 AM, Duncan Murdoch <murdoch.dun...@gmail.com> 
>> wrote:
>> 
>> On 29/12/2016 1:44 PM, Roy Mendelssohn - NOAA Federal wrote:
>>> Thanks,  but as I said,  my next question is how best to proceed with CRAN. 
>>>  I do not want to waste peoples' time with a submission that I know before 
>>> hand will be rejected.   Can I submit with this warning?
>> 
>> I'd recommend waiting a few days.  If you really want to submit soon, you 
>> can figure out which is the offending command, and wrap it in something that 
>> suppresses the warning (e.g. suppressWarnings(), assuming the conversion to 
>> an error happens later).
>> 
>> I don't think your package would be accepted if the vignette won't build on 
>> R-devel.
>> 
>> Duncan Murdoch
>> 
>>> -Roy
>>> 
>>> 
>>>> On Dec 29, 2016, at 10:38 AM, Duncan Murdoch <murdoch.dun...@gmail.com> 
>>>> wrote:
>>>> 
>>>> On 29/12/2016 1:24 PM, Ben Bolker wrote:
>>>>> Sorry, correction/clarification to my last post: it's *not* a bug in
>>>>> ggplot2, rather apparently (?) it's something in base R that has broken
>>>>> tests in both data.table and ggplot2. (Since your code calls ggplot,
>>>>> though, it's presumably in there somewhere, and (?) not your problem.)
>>>> 
>>>> The NEWS item is here:
>>>> 
>>>> http://developer.r-project.org/blosxom.cgi/R-devel/2016/12/28#n2016-12-28
>>>> 
>>>> The issue is discussed in a bit more detail on R-devel (subject "[Rd] 
>>>> Unexpected I(NULL) output") and 
>>>> <https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17198>.
>>>> 
>>>> Overall it seems like a good idea:  some code (perhaps in ggplot2, I 
>>>> haven't tried to track it down) appears to be trying to set attributes on 
>>>> NULL.  This will silently fail in versions of R prior to R-devel rev 
>>>> 71841, and will fail with a warning in that version or later.  (Since the 
>>>> change to R-devel is very recent, it may change again.)
>>>> 
>>>> Duncan Murdoch
>>>> 
>>>>> 
>>>>> cheers
>>>>>  Ben
>>>>> 
>>>>> 
>>>>> 
>>>>> On 16-12-29 01:16 PM, Roy Mendelssohn - NOAA Federal wrote:
>>>>>> Hi All:
>>>>>> 
>>>>>> I am working on a new submission of my xtractomatic package  (the
>>>>>> main change being the use of https).  I develop on a Mac.  When I run
>>>>>> on the Mac:
>>>>>> 
>>>>>> devtools::check()
>>>>>> 
>>>>>> I get no errors, notes, or warnings.  However, when I run
>>>>>> devtools::build_win(), the response I get back isL
>>>>>> 
>>>>>> 
>>>>>>> * checking for unstated dependencies in vignettes ... OK * checking
>>>>>>> package vignettes in 'inst/doc' ... OK * checking re-building of
>>>>>>> vignette outputs ... WARNING Error in re-building vignettes: ...
>>>>>>> Quitting from lines 248-261 (Usingxtractomatic.Rmd) Error:
>>>>>

Re: [R-pkg-devel] warning from win_build

[Roy Mendelssohn - NOAA Federal]

Thanks.  I can wait.  I will also see if I can figure out a work around in the 
meantime.  Is the submission to winbuild automated?  That is really the only 
way I have to check, but I don't want to keep on checking if someone's time is 
being wasted by that.  If automated,  the I don't mind making repeated 
submissions.

Thanks again,

-Roy



> On Dec 29, 2016, at 11:40 AM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
> 
> On 29/12/2016 1:44 PM, Roy Mendelssohn - NOAA Federal wrote:
>> Thanks,  but as I said,  my next question is how best to proceed with CRAN.  
>> I do not want to waste peoples' time with a submission that I know before 
>> hand will be rejected.   Can I submit with this warning?
> 
> I'd recommend waiting a few days.  If you really want to submit soon, you can 
> figure out which is the offending command, and wrap it in something that 
> suppresses the warning (e.g. suppressWarnings(), assuming the conversion to 
> an error happens later).
> 
> I don't think your package would be accepted if the vignette won't build on 
> R-devel.
> 
> Duncan Murdoch
> 
>> -Roy
>> 
>> 
>>> On Dec 29, 2016, at 10:38 AM, Duncan Murdoch <murdoch.dun...@gmail.com> 
>>> wrote:
>>> 
>>> On 29/12/2016 1:24 PM, Ben Bolker wrote:
>>>> Sorry, correction/clarification to my last post: it's *not* a bug in
>>>> ggplot2, rather apparently (?) it's something in base R that has broken
>>>> tests in both data.table and ggplot2. (Since your code calls ggplot,
>>>> though, it's presumably in there somewhere, and (?) not your problem.)
>>> 
>>> The NEWS item is here:
>>> 
>>> http://developer.r-project.org/blosxom.cgi/R-devel/2016/12/28#n2016-12-28
>>> 
>>> The issue is discussed in a bit more detail on R-devel (subject "[Rd] 
>>> Unexpected I(NULL) output") and 
>>> <https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17198>.
>>> 
>>> Overall it seems like a good idea:  some code (perhaps in ggplot2, I 
>>> haven't tried to track it down) appears to be trying to set attributes on 
>>> NULL.  This will silently fail in versions of R prior to R-devel rev 71841, 
>>> and will fail with a warning in that version or later.  (Since the change 
>>> to R-devel is very recent, it may change again.)
>>> 
>>> Duncan Murdoch
>>> 
>>>> 
>>>> cheers
>>>>   Ben
>>>> 
>>>> 
>>>> 
>>>> On 16-12-29 01:16 PM, Roy Mendelssohn - NOAA Federal wrote:
>>>>> Hi All:
>>>>> 
>>>>> I am working on a new submission of my xtractomatic package  (the
>>>>> main change being the use of https).  I develop on a Mac.  When I run
>>>>> on the Mac:
>>>>> 
>>>>> devtools::check()
>>>>> 
>>>>> I get no errors, notes, or warnings.  However, when I run
>>>>> devtools::build_win(), the response I get back isL
>>>>> 
>>>>> 
>>>>>> * checking for unstated dependencies in vignettes ... OK * checking
>>>>>> package vignettes in 'inst/doc' ... OK * checking re-building of
>>>>>> vignette outputs ... WARNING Error in re-building vignettes: ...
>>>>>> Quitting from lines 248-261 (Usingxtractomatic.Rmd) Error:
>>>>>> processing vignette 'Usingxtractomatic.Rmd' failed with
>>>>>> diagnostics: (converted from warning) Calling 'structure(NULL, *)'
>>>>>> is deprecated, as NULL cannot have attributes. Consider
>>>>>> 'structure(list(), *)' instead. Execution halted
>>>>>> 
>>>>> 
>>>>> So this error is from my Vignette.  The offending lines appear to
>>>>> be:
>>>>> 
>>>>>> ```{r topotagPlot, fig.align = 'center', fig.width = 6, fig.height
>>>>>> = 4, warning = FALSE} require("ggplot2") alldata <- cbind(tagData,
>>>>>> topo) alldata$lon <- alldata$lon - 360 z <- ggplot(alldata, aes(x =
>>>>>> lon,y = lat)) + geom_point(aes(colour = mean), size = 2.) +
>>>>>> scale_shape_manual(values = c(19, 1)) z + geom_polygon(data = w,
>>>>>> aes(x = long, y = lat, group = group), fill = "grey80") +
>>>>>> theme_bw() + scale_colour_gradient("Depth") + coord_fixed(1.3, xlim
>>>>>> = xlim, ylim = ylim) + ggtitle("Bathymetry at marlin tag
>>>>>> locations")
>&g

Re: [R-pkg-devel] warning from win_build

[Roy Mendelssohn - NOAA Federal]

Thanks,  but as I said,  my next question is how best to proceed with CRAN.  I 
do not want to waste peoples' time with a submission that I know before hand 
will be rejected.   Can I submit with this warning?

-Roy


> On Dec 29, 2016, at 10:38 AM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
> 
> On 29/12/2016 1:24 PM, Ben Bolker wrote:
>>  Sorry, correction/clarification to my last post: it's *not* a bug in
>> ggplot2, rather apparently (?) it's something in base R that has broken
>> tests in both data.table and ggplot2. (Since your code calls ggplot,
>> though, it's presumably in there somewhere, and (?) not your problem.)
> 
> The NEWS item is here:
> 
> http://developer.r-project.org/blosxom.cgi/R-devel/2016/12/28#n2016-12-28
> 
> The issue is discussed in a bit more detail on R-devel (subject "[Rd] 
> Unexpected I(NULL) output") and 
> <https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17198>.
> 
> Overall it seems like a good idea:  some code (perhaps in ggplot2, I haven't 
> tried to track it down) appears to be trying to set attributes on NULL.  This 
> will silently fail in versions of R prior to R-devel rev 71841, and will fail 
> with a warning in that version or later.  (Since the change to R-devel is 
> very recent, it may change again.)
> 
> Duncan Murdoch
> 
>> 
>>  cheers
>>Ben
>> 
>> 
>> 
>> On 16-12-29 01:16 PM, Roy Mendelssohn - NOAA Federal wrote:
>>> Hi All:
>>> 
>>> I am working on a new submission of my xtractomatic package  (the
>>> main change being the use of https).  I develop on a Mac.  When I run
>>> on the Mac:
>>> 
>>> devtools::check()
>>> 
>>> I get no errors, notes, or warnings.  However, when I run
>>> devtools::build_win(), the response I get back isL
>>> 
>>> 
>>>> * checking for unstated dependencies in vignettes ... OK * checking
>>>> package vignettes in 'inst/doc' ... OK * checking re-building of
>>>> vignette outputs ... WARNING Error in re-building vignettes: ...
>>>> Quitting from lines 248-261 (Usingxtractomatic.Rmd) Error:
>>>> processing vignette 'Usingxtractomatic.Rmd' failed with
>>>> diagnostics: (converted from warning) Calling 'structure(NULL, *)'
>>>> is deprecated, as NULL cannot have attributes. Consider
>>>> 'structure(list(), *)' instead. Execution halted
>>>> 
>>> 
>>> So this error is from my Vignette.  The offending lines appear to
>>> be:
>>> 
>>>> ```{r topotagPlot, fig.align = 'center', fig.width = 6, fig.height
>>>> = 4, warning = FALSE} require("ggplot2") alldata <- cbind(tagData,
>>>> topo) alldata$lon <- alldata$lon - 360 z <- ggplot(alldata, aes(x =
>>>> lon,y = lat)) + geom_point(aes(colour = mean), size = 2.) +
>>>> scale_shape_manual(values = c(19, 1)) z + geom_polygon(data = w,
>>>> aes(x = long, y = lat, group = group), fill = "grey80") +
>>>> theme_bw() + scale_colour_gradient("Depth") + coord_fixed(1.3, xlim
>>>> = xlim, ylim = ylim) + ggtitle("Bathymetry at marlin tag
>>>> locations")
>>>> 
>>>> ```
>>>> 
>>> 
>>> 
>>> Now the vignette builds fine on my machine,  and  I can run it by
>>> "hand"  (as an R Notebook, executing each chunk) and it works also.
>>> Looking at the offending code chunk,  I can honestly say I have no
>>> idea what the error message is referring to.When I run by hand,
>>> I have checked that both tagData and topo are properly defined.  But
>>> is that the problem,  is the error message from the  cbind?
>>> 
>>> Thanks for any help.
>>> 
>>> -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: http://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.
&g

Re: [R-pkg-devel] warning from win_build

[Roy Mendelssohn - NOAA Federal]

Thanks, that is a big help because I had no idea what the error was referring 
to,.  Can I put this in my comments to cran and that will be sufficient?  
Normally any warning is sufficient for rejection?

I just want to make certain the updated submission goes a cleanly as possible.

-Roy



> On Dec 29, 2016, at 10:24 AM, Ben Bolker <bbol...@gmail.com> wrote:
> 
>  Sorry, correction/clarification to my last post: it's *not* a bug in
> ggplot2, rather apparently (?) it's something in base R that has broken
> tests in both data.table and ggplot2. (Since your code calls ggplot,
> though, it's presumably in there somewhere, and (?) not your problem.)
> 
>  cheers
>Ben
> 
> 
> 
> On 16-12-29 01:16 PM, Roy Mendelssohn - NOAA Federal wrote:
>> Hi All:
>> 
>> I am working on a new submission of my xtractomatic package  (the
>> main change being the use of https).  I develop on a Mac.  When I run
>> on the Mac:
>> 
>> devtools::check()
>> 
>> I get no errors, notes, or warnings.  However, when I run
>> devtools::build_win(), the response I get back isL
>> 
>> 
>>> * checking for unstated dependencies in vignettes ... OK * checking
>>> package vignettes in 'inst/doc' ... OK * checking re-building of
>>> vignette outputs ... WARNING Error in re-building vignettes: ... 
>>> Quitting from lines 248-261 (Usingxtractomatic.Rmd) Error:
>>> processing vignette 'Usingxtractomatic.Rmd' failed with
>>> diagnostics: (converted from warning) Calling 'structure(NULL, *)'
>>> is deprecated, as NULL cannot have attributes. Consider
>>> 'structure(list(), *)' instead. Execution halted
>>> 
>> 
>> So this error is from my Vignette.  The offending lines appear to
>> be:
>> 
>>> ```{r topotagPlot, fig.align = 'center', fig.width = 6, fig.height
>>> = 4, warning = FALSE} require("ggplot2") alldata <- cbind(tagData,
>>> topo) alldata$lon <- alldata$lon - 360 z <- ggplot(alldata, aes(x =
>>> lon,y = lat)) + geom_point(aes(colour = mean), size = 2.) + 
>>> scale_shape_manual(values = c(19, 1)) z + geom_polygon(data = w,
>>> aes(x = long, y = lat, group = group), fill = "grey80") + 
>>> theme_bw() + scale_colour_gradient("Depth") + coord_fixed(1.3, xlim
>>> = xlim, ylim = ylim) + ggtitle("Bathymetry at marlin tag
>>> locations")
>>> 
>>> ```
>>> 
>> 
>> 
>> Now the vignette builds fine on my machine,  and  I can run it by
>> "hand"  (as an R Notebook, executing each chunk) and it works also.
>> Looking at the offending code chunk,  I can honestly say I have no
>> idea what the error message is referring to.When I run by hand,
>> I have checked that both tagData and topo are properly defined.  But
>> is that the problem,  is the error message from the  cbind?
>> 
>> Thanks for any help.
>> 
>> -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: http://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

**
"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: http://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] Understanding notes from win-builder

[Roy Mendelssohn - NOAA Federal]

Hi Hadley:

> You can use \donttest{} to tell CRAN to not run it as part of their
> automated tests.
> 
> Hadley
> 

Thank you for the responses.  On the response above,  \donttest{} goes where?  
Is that in each R files where I have an example, or somewhere else?

-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 address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://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-pkg-devel] Understanding notes from win-builder

[Roy Mendelssohn - NOAA Federal]

Hi All:

I am working on preparing a package for submission to CRAN, so using devtools i 
submitted the package to win-builder.  I really appreciate that this has been 
setup, so that hopefully any final submission will be smooth.  win-builder 
returned three notes, and I am unclear on them in the sense of not certain what 
I should do to resolve them so hopefully there will  be no notes on submission. 
 The first one is:

> The Title field starts with the package name.
> The Title field should be in title case, current version then in title case:
> 'xtractomatic: An R package for accessing environmental data'
> 'Xtractomatic: An R Package for Accessing Environmental Data'
> 

the package name is "xtractomatic", but is the last line what is preferred in 
the DESCRIPTION file?

The other two notes are essentially the same:

> * checking examples ...
> ** running examples for arch 'i386' ... [87s] NOTE
> Examples with CPU or elapsed time > 10s
>user system elapsed
> xtracto3.29   0.81   36.49
> xtracto_3D 3.14   0.64   31.40
> xtractogon 0.92   0.20   10.73
> ** running examples for arch 'x64' ... [104s] NOTE
> Examples with CPU or elapsed time > 10s
>user system elapsed
> xtracto2.83   0.64   43.68
> xtracto_3D 2.58   0.72   43.60
> 

I assume the problem here is the amount of time to run the examples.  The 
problem is that what this package does is download data from a remote server, 
and times can vary a lot on the examples.  Is this a show stopper when I submit 
to CRAN?  I can try to simplify the examples to cut down on the time.  
Alternatively, will it help to include this in the cram-comments.md file?

Any advice will be greatly appreciated.

-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 address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://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
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Re: [R-pkg-devel] duplicate function during build

[Roy Mendelssohn - NOAA Federal]

I don't know if ctags works with R files,  but ctags does a similar thing as 
you are asking for other languages,  and can be integrated into git using 
hooks, as in:

https://robots.thoughtbot.com/use-git-hooks-to-automate-annoying-tasks

Don't know if this helps,  but thought I would pass it along.

-Roy

> On Jul 23, 2016, at 10:20 AM, ProfJCNash  wrote:
> 
> Thanks Sven. That indeed works. And if anyone has ideas how it could be
> put into R so Windows users could benefit, I'm sure it would be useful
> in checks of packages.
> 
> In other investigations of this, I realized that install.R has to
> prepare the .rdb and .rdx files and at that stage duplication might be
> detected. If install.R puts both versions of a duplicated name into
> these files, then the lazy load of library() or require() could be a
> place where detection would be useful, though only one of the names gets
> actually made available for use. However, my expertise with this
> internal aspect of R is rather weak.
> 
> Cheers, JN
> 
> On 16-07-23 12:04 PM, Sven E. Templer wrote:
>> Despite it might help, learning/using git is not tackling this specific 
>> problem, I suggest code that does:
>> 
>> sed -e 's/^[\ \t]*//' -e 's/#.*//' R/* | awk '/function/{print $1}' | sort | 
>> uniq -d
>> 
>> or
>> 
>> https://gist.github.com/setempler/7fcf2a3a737ce1293e0623d2bb8e08ed
>> (any comments welcome)
>> 
>> If one knows coding R, it might be more productive developing a tiny tool 
>> for that, instead of learning a new (and complex) one (as git).
>> 
>> Nevertheless, git is great!
>> 
>> Best wishes,
>> 
>> Sven
>> 
>> ---
>> 
>> web: www.templer.se
>> twitter: @setempler
>>> On 23 Jul 2016, at 16:17, Hadley Wickham  wrote:
>>> 
>>> I think this sort of meta problem is best solved with svn/git because you
>>> can easily see if the changes you think you made align with the changes you
>>> actually made. Learning svn or git is a lot of work, but the payoff is
>>> worth it.
>>> 
>>> Hadley
>>> 
>>> On Friday, July 22, 2016, ProfJCNash  wrote:
>>> 
 In trying to rationalize some files in a package I'm working on, I
 copied a function from one file to another, but forgot to change the
 name of one of them. It turns out the name of the file containing the
 "old" function was later in collation sequence than the one I was
 planning to be the "new" one. To debug some issues, I put some print()
 and cat() statements in the "new" file, but after building the package,
 they weren't there. Turns out the "old" function got installed, as might
 be expected if files processed in order. Debugging this took about 2
 hours of slightly weird effort with 2 machines and 3 OS distributions
 before I realized the problem. It's fairly obvious that I should expect
 issues in this case, but not so clear how to detect the source of the
 problem.
 
 Question: Has anyone created a script to catch such duplicate functions
 from different files during build? I think a warning message that there
 are duplicate functions could save some time and effort. Maybe it's
 already there, but I saw no obvious message. In this case, I'm only
 working in R.
 
 I've found build.R in the R tarball, which is where I suspect such a
 check should go, and I'm willing to prepare a patch when I figure out
 how this should be done. However, it seems worth asking if anyone has
 needed to do this before. I've already done some searching, but the
 results seem to pick up quite different posts than I need.
 
 Cheers, JN
 
 __
 R-package-devel@r-project.org  mailing list
 https://stat.ethz.ch/mailman/listinfo/r-package-devel
 
>>> 
>>> 
>>> -- 
>>> http://hadley.nz
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> __
>>> 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

**
"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 address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://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 

[R-pkg-devel] Getting a package ready for CRAN - some questions

[Roy Mendelssohn - NOAA Federal]

Hi All:

I am in the midst of some minor revisions to my xtractomatic package, which up 
till now has only been on github.  Since ncdf4 for Windows is now available 
from CRAN  (and many thanks to whomever is responsible for that) I thought I 
would try to get it into CRAN.  Some questions:

1.  The vignette uses a lot of packages that the main code does not - I put 
those in the DESCRIPTION file, under  “Suggests”, is this correct?

2. The vignette uses ggfortify, which was in CRAN for 3.2.x, but is not in CRAN 
for 3.3.x.  Do I assume then that a submission will fail, or will the 
submission work but just without the vignette?  Or can I include in the 
vignette the command to install from github  (using devtools), and then that 
will build?

3. On a remote build, my vignette is likely to fail to build.  That is because 
the vignette downloads a large amount of data in many requests, and if for any 
reason any one of the downloads fail or times out, the vignette build will 
fail.  As above, will this cause the entire submission to fail, or just the 
vignette to fail?  And is there anyway to provide a pre-built vignette in the 
submission?

I am asking all of this so I am certain of the answers.  I know the CRAN team 
does a lot of work, and the more I can be certain that my submission will work 
the easier it will be for everybody.

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 address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://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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