[R-pkg-devel] "Version contains leading zeroes" note: clarity

[Ben Bolker]

  Hi folks,

  I got the dreaded

Version contains leading zeroes

NOTE from a package check - the version was 0.0.1.000.

until I dug into the code and found the regex "(^|[.-])0[0-9]+" I didn't 
realize the restriction was on leading zeroes *within a version 
component* - I was interpreting it as leftmost in the whole version 
(i.e., the initial 0).


  I eventually found the documentation in ?package_version (feels like 
it should also be pointed to somewhere in Writing R Extensions?


Numeric versions are sequences of one or more non-negative
 integers, usually (e.g., in package ‘DESCRIPTION’ files)
 represented as character strings with the elements of the sequence
 concatenated and separated by single ‘.’ or ‘-’ characters.  R
 package versions consist of at least two such integers, an R
 system version of exactly three (major, minor and patchlevel).

Doesn't say anything about leading zero(e)s here ...

  "Zeroes" looks weird to me, but I see that "zeroes" is used on 26 
lines in .Rd files in the R code base, while "zeros" is used on 36 lines 
... so close to a tie. (Maybe someone wants to clean this up ... ? 
Maybe a mini-project for the R bug sprint at the end of the summer?


  Also, I'm sure this has been asked a few 100 times but: a new-to-CRAN 
maintainer triggers a NOTE.  Is there any way that a new user would know 
that this was informational only?  (There is also a 
Note_to_CRAN_maintainers 
: 
wouldn't that be more appropriate here?)


  cheers
   Ben Bolker

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Re: [R-pkg-devel] Package PowerSDI NOTES

[Ben Bolker]

  See also

https://ropensci.org/blog/2022/01/21/ropensci-news-digest-january-2022/#to-quote-or-not-to-quote-non-existing-words-in-description

https://stat.ethz.ch/R-manual/R-patched/library/utils/html/aspell-utils.html

On 2023-07-18 3:11 p.m., Duncan Murdoch wrote:

On 18/07/2023 12:37 p.m., Gabriel Constantino Blain wrote:

Dears,
I submitted my R package to CRAN.
However, it didn't pass the CRAN checks because of 2 notes:
Note 1:
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: CRAN incoming feasibility, Result: NOTE
   Maintainer: 'Gabriel Constantino Blain '
   New submission
 Possibly misspelled words in DESCRIPTION:
 EP (14:45)
 NASAPOWER (11:18)
 OperatSDI (12:9)
 PowerSDI (7:18, 13:9)
 SPEI (3:31, 7:50, 10:20)
 SPI (3:23, 7:42, 10:12)
 ScientSDI (9:19)
 evapotranspitation (13:44)
 subperiods (15:76)
Note 2:
Flavor: r-devel-windows-x86_64
Check: examples, Result: NOTE
   Examples with CPU (user + system) or elapsed time > 10s
  user system elapsed
   ScientSDI 82.71   0.75   88.00
   Reference 29.75   0.05   29.80
   Accuracy  10.02   1.11   11.12
Flavor: r-devel-linux-x86_64-debian-gcc
Check: examples, Result: NOTE
   Examples with CPU (user + system) or elapsed time > 5s
   user system elapsed
   ScientSDI 52.674  0.176  57.765
   Reference 20.749  0.148  20.898
   Accuracy   6.001  0.024   6.024

Regarding note 1, not all the words are misspelled,
EP, SPI and SPEI are acronyms
OperatSDI and ScientSDI are functions of my package
PowerSDI is the name of my package's name
  NASAPOWER is the project's name.


Writing R Extensions section 1.1.1 describes some rules for quoting 
non-English words.  I think they imply OperatSDI, ScientSDI and PowerSDI 
should be in single quotes.  I am not sure whether that also applies to 
your other non-English words.


Duncan Murdoch



Regarding note 2, I don't know what's wrong. Is it related to the time 
to run the examples (>5s)? If is it so, it is not an error. There are 
so many calculations that it does take some time to do it.


The package is available at https://github.com/gabrielblain/PowerSDI
I really appreciate any help you can provide.
Best regards
Gabriel

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Re: [R-pkg-devel] Package PowerSDI NOTES

[Duncan Murdoch]

On 18/07/2023 12:37 p.m., Gabriel Constantino Blain wrote:

Dears,
I submitted my R package to CRAN.
However, it didn't pass the CRAN checks because of 2 notes:
Note 1:
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: CRAN incoming feasibility, Result: NOTE
   Maintainer: 'Gabriel Constantino Blain '
   New submission
 Possibly misspelled words in DESCRIPTION:
 EP (14:45)
 NASAPOWER (11:18)
 OperatSDI (12:9)
 PowerSDI (7:18, 13:9)
 SPEI (3:31, 7:50, 10:20)
 SPI (3:23, 7:42, 10:12)
 ScientSDI (9:19)
 evapotranspitation (13:44)
 subperiods (15:76)
Note 2:
Flavor: r-devel-windows-x86_64
Check: examples, Result: NOTE
   Examples with CPU (user + system) or elapsed time > 10s
  user system elapsed
   ScientSDI 82.71   0.75   88.00
   Reference 29.75   0.05   29.80
   Accuracy  10.02   1.11   11.12
Flavor: r-devel-linux-x86_64-debian-gcc
Check: examples, Result: NOTE
   Examples with CPU (user + system) or elapsed time > 5s
   user system elapsed
   ScientSDI 52.674  0.176  57.765
   Reference 20.749  0.148  20.898
   Accuracy   6.001  0.024   6.024

Regarding note 1, not all the words are misspelled,
EP, SPI and SPEI are acronyms
OperatSDI and ScientSDI are functions of my package
PowerSDI is the name of my package's name
  NASAPOWER is the project's name.


Writing R Extensions section 1.1.1 describes some rules for quoting 
non-English words.  I think they imply OperatSDI, ScientSDI and PowerSDI 
should be in single quotes.  I am not sure whether that also applies to 
your other non-English words.


Duncan Murdoch



Regarding note 2, I don't know what's wrong. Is it related to the time to run the 
examples (>5s)? If is it so, it is not an error. There are so many calculations 
that it does take some time to do it.

The package is available at https://github.com/gabrielblain/PowerSDI
I really appreciate any help you can provide.
Best regards
Gabriel

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Re: [R-pkg-devel] Package PowerSDI NOTES

[Ivan Krylov]

On Tue, 18 Jul 2023 16:37:46 +
Gabriel Constantino Blain  wrote:

> Regarding note 1, not all the words are misspelled,

This is fine, especially if you add a comment to your package
submission.

> Regarding note 2, I don't know what's wrong. Is it related to the
> time to run the examples (>5s)? If is it so, it is not an error.
> There are so many calculations that it does take some time to do it.

I'm sorry, but it's a policy of CRAN to require examples that run "for
no more than a few seconds each":
https://cran.r-project.org/web/packages/policies.html

I know it may be non-trivial, but I hope it's possible to reduce the
amount of data processed by your examples until they take around 5
seconds or less on a typical computer. For example, could it be
possible to reduce the date range of the ScientSDI example to one year
and/or increase(?) the TS parameter?

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Package PowerSDI NOTES

[Avraham Adler]

Hello, Gabriel. 

CRAN policy is to rarely, if ever, allow long-running examples. It would be 
best if you could give an example of the function which requires as little run 
time as possible. Perhaps pre-compute some stages?

Avi

Sent from my iPhone

> On Jul 18, 2023, at 9:07 PM, Gabriel Constantino Blain 
>  wrote:
> 
> Dears,
> I submitted my R package to CRAN.
> However, it didn't pass the CRAN checks because of 2 notes:
> Note 1:
> Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
> Check: CRAN incoming feasibility, Result: NOTE
>  Maintainer: 'Gabriel Constantino Blain '
>  New submission
>Possibly misspelled words in DESCRIPTION:
>EP (14:45)
>NASAPOWER (11:18)
>OperatSDI (12:9)
>PowerSDI (7:18, 13:9)
>SPEI (3:31, 7:50, 10:20)
>SPI (3:23, 7:42, 10:12)
>ScientSDI (9:19)
>evapotranspitation (13:44)
>subperiods (15:76)
> Note 2:
> Flavor: r-devel-windows-x86_64
> Check: examples, Result: NOTE
>  Examples with CPU (user + system) or elapsed time > 10s
> user system elapsed
>  ScientSDI 82.71   0.75   88.00
>  Reference 29.75   0.05   29.80
>  Accuracy  10.02   1.11   11.12
> Flavor: r-devel-linux-x86_64-debian-gcc
> Check: examples, Result: NOTE
>  Examples with CPU (user + system) or elapsed time > 5s
>  user system elapsed
>  ScientSDI 52.674  0.176  57.765
>  Reference 20.749  0.148  20.898
>  Accuracy   6.001  0.024   6.024
> 
> Regarding note 1, not all the words are misspelled,
> EP, SPI and SPEI are acronyms
> OperatSDI and ScientSDI are functions of my package
> PowerSDI is the name of my package's name
> NASAPOWER is the project's name.
> 
> Regarding note 2, I don't know what's wrong. Is it related to the time to run 
> the examples (>5s)? If is it so, it is not an error. There are so many 
> calculations that it does take some time to do it.
> 
> The package is available at https://github.com/gabrielblain/PowerSDI
> I really appreciate any help you can provide.
> Best regards
> Gabriel
> 
>[[alternative HTML version deleted]]
> 
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Re: [R-pkg-devel] Check package without suggests

[William Gearty]

Hi John,

You need to set the R CMD check environment variable
_R_CHECK_FORCE_SUGGESTS_ to FALSE/0. You should be able to do this
with the env_vars
argument in rhub::check(). You can also achieve this with github actions by
customizing your yaml file (example here:
https://github.com/willgearty/deeptime/blob/master/.github/workflows/R-CMD-check.yaml#L57
).

Best,
Will

--
*William Gearty*
*Lerner-Gray Postdoctoral Research Fellow*
Division of Paleontology
American Museum of Natural History
williamgearty.com



On Tue, Jul 18, 2023 at 10:38 AM John Harrold 
wrote:

> Howdy Folks,
>
> I recent had a package start failing because I wasn't checking properly in
> my tests to make sure my suggested packages were installed before running
> tests. I think this is something new running on CRAN where packages are
> tested with only the packages specified as Imports in the DESCRIPTION file
> are installed. It took me a bit of back and forth to get all of these
> issues worked out.  I was wondering if anyone has a good way to run R CMD
> check with only the imports installed?  A github action, or a
> specific platform on rhub?
>
> Thank you,
>
> John
> :wq
>
> [[alternative HTML version deleted]]
>
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>

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[R-pkg-devel] Package PowerSDI NOTES

[Gabriel Constantino Blain]

Dears,
I submitted my R package to CRAN.
However, it didn't pass the CRAN checks because of 2 notes:
Note 1:
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: 'Gabriel Constantino Blain '
  New submission
Possibly misspelled words in DESCRIPTION:
EP (14:45)
NASAPOWER (11:18)
OperatSDI (12:9)
PowerSDI (7:18, 13:9)
SPEI (3:31, 7:50, 10:20)
SPI (3:23, 7:42, 10:12)
ScientSDI (9:19)
evapotranspitation (13:44)
subperiods (15:76)
Note 2:
Flavor: r-devel-windows-x86_64
Check: examples, Result: NOTE
  Examples with CPU (user + system) or elapsed time > 10s
 user system elapsed
  ScientSDI 82.71   0.75   88.00
  Reference 29.75   0.05   29.80
  Accuracy  10.02   1.11   11.12
Flavor: r-devel-linux-x86_64-debian-gcc
Check: examples, Result: NOTE
  Examples with CPU (user + system) or elapsed time > 5s
  user system elapsed
  ScientSDI 52.674  0.176  57.765
  Reference 20.749  0.148  20.898
  Accuracy   6.001  0.024   6.024

Regarding note 1, not all the words are misspelled,
EP, SPI and SPEI are acronyms
OperatSDI and ScientSDI are functions of my package
PowerSDI is the name of my package's name
 NASAPOWER is the project's name.

Regarding note 2, I don't know what's wrong. Is it related to the time to run 
the examples (>5s)? If is it so, it is not an error. There are so many 
calculations that it does take some time to do it.

The package is available at https://github.com/gabrielblain/PowerSDI
I really appreciate any help you can provide.
Best regards
Gabriel

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Re: [R-pkg-devel] Check package without suggests

[John Harrold]

I want to check my package to make sure I'm properly using suggested
packages. I'm trying to catch mistakes where I forgot to do what you're
suggesting.

On Tue, Jul 18, 2023 at 7:58 AM Serguei Sokol 
wrote:

> Is it possible that you have complicated the task unnecessarily?
> Normally, you can just do
>
> if (requireNamespace("", quietly=TRUE)) {
>   # do the tests involving 
> }
>
> Wasn't that enough?
>
> Best,
> Serguei.
>
>
> Le 18/07/2023 à 16:37, John Harrold a écrit :
> > Howdy Folks,
> >
> > I recent had a package start failing because I wasn't checking properly
> in
> > my tests to make sure my suggested packages were installed before running
> > tests. I think this is something new running on CRAN where packages are
> > tested with only the packages specified as Imports in the DESCRIPTION
> file
> > are installed. It took me a bit of back and forth to get all of these
> > issues worked out.  I was wondering if anyone has a good way to run R CMD
> > check with only the imports installed?  A github action, or a
> > specific platform on rhub?
> >
> > Thank you,
> >
> > John
> > :wq
> >
> >   [[alternative HTML version deleted]]
> >
> > __
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> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>

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Re: [R-pkg-devel] Check package without suggests

[Ivan Krylov]

В Tue, 18 Jul 2023 07:37:40 -0700
John Harrold  пишет:

> I was wondering if anyone has a good way to run R CMD
> check with only the imports installed?

According to "R Internals", running R CMD check with the environment
variable _R_CHECK_DEPENDS_ONLY_ set to "TRUE" will populate a temporary
library with only the hard dependencies of the package (Depends and
Imports) before running the tests.

If this works, you should see a NOTE:

* checking package dependencies ... NOTE
Packages which this enhances but not available for checking: <...>

(This NOTE also happens during the CRAN check but doesn't count against
your package.)

One caveat is that the library pointed to by the .Library variable is
also available during the check. In a packaged R it's a system
directory where non-base or recommended packages are not normally
installed, so _R_CHECK_DEPENDS_ONLY_ works. If you're running a custom
build of R with a writeable .Library (say, a copy of R-devel in your
home directory), the packages end up being installed there by default
and therefore available to the package being checked, despite
_R_CHECK_DEPENDS_ONLY_=TRUE. For recommended packages, there exists a
separate environment variable _R_CHECK_NO_RECOMMENDED_=TRUE, which
makes R CMD check create fake recommended packages in the temporary
library, which fail to load.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Check package without suggests

[Serguei Sokol]

Is it possible that you have complicated the task unnecessarily?
Normally, you can just do

if (requireNamespace("", quietly=TRUE)) {
 # do the tests involving 
}

Wasn't that enough?

Best,
Serguei.


Le 18/07/2023 à 16:37, John Harrold a écrit :

Howdy Folks,

I recent had a package start failing because I wasn't checking properly in
my tests to make sure my suggested packages were installed before running
tests. I think this is something new running on CRAN where packages are
tested with only the packages specified as Imports in the DESCRIPTION file
are installed. It took me a bit of back and forth to get all of these
issues worked out.  I was wondering if anyone has a good way to run R CMD
check with only the imports installed?  A github action, or a
specific platform on rhub?

Thank you,

John
:wq

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[R-pkg-devel] Check package without suggests

[John Harrold]

Howdy Folks,

I recent had a package start failing because I wasn't checking properly in
my tests to make sure my suggested packages were installed before running
tests. I think this is something new running on CRAN where packages are
tested with only the packages specified as Imports in the DESCRIPTION file
are installed. It took me a bit of back and forth to get all of these
issues worked out.  I was wondering if anyone has a good way to run R CMD
check with only the imports installed?  A github action, or a
specific platform on rhub?

Thank you,

John
:wq

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