Re: [R-pkg-devel] Package submission to CRAN not passing incoming checks

[Ivan Krylov via R-package-devel]

Dear Isaac,

В Mon, 22 Apr 2024 17:00:27 +
"Petersen, Isaac T"  пишет:

> This my first post--I read the posting guidelines, but my apologies
> in advance if I make a mistake.

Welcome to R-package-devel! You're doing just fine.

> 1) The first note <...> includes the contents of the LICENSE file

It's multiple NOTEs in a trench coat. Kasper has addressed the "large
version components" and the DOIs interpreted as file URIs, but there's
one more.

The ' + file LICENSE' syntax has two uses: (1)
for when the terms of the license is a template, requiring the author
of the software to substitute some information (e.g. the year and the
copyright holder for MIT) and (2) for when a package puts additional
restrictions on the base license.

(Hmm. Only case (2) is currently described at
; case
(1) is only described inside the license files.)

The CRAN team has expressed a preference for the package authors not to
put 2 twisty little copies of standard licenses, all slightly
different, inside their packages. Since you're not restricting CC BY
4.0, it's enough to say 'License: CC BY 4.0'. If you'd like a full copy
of the license text in your source code repository, that's fine, but
you'll need to list the file in .Rbuildignore:
https://cran.r-project.org/doc/manuals/R-exts.html#Building-package-tarballs

Speaking of the Creative Commons license: the choice of a license for
your code is obviously yours, but Creative Commons themselves recommend
against using their licenses for software:
.
I can't recommend you a license - that would be politically motivated
meddling in foreign affairs - but the lists linked by the CC FAQ and
Writing R Extensions section 1.1.2 should provide a good starting point.

> Here are the results from win-builder:
> https://win-builder.r-project.org/incoming_pretest/petersenlab_0.1.2-9033_20240415_212322/

There is one more NOTE:

>> * checking examples ... [437s/438s] NOTE
>> Examples with CPU (user + system) or elapsed time > 5s
>>user system elapsed
>> load_or_install 349.410 37.410 387.233
>> vwReg35.199  0.379  35.606
 
The examples are not only for the user to read in the help page; they
are also for the user to run example(vwReg) and see your code in action
(and for R CMD check to see whether they crash, including regularly on
CRAN).

For vwReg, try reducing the number of regressions you are running
(since your dataset is mtcars, which is already very compact).

For load_or_install, we have the additional issue that running
example(load_or_install) modifies the contents of the R library and the
search path, which belong to the user. The CRAN policy forbids such
modifications: 

Examples in general should change as little of the global state of the
R session and the underlying computer as possible. I suggest wrapping
the example in \dontrun{} (since everything about load_or_install() is
about altering global state) and creating a test for the function in
tests/*.R.

The test should set up a new library under tempdir(), run
load_or_install(), check the outcomes (that the desired package is
attached, etc.) and clean up after itself. There's also the matter of
the package not failing without a connection to the Internet, which is
another CRAN policy requirement. You might have to bring a very small
test package in inst/extdata just for load_or_install() to install and
load it, so that R CMD check won't fail when running offline.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Package submission to CRAN not passing incoming checks

[Kasper Daniel Hansen]

1. The version number complaint is the use of 0.1.2-9033. It is complaining
about 9033. Personally, I would not use the - style, but that is a
personal choice I guess. R-exts says
  "The mandatory ‘Version’ field gives the version of the package. This is
a sequence of at least *two* (and usually three) non-negative integers
separated by single ‘.’ or ‘-’ characters. The canonical form is as shown
in the example, and a version such as ‘0.01’ or ‘0.01.0’ will be handled as
if it were ‘0.1-0’. It is *not* a decimal number, so for example 0.9 < 0.75
since 9 < 75."
2. Those are not URLs, they are DOIs. The Rd format has a \doi{} command
you should use
3. If your examples generate files, I would use the tempfile() command from
base R.

On Mon, Apr 22, 2024 at 8:25 PM Petersen, Isaac T <
isaac-t-peter...@uiowa.edu> wrote:

> Dear R-package-devel,
>
> This my first post--I read the posting guidelines, but my apologies in
> advance if I make a mistake.
>
> I am trying to post my R package to CRAN. I just submitted it to CRAN but
> received a note that the package "does not pass the incoming checks
> automatically".
>
> Here are the results from win-builder:
> https://win-builder.r-project.org/incoming_pretest/petersenlab_0.1.2-9033_20240415_212322/
>
> As far as I can tell, there are 3 notes to address. However, I'm not sure
> how to address them.
>
> 1) The first note appears to be "Version contains large components", which
> includes the contents of the LICENSE file (CC BY 4.0). I'm not sure if this
> is a problem that needs to be addressed (or how to address it).
>
> 2) The second note says:
>
> "Found the following (possibly) invalid file URIs:
>   URI: 10.1177/0146621613475471
> From: man/itemInformation.Rd
>   URI: 10.1177/0146621613475471
> From: man/standardErrorIRT.Rd"
>
> However, I verified that those DOIs resolve correctly, so I'm not sure how
> to address this note.
>
> 3) The third note (in the Debian but not Windows version) says:
>
> "* checking for non-standard things in the check directory ... NOTE
> Found the following files/directories:
>   ‘encryptionKey.RData’ ‘encrypytedCredentials.txt’"
>
> These files are generated in the examples for one of the functions to
> demonstrate how to read data using an encryption key:
> https://github.com/DevPsyLab/petersenlab/blob/9ece9d7dc32727c1315a03bc2810cc9c957971d1/R/readEncryptedData.R#L24.
> I'm not sure if this is a problem that needs to be addressed (or how to
> address it).
>
> The source code for my R package (petersenlab) is here:
> https://github.com/DevPsyLab/petersenlab
>
> Thanks very much in advance,
> Isaac
>
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>
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>


-- 
Best,
Kasper

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Re: [R-pkg-devel] Package submission to CRAN

[Brodie Gaslam via R-package-devel]

I would just increment the version.  This is the from the CRAN
re-submission policy[1]:

> Updates to previously-published packages must have an increased version. 
> Increasing the version number at each submission reduces confusion so is 
> preferred even when a previous submission was not accepted.

You could always add NEWS entry explaining what the new version
is, then the package will not be exactly the same anymore ;).

Best,

B.


[1]: https://cran.r-project.org/web/packages/policies.html#Re_002dsubmission



On Tuesday, October 19, 2021, 08:38:01 AM EDT, Simon Bonner 
 wrote: 





Hi all,

I have a question re package submission that I'm hoping someone might be able 
to help with.

A package I maintain (dalmatian) was archived last year because one of the 
packages it depends on (dglm) was removed from CRAN. The dglm package has been 
fixed and is back on CRAN, and I have resubmitted my package. There have been 
no changes to my package and I resubmitted the same version with the same 
version number. I noted this in my submission.

All checks passed, but I received the following from log CRAN-pretest:

Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: WARNING
  Maintainer: 'Simon Bonner simon.bon...@uwo.ca'

  New submission

  Package was archived on CRAN

  Insufficient package version (submitted: 0.6.1, existing: 0.6.1)

  CRAN repository db overrides:
    X-CRAN-Comment: Archived on 2020-10-18 as requires archived package
      'dglm'.

  This build time stamp is over a month old.

It seems that I am not allowed to submit the package with the same version, but 
 it also seems odd to increment the version to get around this when nothing at 
all has changed in the package.

Is there another solution?

Thanks,

Simon

-
Simon Bonner (he/him)
Associate Professor of Environmetrics
Vice-Director, Western Data Science Solutions
Department of Statistical and Actuarial Sciences
University of Western Ontario

Office: Western Science Centre rm 276

Email: sbonn...@uwo.ca | Telephone: 519-661-2111 x88205 
| Fax: 519-661-3813
Twitter: @bonnerstatslab | Website: http://simon.bonners.ca/bonner-lab/wpblog/


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Re: [R-pkg-devel] Package Submission to CRAN

[Akshit Achara]

Dear Uwe,

Thanks for the suggestions, I was able to install my package without the
header files or library on the system.

Thanks,
Akshit Achara



On Sat, Nov 14, 2020 at 8:02 PM Uwe Ligges 
wrote:

> Write to c...@r-project.org, explain how to install the third party
> software (availability and names of Debian packages etc.) and the CRAN
> team will decide whether the software will be isntalled on (a subset of)
> CRAN machines.
>
> Best,
> Uwe Ligges
>
>
>
> On 09.11.2020 19:24, Akshit Achara wrote:
> > Hey everyone,
> >
> > I have created a package rminizinc
> >  that depends on a third
> party
> > C++ API
> > which is used in some of the Rcpp files. The third party header files
> need
> > to be present for their compilation or the package doesn't install.
> >
> > I wish to submit the package to CRAN but the CRAN servers will not have
> > the third party library. Is there any way I can install the package
> without
> > having the third party library on my system?
> >
> > Thanks,
> > Akshit Achara
> >
> >   [[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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Re: [R-pkg-devel] Package Submission to CRAN

[Uwe Ligges]

Write to c...@r-project.org, explain how to install the third party 
software (availability and names of Debian packages etc.) and the CRAN 
team will decide whether the software will be isntalled on (a subset of) 
CRAN machines.


Best,
Uwe Ligges



On 09.11.2020 19:24, Akshit Achara wrote:

Hey everyone,

I have created a package rminizinc
 that depends on a third party
C++ API
which is used in some of the Rcpp files. The third party header files need
to be present for their compilation or the package doesn't install.

I wish to submit the package to CRAN but the CRAN servers will not have
the third party library. Is there any way I can install the package without
having the third party library on my system?

Thanks,
Akshit Achara

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