Re: [R-pkg-devel] Questions regarding a new (seperated package) and how to submit them to cran

[Bernd . Gruber]

Thanks, just to make sure:

In the policy I find the entry:

Additional_repositories:

The ‘Additional_repositories’ field is a comma-separated list of repository 
URLs where the packages named in the other fields may be found. It is currently 
used by R CMD check to check that the packages can be found, at least as source 
packages (which can be installed on any platform).

And here I would have to provide an url that links to the tar.gz file of the 
package, or can I also provide

The ‘Additional_repositories’ field is a comma-separated list of repository 
URLs where the packages named in the other fields may be found. It is currently 
used by R CMD check to check that the packages can be found, at least as source 
packages (which can be installed on any platform).

github::green-striped-gecko/dartR.popgenomics

similar to the Remotes: field (which I think is not possible to use).

Thanks,


==
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 _.--..---"-,--c_
Professor Ecological Modelling  \|..'   ._O__)_
Tel: (02) 6206 3804 ,=._.+   _ \..--( /
Fax: (02) 6201 2328   \\.-''_.-' \ ( \_
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From: Uwe Ligges 
Sent: Sunday, 25 June 2023 20:51
To: Bernd.Gruber 
Cc: r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] Questions regarding a new (seperated package) and 
how to submit them to cran



On 25.06.2023 09:00, Bernd.Gruber wrote:
> Hi,
>
> Thanks for the advice.
>
> Still not 100% sure if that is okay to submit to CRAN.
>
> As mentioned I have new packages that have others in the suggest (and yes the 
> examples/tests run fine by making the dependent),
>
> But if I have a package that is not yet on CRAN in the suggest I see that 
> running winbuilder.
>
> Suggests or Enhances not in mainstream repositories:
> dartR.sim

If it is not in a mainstream repo, you can declare where users can get
it from, see the explanation in the CRAN policies how to declare it.



> * checking package namespace information ... OK
> * checking package dependencies ... NOTE
> Package suggested but not available for checking: 'dartR.sim'

This is OK, once the former is explained.

Best,
Uwe Ligges


>
>
>
>
> Can I explain when I submit that dartR.sim will be there (as mentioned the 
> examples run fine), but obviously is not yet on CRAN.
>
> I assume the same would happen if I put the new packages in Enhances…
>
> Regards, Bernd
>
>
>
>
> From: Thierry Onkelinx 
> mailto:thierry.onkel...@inbo.be>>
> Sent: Friday, June 23, 2023 5:51 PM
> To: Simon Urbanek 
> mailto:simon.urba...@r-project.org>>
> Cc: Bernd.Gruber 
> mailto:bernd.gru...@canberra.edu.au>>; 
> r-package-devel@r-project.org<mailto:r-package-devel@r-project.org>
> Subject: Re: [R-pkg-devel] Questions regarding a new (seperated package) and 
> how to submit them to cran
>
> Dear Bernd,
>
> You could contact the maintainer of the spatstat package. They did the same 
> thing (splitting a large package into several smaller ones) a few years ago.
>
> Having the base package suggesting an add-on and the add-on depending on or 
> suggesting the base package might create an unwanted loop.
>
> 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<mailto:thierry.onkel...@inbo.be<mailto:thierry.onkel...@inbo.be%3cmailto:thierry.onkel...@inbo.be>>
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be<http://www.inbo.be><http://www.inbo.be<http://www.inbo.be>>
> ///

Re: [R-pkg-devel] Nickname allowed in description when submitting to CRAN?

[Bernd . Gruber]

Thanks for the advice. Revision sounds perfectly plausible to me. I will test 
via winbuilder and may use it.

Regards, Bernd


==
Dr Bernd Gruber  )/_  
 _.--..---"-,--c_ 
Professor Ecological Modelling  \|..'   ._O__)_ 
 
Tel: (02) 6206 3804 ,=._.+   _ \..--( /   
Fax: (02) 6201 2328   \\.-''_.-' \ ( \_   
Institute for Applied Ecology  `'''   `\__   /\   
Faculty of Science and Technology  ') 
University of Canberra   ACT 2601 AUSTRALIA
Email: bernd.gru...@canberra.edu.au
WWW: bernd-gruber

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-Original Message-
From: Ivan Krylov  
Sent: Sunday, 25 June 2023 17:35
To: Bernd.Gruber 
Cc: r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] Nickname allowed in description when submitting to 
CRAN?

В Sun, 25 Jun 2023 06:30:39 +
Bernd.Gruber  пишет:

> I read in some stackexchange answers that it is possible to add the 
> keyword
> 
> Nickname:
> 
> to the description file. It works fine when I check the package but 
> winbuilder comes back with a note:
> 
> Unknown, possibly misspelled, fields in DESCRIPTION:
>   'Nickname'
> 
> So the question is, is there a way to have a nickname for a version of 
> an R package and if so, how would that be done.

I'm afraid it's not exactly documented (and therefore may be subject to 
change), but this NOTE is currently produced for every DESCRIPTION field unless 
it's mentioned in tools:::.get_standard_DESCRIPTION_fields() or starts with a 
number of prefixes (such as X-CRAN, X-schema.org, Repository/R-Forge, VCS/, and 
Config/).

I see "Revision" in the list of standard DESCRIPTION fields.
Conveniently, it doesn't seem to be used by base R packages. Would it be 
acceptable to use "Revision" instead of "Nickname"?

An alternative option would be to file a wishlist ticket asking for "Nickname" 
to be added to the list, but then your package will have to wait until that 
change propagates to the next release of R.

--
Best regards,
Ivan

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Re: [R-pkg-devel] Questions regarding a new (seperated package) and how to submit them to cran

[Bernd . Gruber]

Hi,

Thanks for the advice.

Still not 100% sure if that is okay to submit to CRAN.

As mentioned I have new packages that have others in the suggest (and yes the 
examples/tests run fine by making the dependent),

But if I have a package that is not yet on CRAN in the suggest I see that 
running winbuilder.

Suggests or Enhances not in mainstream repositories:
  dartR.sim

* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'dartR.sim'





Can I explain when I submit that  dartR.sim will be there (as mentioned the 
examples run fine), but obviously is not yet on CRAN.

I assume the same would happen if I put the new packages in Enhances…

Regards, Bernd




From: Thierry Onkelinx 
Sent: Friday, June 23, 2023 5:51 PM
To: Simon Urbanek 
Cc: Bernd.Gruber ; r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] Questions regarding a new (seperated package) and 
how to submit them to cran

Dear Bernd,

You could contact the maintainer of the spatstat package. They did the same 
thing (splitting a large package into several smaller ones) a few years ago.

Having the base package suggesting an add-on and the add-on depending on or 
suggesting the base package might create an unwanted loop.

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
///

[https://inbo-website-prd-532750756126.s3-eu-west-1.amazonaws.com/inbologoleeuw_nl.png]


Op vr 23 jun 2023 om 06:52 schreef Simon Urbanek 
mailto:simon.urba...@r-project.org>>:
Bernd,

the sequence in which you submit doesn't matter - the packages have to work 
regardless of the sequence. Suggests means that the dependency is optional, not 
that it can break tests. You have to skip the tests that cannot be run due to 
missing dependencies (see 1.1.3.1 in R-exts)

Cheers,
Simon



> On Jun 23, 2023, at 2:35 PM, Bernd.Gruber 
> mailto:bernd.gru...@canberra.edu.au>> wrote:
>
> Hi,
>
> I have a question regarding the separation of a package into smaller pieces 
> (to avoid long testing/installation times and more important to avoid to many 
> dependencies)
>
> I am the maintainer of an R package (dartR) which has grown and is now at the 
> limit in terms of testing/run time and also dependencies. To further develop 
> the package we started to break the package into smaller packages namely
>
>
> Two core packages (dartR.base and dartR.data) and here dartR.base has 
> dartR.data in the depends. (dartR.base is 60% of the previous package) and 
> dartR.data is our data.package for test data (dartR.data is already on CRAN)
>
>
>
>
> Next to the two core packages we also have 3 more addon packages that deal 
> with specialised analysis
>
> dartR.sim
> dartR.spatial
> dartR.popgenomics.
>
> Those packages depend on dartR.base and dartR.data.
>
> All addon packages and core packages should have the other addon packages as 
> suggests, hence here comes the question.
>
>
> How do I submit the packages?  All of them at once? Or step by step.
>
> If I submit step by step (e.g. dartR.base) it obviously cannot have the other 
> dartR addon packages as suggests (cannot be tested and will break the CRAN 
> tests).
>
> So would be the correct way to:
> Submit dartR.base (without dartR.sim, dartR.spatial and dartR.popgenomics in 
> the suggest.)
> Then submit dartR.sim, then dartR.spatial and finally dartR.popgenomics (all 
> without suggests of the other packages)
>
> And finally update all packages (only their description file and add the 
> suggests once they are on CRAN).
>
> Hope that makes sense and thanks in advance,
>
> Bernd
>

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[R-pkg-devel] Nickname allowed in description when submitting to CRAN?

[Bernd . Gruber]

Hi,
I know that sounds like a useless feature, but it happens that people are 
better in recognising names than numbers.

And here is the question. I read in some stackexchange answers that it is 
possible to add the keyword

Nickname:

to the description file. It works fine when I check the package but winbuilder 
comes back with a note:

Unknown, possibly misspelled, fields in DESCRIPTION:
  'Nickname'

So the question is, is there a way to have a nickname for a version of an R 
package and if so, how would that be done.

Thanks in advance


==
Dr Bernd Gruber  )/_
 _.--..---"-,--c_
Professor Ecological Modelling  \|..'   ._O__)_
Tel: (02) 6206 3804 ,=._.+   _ \..--( /
Fax: (02) 6201 2328   \\.-''_.-' \ (
 \_
Institute for Applied Ecology  `'''   `\__   /\
Faculty of Science and Technology  ')
University of Canberra   ACT 2601 AUSTRALIA
Email: bernd.gru...@canberra.edu.au<mailto:bernd.gru...@canberra.edu.au>
WWW: 
bernd-gruber<https://researchprofiles.canberra.edu.au/en/persons/bernd-gruber>

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[R-pkg-devel] Questions regarding a new (seperated package) and how to submit them to cran

[Bernd . Gruber]

Hi,

I have a question regarding the separation of a package into smaller pieces (to 
avoid long testing/installation times and more important to avoid to many 
dependencies)

I am the maintainer of an R package (dartR) which has grown and is now at the 
limit in terms of testing/run time and also dependencies. To further develop 
the package we started to break the package into smaller packages namely


Two core packages (dartR.base and dartR.data) and here dartR.base has 
dartR.data in the depends. (dartR.base is 60% of the previous package) and 
dartR.data is our data.package for test data (dartR.data is already on CRAN)




Next to the two core packages we also have 3 more addon packages that deal with 
specialised analysis

dartR.sim
dartR.spatial
dartR.popgenomics.

Those packages depend on dartR.base and dartR.data.

All addon packages and core packages should have the other addon packages as 
suggests, hence here comes the question.


How do I submit the packages?  All of them at once? Or step by step.

If I submit step by step (e.g. dartR.base) it obviously cannot have the other 
dartR addon packages as suggests (cannot be tested and will break the CRAN 
tests).

So would be the correct way to:
Submit dartR.base (without dartR.sim, dartR.spatial and dartR.popgenomics in 
the suggest.)
Then submit dartR.sim, then dartR.spatial and finally dartR.popgenomics (all 
without suggests of the other packages)

And finally update all packages (only their description file and add the 
suggests once they are on CRAN).

Hope that makes sense and thanks in advance,

Bernd





==
Dr Bernd Gruber  )/_
 _.--..---"-,--c_
Professor Ecological Modelling  \|..'   ._O__)_
Tel: (02) 6206 3804 ,=._.+   _ \..--( /
Fax: (02) 6201 2328   \\.-''_.-' \ ( \_
Institute for Applied Ecology  `'''   `\__   /\
Faculty of Science and Technology  ')
University of Canberra   ACT 2601 AUSTRALIA
Email: bernd.gru...@canberra.edu.au<mailto:bernd.gru...@canberra.edu.au>
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[R-pkg-devel] How to request for an Non Maintainer update - NMU

[Bernd . Gruber]

Hi everyone,

I am the maintainer of a package (dartR) that depends on ggtern (a package that 
seems not to be maintained anymore).
Currently the package was removed from CRAN (about 4 weeks ago) due to a simple 
error, which can be easily fixed. This was kindly achieved by Roger Bivand 
(simply the remove of a backslash does the trick).

In an github exchange he also suggested to have an non maintainer update (NMU) 
for the package in the short term (and find a replacement of orphan the package 
and find a new maintainer in the long term).

Here is my first question as I did not find an answer googling it.

How can I ask, request for an NMU? Would I simply write to CRAN and describe 
the situation and send the files that need to be replaced?

The second question is, how I would request to orphan the package and what is 
the procedure to find a new maintainer (as it relies on ggplot code and this is 
not really my strength, hence I would try to find someone else to take over).

Thanks a lot, Bernd



==
Dr Bernd Gruber  )/_
 _.--..---"-,--c_
Professor Ecological Modelling  \|..'   ._O__)_
Tel: (02) 6206 3804 ,=._.+   _ \..--( /
Fax: (02) 6201 2328   \\.-''_.-' \ ( \_
Institute for Applied Ecology  `'''   `\__   /\
Faculty of Science and Technology  ')
University of Canberra   ACT 2601 AUSTRALIA
Email: bernd.gru...@canberra.edu.au<mailto:bernd.gru...@canberra.edu.au>
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[R-pkg-devel] [UNCLASSIFIED] Remotes in description when submitting a package until a dependency is fixed

[Bernd . Gruber]

Hi,

I have a package (dartR) that needs to be updated by CRAN (and got a time set 
until a certain date). It depends on a package that is currently showing errors 
in the CRAN results and therefore fails. The maintainer of that package is 
busily trying to rectify the error (as can be seen be repeated submissions in 
the last weeks), but was not able yet to fix it. As we are running out of time 
my approach would be to have a version of the package that fixes it and use 
Remotes: in the description. It runs fine without errors.

In the R-packages book I read the following:

"It's important to note that you should not submit your package to CRAN in the 
intermediate state, meaning with a Remotes field and with a dependency required 
at a version that's not available from CRAN or Bioconductor. For CRAN packages, 
this can only be a temporary development state, eventually resolved when the 
dependency updates on CRAN and you can bump your minimum version accordingly."

So is it okay to submit our package with a remote statement until the 
maintainer of the other package has fixed their issues?

Thanks in advance,
Bernd


==
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 _.--..---"-,--c_
Professor Ecological Modelling  \|..'   ._O__)_
Tel: (02) 6206 3804 ,=._.+   _ \..--( /
Fax: (02) 6201 2328   \\.-''_.-' \ ( \_
Institute for Applied Ecology  `'''   `\__   /\
Faculty of Science and Technology  ')
University of Canberra   ACT 2601 AUSTRALIA
Email: bernd.gru...@canberra.edu.au<mailto:bernd.gru...@canberra.edu.au>
WWW: 
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Re: [R-pkg-devel] two functions with the same name when importing

[Bernd . Gruber]

@Martin Morgan

Thanks to your hint if found this:

@rawNamespace import(adegenet, except = plot)

which works beautifully  and no need to go through each Namespace function.

Thanks again to everyone.




From: Martin Morgan 
Sent: Thursday, 7 November 2019 8:34 PM
To: Duncan Murdoch ; Bernd.Gruber 
; r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] two functions with the same name when importing

RShowDoc("R-exts") setion 1.5.1 Specifying imports and exports indicates that 
imports() has an except= argument, so

import(adegenet, except = plot)

might do the trick. Use it in your package as `adegenet::plot()`.

Martin Morgan

On 11/6/19, 8:31 PM, "R-package-devel on behalf of Duncan Murdoch" 
mailto:r-package-devel-boun...@r-project.org%20on%20behalf%20of%20murdoch.dun...@gmail.com>>
 wrote:

On 06/11/2019 6:50 p.m., Bernd.Gruber wrote:
> Hi,
>
> I have a problem regarding the name of two functions and I know the "correct" 
> way is to use importFrom to make sure only specified functions are imported. 
> But my problem is that my package really depends on another package
> adegenet as I basically use 90% of the say >100 functions.
>
> So when I import all of adegenet I get:
>
> 2: replacing previous import 'adegenet::plot' by 'graphics::plot' when 
> loading 'dartR'
>
>
> So in essence I think adegenet is importing a plot function which collides 
> with the basic plot function. Is there anything I can do, without going 
> through 100 functions and using importFrom
>
> In addition I actually need the plot function from adegenet, so I would need 
> to rename it as well somehow.
>
> Any hint how to solve this would be highly appreciated.

Just get a copy of the adegenet NAMESPACE file to get all of its
exports. Edit the list down to the ones you use, and use a text editor
to change the export directives to importFrom directives. It's not
really that hard.

The path to the NAMESPACE file is given by

system.file("NAMESPACE", package="adegenet")

Duncan Murdoch

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[R-pkg-devel] two functions with the same name when importing

[Bernd . Gruber]

Hi,

I have a problem regarding the name of two functions and I know the "correct" 
way is to use importFrom to make sure only specified functions are imported. 
But my problem is that my package really depends on another package
adegenet as I basically use 90% of the say >100 functions.

So when I import all of adegenet I get:

2: replacing previous import 'adegenet::plot' by 'graphics::plot' when loading 
'dartR'


So in essence I think adegenet is importing a plot function which collides with 
the basic plot function. Is there anything I can do, without going through 100 
functions and using importFrom

In addition I actually need the plot function from adegenet, so I would need to 
rename it as well somehow.

Any hint how to solve this would be highly appreciated.

Regards, Bernd





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[R-pkg-devel] Note issued though package is in depends (or imports)

[Bernd . Gruber]

Hi,

I had a package on cran for a while.

Since the latest update/recompile I get the Note (not via R-studio, but running 
Rstudio to compile)


NOTE


checking data for non-ASCII characters ... NOTE
  Error in .requirePackage(package) :
unable to find required package 'raster'
  Calls:  ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted




when I test the package.

Unfortunately I am stuck here as I do not know why this Note is issued.

My suspicion is that I have an internal data set of type raster that throws the 
error. But I have the raster package in the depends in my description file also 
I tried to put it into imports.

Or add an @import raster into the roxygen description of the data set. Nothing 
seems to work and the Note still occurs.

Anyone has a similar idea and or is there an idea how can I reproduce the Note 
(as said under R-studio I cannot see it, it compiles fine without Note) only on 
win-builder I get that.

Any advice would be highly appreciated.

Regards, Bernd




==
Dr Bernd Gruber  )/_
 _.--..---"-,--c_
Associate Professor \|..'   ._O__)_
Tel: (02) 6206 3804 ,=._.+   _ \..--( /
Fax: (02) 6201 2328   \\.-''_.-' \ ( \_
Institute for Applied Ecology  `'''   `\__   /\
Faculty of Science and Technology  ')
University of Canberra   ACT 2601 AUSTRALIA
Email: bernd.gru...@canberra.edu.au<mailto:bernd.gru...@canberra.edu.au>
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