Re: [R-pkg-devel] Warning from orphaned package on check page

Duncan Murdoch Thu, 09 Nov 2023 07:49:09 -0800

I have volunteered to take over maintenance of plotrix. I should besubmitting a version without the "orphaned" designation soon.

(If anyone else would rather be maintainer, please get in touch with meoffline.)


Duncan Murdoch

On 09/11/2023 9:47 a.m., Liam J. Revell wrote:

Thank you Georgi & Ivan for your comments.

Because of the way 'plotrix' is written, it turns out to be very easy to
copy the imported functions into a new source file in my package (let's
say, plotrix_fn.R) and remove the dependency.

What I've actually done is move 'plotrix' to Suggests, and then have R
check to see if plotrix is installed to determine which version of each
function to use. E.g.:

      arctext<-if(.check.pkg("plotrix")) plotrix::arctext else Arctext

in which 'arctext' is the function name exported by plotrix and Arctext
is the copy in my package.

I believe this is permitted under GPL-3. Can someone with more
experience in this recommend how the original authors of plotrix should
be properly credited?

Thanks again for this constructive feedback.

All the best, Liam

Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R (Princeton University Press,
2022)


On 11/9/2023 6:42 AM, Georgi Boshnakov wrote:


        
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CAUTION: EXTERNAL SENDER
Orphaned packages can't be listed in DEPENDS and IMPORTS fields in
file DESCRIPTION. They can be in SUGGESTS but calls of functions from
them should be guarded, eg with a message to install the offending
package. In examples and tests the usage should be conditional on the
package beinginstalled.

Another option is to take over maintenance of that package. In your
case, with so many dependencies someone may be working on bringing it
back.

Georgi Boshnakov

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------------------------------------------------------------------------
*From:* R-package-devel <r-package-devel-boun...@r-project.org> on
behalf of Liam J. Revell <liam.rev...@umb.edu>
*Sent:* Thursday, November 9, 2023 11:30:05 AM
*To:* Alexandre Courtiol <alexandre.court...@gmail.com>
*Cc:* r-package-devel@r-project.org <r-package-devel@r-project.org>
*Subject:* Re: [R-pkg-devel] Warning from orphaned package on check page
My apologies for the lack of clarity.

plotrix has been orphaned so my package results page now says

      checking package dependencies ... WARNING
      Requires orphaned package: ‘plotrix’

CRAN incoming requires maintainers to certify: 'I have fixed all
problems shown on the package check page.' Since I can't unorphan
plotrix, I can't certify this statement & thus can't get a new version
of my package on CRAN. Advice on how to proceed is welcomed.

Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web:
https://urldefense.com/v3/__http://faculty.umb.edu/liam.revell/__;!!PDiH4ENfjr2_Jw!EUF27KhzseEpywIN0EnjFB_d4JQ9VgFwYWOCrNH1U9F6Bqh9SOqbi57oq38wPjZFM-40ALcQXaITFEjCuIgQOW0aznrXaHjdobg$
<https://urldefense.com/v3/__http://faculty.umb.edu/liam.revell/__;!!PDiH4ENfjr2_Jw!EUF27KhzseEpywIN0EnjFB_d4JQ9VgFwYWOCrNH1U9F6Bqh9SOqbi57oq38wPjZFM-40ALcQXaITFEjCuIgQOW0aznrXaHjdobg$>
[faculty[.]umb[.]edu]
Book: Phylogenetic Comparative Methods in R (Princeton University Press,
2022)

On 11/9/2023 4:10 AM, Alexandre Courtiol wrote:



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CAUTION: EXTERNAL SENDER
Dear Liam,
I don't understand your question: if your package has plotrix listed
as a dependency, it won't affect plotrix.
Only the opposite would be true. Could you please clarify and indicate
which package you are referring to?
Thanks,
Alex



On Thu, 9 Nov 2023 at 09:57, Liam J. Revell <liam.rev...@umb.edu> wrote:

      Dear colleagues.

      I'm trying to update a package on CRAN containing a dependency
      (specifically, on the popular graphing package 'plotrix') that has
      been
      orphaned because the maintainer is deceased.

      'plotrix' is imported by well over 100 other CRAN packages, so I
      hope it
      is not removed from CRAN. On the other hand, I don't want to certify
      that 'I have fixed all problems shown on the package check page'
      if this
      is not, in fact, the case.

      Can anyone comment on how one might proceed in this situation?

      Thank you. -- Liam

      --
      Liam J. Revell
      Professor of Biology, University of Massachusetts Boston
      Web:

https://urldefense.com/v3/__http://faculty.umb.edu/liam.revell/__;!!PDiH4ENfjr2_Jw!EUF27KhzseEpywIN0EnjFB_d4JQ9VgFwYWOCrNH1U9F6Bqh9SOqbi57oq38wPjZFM-40ALcQXaITFEjCuIgQOW0aznrXaHjdobg$
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      Book: Phylogenetic Comparative Methods in R (Princeton University
      Press,
      2022)

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--
Alexandre Courtiol,

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Re: [R-pkg-devel] Warning from orphaned package on check page

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