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

Liam J. Revell ||@m@reve|| @end|ng |rom umb@edu
Thu Nov 9 15:47:08 CET 2023 

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:
>
> 	
> You don't often get email from georgi.boshnakov using manchester.ac.uk. 
> Learn why this is important 
> <https://aka.ms/LearnAboutSenderIdentification>
> 	
>
> 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
>
> Sent from Outlook for Android 
> <https://aka.ms/AAb9ysg>
> ------------------------------------------------------------------------
> *From:* R-package-devel <r-package-devel-bounces using r-project.org> on 
> behalf of Liam J. Revell <liam.revell using umb.edu>
> *Sent:* Thursday, November 9, 2023 11:30:05 AM
> *To:* Alexandre Courtiol <alexandre.courtiol using gmail.com>
> *Cc:* r-package-devel using r-project.org <r-package-devel using 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$> 
> [faculty[.]umb[.]edu]
> Book: Phylogenetic Comparative Methods in R (Princeton University Press,
> 2022)
>
> On 11/9/2023 4:10 AM, Alexandre Courtiol wrote:
> >
> >
> > You don't often get email from alexandre.courtiol using gmail.com. Learn why
> > this is important 
> <https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!PDiH4ENfjr2_Jw!EUF27KhzseEpywIN0EnjFB_d4JQ9VgFwYWOCrNH1U9F6Bqh9SOqbi57oq38wPjZFM-40ALcQXaITFEjCuIgQOW0aznrXKg7CKCI$ 
> [aka[.]ms]>
> >
> >
> > 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.revell using 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$ 
> <https://urldefense.com/v3/__http://faculty.umb.edu/liam.revell/__;!!PDiH4ENfjr2_Jw!EUF27KhzseEpywIN0EnjFB_d4JQ9VgFwYWOCrNH1U9F6Bqh9SOqbi57oq38wPjZFM-40ALcQXaITFEjCuIgQOW0aznrXaHjdobg$> 
> [faculty[.]umb[.]edu]
> > 
> <https://urldefense.com/v3/__http://faculty.umb.edu/liam.revell/__;!!PDiH4ENfjr2_Jw!EUF27KhzseEpywIN0EnjFB_d4JQ9VgFwYWOCrNH1U9F6Bqh9SOqbi57oq38wPjZFM-40ALcQXaITFEjCuIgQOW0aznrXaHjdobg$ 
> [faculty[.]umb[.]edu]>
> >     Book: Phylogenetic Comparative Methods in R (Princeton University
> >     Press,
> >     2022)
> >
> > ______________________________________________
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> >
> >
> > --
> > Alexandre Courtiol, 
> https://urldefense.com/v3/__http://www.datazoogang.de/__;!!PDiH4ENfjr2_Jw!EUF27KhzseEpywIN0EnjFB_d4JQ9VgFwYWOCrNH1U9F6Bqh9SOqbi57oq38wPjZFM-40ALcQXaITFEjCuIgQOW0aznrXtwIJCmI$ 
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> [datazoogang[.]de]
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