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

Thu Nov 9 16:48:38 CET 2023

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

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

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:
>>
>> 	
>> 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)
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>>
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>> [stat[.]ethz[.]ch]
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>> [stat[.]ethz[.]ch]>
>>>
>>>
>>>
>>> --
>>> 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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