[R-pkg-devel] Question about preventing CRAN package archival
Ben Bolker
bbo|ker @end|ng |rom gm@||@com
Wed Jun 2 22:30:43 CEST 2021
Write to the CRAN maintainers and let them know about the situation,
hopefully that would prevent archiving.
On 6/2/21 4:16 PM, Ben Staton wrote:
> Hi Everyone, thank you all for your responses.
>
> I agree that I can replicate the three functions within matrixcalc that I
> need with ease, even without copying and pasting the original code found in
> that package and thus not creating any licensing issues.
>
> I have checked the CRAN incoming boards (here
> <https://lockedata.github.io/cransays/articles/dashboard.html>), and they
> actually have a new version of matrixcalc coming through so hopefully this
> issue will be resolved without my intervention.
>
> On a related note, suppose that this issue does not get resolved before the
> archival date, and my package gets archived. What would be the path for me
> to have CRAN remove it from the archived list? Is it basically (1) fix the
> issue that caused initial archival and (2) resubmit?
>
> Thank you,
> Ben
>
> On Wed, Jun 2, 2021 at 12:48 PM Spencer Graves <
> spencer.graves using effectivedefense.org> wrote:
>
>> The CRAN maintainers almost certainly have tried to contact the
>> maintainer. You can ask if he plans to fix the bug. If not, if it's
>> that easy to fix, you could offer to both the maintainers of both
>> matrixcalc and CRAN to take over maintenance.
>>
>>
>> Spencer
>>
>>
>> On 6/2/21 2:41 PM, Roy Mendelssohn - NOAA Federal via R-package-devel
>> wrote:
>>> After looking up matrixcalc on CRAN, I would recommend contacting the
>> maintainer, who is listed as:
>>>
>>>> Frederick Novomestky <fnovomes at poly.edu>
>>>
>>>
>>> The reason I say this is what is blowing up the package in the nightly
>> builds is a careless error in one Example:
>>>
>>>> > x <- matrix( c( 2, 4, 2, 1, 3, 1, 5, 2, 1, 2, 3, 3 ), nrow=4,
>> ncol=4, byrow=TRUE )
>>>> Error in matrix(c(2, 4, 2, 1, 3, 1, 5, 2, 1, 2, 3, 3), nrow = 4,
>> ncol = 4, :
>>>> data length differs from size of matrix: [12 != 4 x 4]
>>>>
>>>
>>> That should be pretty easy for the maintainer to fix and to resubmit.
>>>
>>> -Roy
>>>
>>>
>>>> On Jun 2, 2021, at 10:36 AM, Ben Staton <statonbe using gmail.com> wrote:
>>>>
>>>> My package uses the MIT license, so would that not meet the
>> compatibility
>>>> requirements?
>>>>
>>>> I will attempt to reach out to the package author - thanks for your
>> help!
>>>>
>>>> On Wed, Jun 2, 2021 at 10:31 AM Ben Bolker <bbolker using gmail.com> wrote:
>>>>
>>>>> That all sounds exactly right.
>>>>> GPL >= 2 allows you to use the material without asking permission as
>>>>> long as your package is compatibly licensed (e.g. also GPL).
>>>>> Under normal circumstances it would be polite to ask permission, but
>>>>> if the reason for doing this is that the maintainer is unreachable in
>>>>> the first place ...
>>>>>
>>>>> If you want to try a little harder, it seems quite possible that you
>>>>> can reach the matrixcalc maintainer at the (personal) e-mail address
>>>>> shown in this page:
>>>>>
>>>>>
>> https://www.facebook.com/photo/?fbid=10208324530363130&set=ecnf.1000413042
>>>>>
>>>>> (Possibly an identity confusion, but I rate that as unlikely based
>> on
>>>>> other facebook snooping)
>>>>>
>>>>> I don't think a short, polite e-mail request would be out of bounds,
>>>>> they can always ignore it or tell you to go away.
>>>>>
>>>>> cheers
>>>>> Ben Bolker
>>>>>
>>>>> On 6/2/21 1:15 PM, Ben Staton wrote:
>>>>>> Hello,
>>>>>>
>>>>>> Thank you for your detailed list of solutions.
>>>>>>
>>>>>> I was initially tempted to go with option 1 (move matrixcalc to
>> suggests
>>>>>> and check for its existence before using functions that rely on it),
>> but
>>>>> as
>>>>>> mentioned, this is not a long term fix.
>>>>>>
>>>>>> I unfortunately can't take on the responsibilities of option 2
>> (becoming
>>>>>> the package maintainer) -- there is much that this package does that
>> I do
>>>>>> not understand, and do not wish to feign authority!
>>>>>>
>>>>>> I plan to take option 3 (copy the needed functions into my package).
>>>>> There
>>>>>> are only three functions I need from matrixcalc, and all three are
>> fairly
>>>>>> simple (is.square.matrix
>>>>>> <https://rdrr.io/cran/matrixcalc/src/R/is.square.matrix.R>,
>>>>>> is.symmetric.matrix
>>>>>> <https://rdrr.io/cran/matrixcalc/src/R/is.symmetric.matrix.R>, and
>>>>>> is.positive.definite
>>>>>> <https://rdrr.io/cran/matrixcalc/src/R/is.positive.definite.R>) and
>>>>> there
>>>>>> is only one function in postpack that needs them. I plan to define
>> them
>>>>>> within the postpack function. matrixcalc is licensed under GPL >= 2
>> and
>>>>>> based on my scan of the license text, this is allowed. Is that
>> correct?
>>>>>>
>>>>>> Regarding option 4 (contacting the matrixcalc maintainer), the
>> original
>>>>>> email from CRAN mentioned that they have attempted to contact the
>> package
>>>>>> author with no response.
>>>>>>
>>>>>> Thank you!
>>>>>>
>>>>>> On Wed, Jun 2, 2021 at 9:52 AM J C Nash <profjcnash using gmail.com> wrote:
>>>>>>
>>>>>>> I just downloaded the source matrixcalc package to see what it
>>>>> contained.
>>>>>>> The functions
>>>>>>> I looked at seem fairly straightforward and the OP could likely
>> develop
>>>>>>> equivalent features
>>>>>>> in his own code, possibly avoiding a function call. Avoiding the
>>>>> function
>>>>>>> call means NAMESPACE etc. are not involved, so fewer places for
>> getting
>>>>>>> into
>>>>>>> trouble, assuming the inline code works properly.
>>>>>>>
>>>>>>> JN
>>>>>>>
>>>>>>>
>>>>>>> On 2021-06-02 12:37 p.m., Duncan Murdoch wrote:
>>>>>>>> On 02/06/2021 12:13 p.m., Ben Staton wrote:
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> I received an email notice from CRAN indicating that my R package
>>>>>>>>> ('postpack') will be archived soon if I do not take any action and
>> I
>>>>>>> want
>>>>>>>>> to avoid that outcome. The issue is not caused by my package, but
>>>>>>> instead a
>>>>>>>>> package that my package depends on:
>>>>>>>>>
>>>>>>>>> "... package 'matrixcalc' is now scheduled for archival on
>> 2021-06-09,
>>>>>>>>> and archiving this will necessitate also archiving its strong
>> reverse
>>>>>>>>> dependencies."
>>>>>>>>>
>>>>>>>>> Evidently, xyz has been returning errors on new R builds prompting
>>>>> CRAN
>>>>>>> to
>>>>>>>>> list it as a package to be archived. My package, 'postpack' has
>>>>>>>>> 'matrixcalc' listed in the Imports field, which I assume is why I
>>>>>>> received
>>>>>>>>> this email.
>>>>>>>>>
>>>>>>>>> I want to keep 'postpack' active and don't want it to be archived.
>> I
>>>>>>> still
>>>>>>>>> need package 'matrixcalc' for my package, but not for most
>> functions.
>>>>>>> Could
>>>>>>>>> I simply move package 'matrixcalc' to the Suggests list and submit
>> the
>>>>>>> new
>>>>>>>>> version to CRAN to remove the "Strong Reverse Dependency" issue
>> that
>>>>>>>>> triggered this email to avoid CRAN from archiving my package?
>>>>>>>>
>>>>>>>> That's part of one solution, but not the best solution.
>>>>>>>>
>>>>>>>> If you move it to Suggests, you should make sure that your package
>>>>>>> checks for it before every use, and falls back to
>>>>>>>> some other calculation if it is not present. Be aware that once it
>> is
>>>>>>> archived, almost none of your users will have it
>>>>>>>> available, so this is kind of like dropping the functions that it
>>>>>>> supports.
>>>>>>>>
>>>>>>>> Another solution which would be great for the community might be for
>>>>> you
>>>>>>> to offer to take over as maintainer of
>>>>>>>> matrixcalc. Then you'd fix whatever problems it has, and you
>> wouldn't
>>>>>>> need to worry about it. I haven't looked at the
>>>>>>>> issues so I don't know if this is feasible.
>>>>>>>>
>>>>>>>> A third choice would be for you to copy the functions you need from
>>>>>>> matrixcalc into your own package so you can drop the
>>>>>>>> dependency. This is generally legal under the licenses that CRAN
>>>>>>> accepts, but you should check anyway.
>>>>>>>>
>>>>>>>> A fourth choice would be for you to contact the matrixcalc
>> maintainer,
>>>>>>> and help them to fix the issues so that
>>>>>>>> matrixcalc doesn't get archived. They may or may not be willing to
>>>>> work
>>>>>>> with you.
>>>>>>>>
>>>>>>>> I'd say my third choice is the best choice in the short term, and
>> 2nd
>>>>> or
>>>>>>> 4th would be good long term solutions.
>>>>>>>>
>>>>>>>> Duncan Murdoch
>>>>>>>>
>>>>>>>> ______________________________________________
>>>>>>>> R-package-devel using r-project.org mailing list
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>>>
>>>>>>
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>>>>>>
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>>>>>>
>>>>>
>>>>> ______________________________________________
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>>>
>>> **********************
>>> "The contents of this message do not reflect any position of the U.S.
>> Government or NOAA."
>>> **********************
>>> Roy Mendelssohn
>>> Supervisory Operations Research Analyst
>>> NOAA/NMFS
>>> Environmental Research Division
>>> Southwest Fisheries Science Center
>>> ***Note new street address***
>>> 110 McAllister Way
>>> Santa Cruz, CA 95060
>>> Phone: (831)-420-3666
>>> Fax: (831) 420-3980
>>> e-mail: Roy.Mendelssohn using noaa.gov www: https://www.pfeg.noaa.gov/
>>>
>>> "Old age and treachery will overcome youth and skill."
>>> "From those who have been given much, much will be expected"
>>> "the arc of the moral universe is long, but it bends toward justice"
>> -MLK Jr.
>>>
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>>
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