[R-pkg-devel] Question about preventing CRAN package archival

Roy Mendelssohn - NOAA Federal roy@mende|@@ohn @end|ng |rom no@@@gov
Wed Jun 2 21:41:58 CEST 2021

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.


> 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
>>>> 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
>>>>> ______________________________________________
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Roy Mendelssohn
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