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

Avraham Adler @vr@h@m@@d|er @end|ng |rom gm@||@com
Wed Jun 2 21:28:25 CEST 2021 

Exactly. Is square is just brow=ncol, is positive definite can be
implemented as a check that all eigenvalues > 0, which can be done with
base, and is.symmetric can be simply brute forced in a loop comparing i,j
with j,i.

The fewer dependencies a package has, the more robust it is. It’s a fine
balance between not reinventing the wheel and ceding too much stability to
other packages.

Thanks,

Avi

On Wed, Jun 2, 2021 at 3:15 PM John Harrold <john.m.harrold using gmail.com>
wrote:

> To add another option. In the past when this has happened to me I've found
> other packages that provide similar functionality.
>
> I'm assuming that is.square just checks the number of columns == number of
> rows? And the others can probably be implemented pretty easily.
>
> On Wed, Jun 2, 2021 at 10:41 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
> > > >>
> > > >
> > > >       [[alternative HTML version deleted]]
> > > >
> > > > ______________________________________________
> > > > R-package-devel using r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > > >
> > >
> > > ______________________________________________
> > > R-package-devel using r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > >
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
>
> --
> John
> :wq
>
>         [[alternative HTML version deleted]]
>
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>
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