[R-pkg-devel] Errors from Suggests or Enhances not in mainstream repositories

Ben Bolker bbolker @ending from gm@il@com
Tue Jul 3 00:41:19 CEST 2018

Thanks, Uwe.  Responses inline.

On Mon, Jul 2, 2018 at 6:23 PM Uwe Ligges
<ligges using statistik.tu-dortmund.de> wrote:
> On 03.07.2018 00:13, Ben Bolker wrote:
> > I got something similar.  I have a few thoughts:
> >
> > (1) you should use  "if (require(citrus)) { ... }" in your examples;
> > "Suggests" and "Enhances" packages are supposed to be *optional*, i.e.
> > examples and tests should be able to run even if they're not installed
> > (I would imagine that "Writing R Extensions" and/or the CRAN policies
> > say something to this effect, but I haven't checked)
> > (2) I can imagine that win-builder is looking for *binary* versions of
> > the package (I'm not sure why this would be the default, and why it
> > couldn't fall back and install from source, but that would be my
> > guess); do you have binary versions, for the appropriate major R
> > version (i.e. 3.5 for release, maybe?? 3.4 for oldrelease??), in your
> > repo. (In my example, I don't; I was going to try compiling a binary
> > version and putting it in the repo. This is a bit of a chicken-and-egg
> > problem if you can't get a binary built because the examples fail, but
> > if you implement step #1 I think it should work).
> >
> > My point (3) is a follow-on question that I would love an answer to,
> > or hints. I get a *message* similar to the one found in throm's
> > win-builder logs, i.e. "Suggests or Enhances not in mainstream
> > repositories: ..." - but since it's not labeled as a WARNING or an
> > ERROR (or even a NOTE), I am wondering what its status is in the
> > CRAN-maintainers' eyes - is it a CRAN-submission-blocking problem? Or
> > a "we'd rather you didn't do that but we'll accept it this time?" or
> > ...
Uwe> Ideally packages are in mainstream repositories.


Uwe> For waek dependencies such as Suggests or Enhances, and if the package
Uwe> is in some repository, you can declare it via the
Uwe> Additional_Repositories field.

  I did that (so did the OP). Speaking for myself (since I'm not sure
of the OP's exact situation), I know that the source tarball is in my
repo, and it gets installed successfully on Linux and MacOS. On
Windows (win-builder), the package is not detected in the repo. I can
try adding a Windows binary to the repo to see if that solves the

  FWIW, one of the off-CRAN packages I Suggest: is INLA (which is
beyond my control). The other is glmmADMB, which includes a binary
blob and can't go on CRAN.  I would like to offer some support for
these packages, if at all possible.

I just don't know if the message about the package *not* being found
in the repo suggested by Additional_repositories: will be
CRAN-blocking (and would prefer not to waste everyone's time by
submitting if it is ...)

Uwe> Finally, if not even in a repository, explain in the Descripton field
Uwe> how to get it.
> Best,
> Uwe Ligges
> >
> >     I'm not asking anyone (except possibly CRAN maintainers) to speak
> > for the CRAN maintainers, but if anyone has any experience or guesses
> > (or pointers to parts of the CRAN policies/Writing R Extensions
> > document that I overlooked) I'd appreciate hearing about it.
> >
> >    cheers
> >       Ben Bolker
> > On Mon, Jul 2, 2018 at 5:28 PM Throm, Allison <throm using wustl.edu> wrote:
> >>
> >> Hi all,
> >>
> >>
> >> I'm trying to submit a package to the CRAN that further examines results from the "citrus" package as done for an accepted publication (available on Github: <https://github.com/nolanlab/citrus>).
> >>
> >>
> >> I do not get any errors when using devtools::check() on my Mac, which already has the citrus package installed. However, I am getting errors during the CRAN submission check <https://win-builder.r-project.org/incoming_pretest/mineCitrus_1.0.0_20180702_172340/>.
> >>
> >>
> >> I've tried searching Stack Overload and other CRAN packages with Additional_repositories fields, but none of the applicable solutions have worked. I'm pretty sure it's the loading of the citrus package that is causing the error and have added the Additional_repositories field with a link the package on Github, but still haven't been able to resolve the issue. There are very specific installation instructions for the package <https://github.com/nolanlab/citrus/wiki/Installing-Citrus>, which may be contributing to issues.
> >>
> >>
> >> How should I properly specify dependencies on the nolanlab/citrus<https://github.com/nolanlab/citrus> Github package for my CRAN package?
> >>
> >>
> >> Thank you in advance,
> >>
> >> Allison
> >>
> >>
> >>
> >>
> >>
> >>
> >>          [[alternative HTML version deleted]]
> >>
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> >
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