[R-pkg-devel] Cryptic fail on GitHub Action (was: Rd cross-references ... NOTE, Undeclared packages ... in Rd xrefs)

[Spencer Graves]

Hi, Hugo, et al.:


	  How can I "set the environment variable _R_CHECK_FORCE_SUGGESTS_" on 
GitHub Actions, as Hugo suggests below?


	  Secondly, I have another cryptic failure on macOS-latest (release):


Run r-lib/actions/setup-pandoc using v1


sudo installer -pkg /Users/runner/work/_temp/pandoc-2.7.3-macOS.pkg 
-target /


Error: The operation was canceled.


	  Any suggestions on this?  This package successfully passed four other 
platforms on GitHub Action [Windows-latest (release) and Ubuntu 
(release, devel, and oldrel-1).


	  Thanks,
	  Spencer Graves
	

On 6/14/22 3:09 AM, hugo.gruson+R using normalesup.org wrote:
> On 14/06/2022 01:01, Spencer Graves wrote:
>  >
>  >
>  > On 6/13/22 5:05 PM, Duncan Murdoch wrote:
>  >> On 13/06/2022 5:11 p.m., Spencer Graves wrote:
>  >>>
>  >>>
>  >>> On 6/13/22 1:26 PM, Duncan Murdoch wrote:
>  >>>> On 13/06/2022 12:12 p.m., Spencer Graves wrote:
>  >>>>> Hello, All:
>  >>>>>
>  >>>>>
>  >>>>>        How do I fix "Rd cross-references ... NOTE
>  >>>>> Undeclared packages ‘EnvStats’, ‘drc’, ‘zoo’, ‘prodlim’, ‘plyr’,
>  >>>>> ‘TRAMPR’, ‘raster’ in Rd xrefs"?
>  >>>>>
>  >>>>>
>  >>>>>        This occurs with
>  >>>>> 
> "https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Ecfun-00check.html" 
> 
>  >>>>>
>  >>>>> and with
>  >>>>> 
> "https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/Ecdat-00check.html". 
> 
>  >>>>>
>  >>>>>     However, this error is not raised on other platforms.  My 
> search for
>  >>>>> this note produced essentially the same message for other 
> packages but
>  >>>>> no advice on how to fix it.
>  >>>>>
>  >>>>>
>  >>>>>        These are references to other packages that I do not use 
> in my
>  >>>>> packages but that some users may wish to consider.  If needed, I 
> will
>  >>>>> add them to "Suggests" for the packages.  However, that seems 
> overkill,
>  >>>>> because I do not use them myself.  ???
>  >>>>
>  >>>> Section 2.5 of Writing R Extensions says "Packages referred to by 
> these
>  >>>> ‘other forms’ should be declared in the DESCRIPTION file, in the
>  >>>> ‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields."  Of those
>  >>>> fields, Suggests looks like the best fit.  You'd use Enhances if your
>  >>>> package provides "methods for classes from these packages, or ways to
>  >>>> handle objects from these packages".
>  >>>
>  >>>
>  >>>       GitHub Actions failed after I added those packages to Suggests:
>  >>>
>  >>>
>  >>> 
> https://github.com/sbgraves237/Ecfun/runs/6869516417?check_suite_focus=true
>  >>
>  >> That log doesn't really give much info about what went wrong.  Maybe 
> some of the packages in the Suggests list weren't available?
>  >
>  >
>  >        Is there a way in GitHub Action to NOT fail when a package is 
> not available -- or at least to give a more useful diagnostic?
> 
> Hi Spencer and all,
> 
> Yes, you can set the environment variable _R_CHECK_FORCE_SUGGESTS_. R 
> CMD check will still run even if some suggested packages are missing. 
> Provided no error is raised by your package when one of these Suggests 
> is missing, you should be fine.
> 
> Best wishes,
> 
> Hugo
> 
>  >
>  >
>  >        There probably is, but I don't know how to find the right 
> manual to read nor any better place to ask for help with that than here.
>  >
>  >
>  >        Thanks, sg
>  >
>  >>
>  >> Duncan Murdoch
>  >
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