[R-pkg-devel] Rd cross-references ... NOTE, Undeclared packages ... in Rd xrefs

[hugo@gruso@+R m@iii@g oii @orm@iesup@org]

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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