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

[Duncan Murdoch]

On 13/06/2022 7:01 p.m., 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?
> 
> 
> 	  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.

Your DESCRIPTION file has a blank line after the list of Suggests 
packages, and that caused dev_package_deps() to die with the error you saw.

I think the blank line is illegal in a DESCRIPTION file:  in the DCF 
format, that separates blocks, and everything is supposed to be in one 
block.  But remotes::dev_package_deps() could perhaps give a more 
informative message, as R CMD INSTALL does.

Duncan Murdoch