[R-pkg-devel] help with CRAN failures (broom.mixed, rstan-related)

[Ben Bolker]

    Thanks both.

Josiah Parry says:

 > Ben, the issue is that {rstan} is not available. Since it is a 
suggested package it is not expected to always be there.

   The thing is that the checks for rstan-based objects *are* 
conditional.  This is actually failing on the tests for brms-based 
objects, which import methods from rstan.  I do test to see whether brms 
is available or not.

   I agree with Ivan's diagnosis that something has happened to the 
rstan installation which leaves brms available but rstan somehow 
(despite the fact that it is a hard dependency for brms) missing ...

   I will ask the CRAN maintainers for guidance.

   cheers
    Ben Bolker


On 9/24/24 11:14, Ivan Krylov wrote:
> В Tue, 24 Sep 2024 10:27:34 -0400
> Ben Bolker <bbolker using gmail.com> пишет:
> 
>>     Weirdly, I can't get this to fail on my local system even if I
>> remove rstan -- maybe rstan needs to be present for brms at install
>> time but not at runtime ... ???
> 
> I'm noticing that despite broom.mixed having Suggests: rstan and it
> being seemingly unable to load, you don't get a NOTE for the missing
> dependency:
> 
>>> checking package dependencies ... NOTE
>>> Packages suggested but not available for checking: 'dotwhisker',
>>> 'glmmADMB'
> 
> At that stage, R CMD check verifies that at least one of the libraries
> contains file.path(PACKAGE_NAME, 'DESCRIPTION'). Later, something else
> needs a valid rstan/Meta/package.rds. (There are also tests for links
> between help pages, but they don't stop the check.) While running the
> tests, methods:::.requirePackage actually tries to load the namespace
> using require() -> ... -> loadNamespace(), which fails.
> 
>> Weirdly, I can't get this to fail on my local system even if I
>> remove rstan -- maybe rstan needs to be present for brms at install
>> time but not at runtime ... ???
> 
> Having only the following files left from a valid 'rstan' installation,
> I can make R CMD check broom.mixed_0.2.9.5.tar.gz reach the same error
> as you're getting:
> 
> rstan
> rstan/Meta
> rstan/Meta/package.rds
> rstan/DESCRIPTION
> 
> Something must have happened on the Fedora machine.
> 

-- 
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
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