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

[Josiah Parry]

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

This is referred to is the "hard" check.

Here is a  GitHub CI workflow I use to perform this check:
https://github.com/JosiahParry/sfdep/blob/008a59b6009d01e5e1625319f6525c1e0bae34a2/.github/workflows/R-CMD-check-hard.yaml#L15

TL;DR if you are using a package conditionally, the examples should also be
conditional.




On Tue, Sep 24, 2024 at 7:27 AM Ben Bolker <bbolker using gmail.com> wrote:

>    broom.mixed is failing tests on Fedora.
>
> With apologies for the mangled formatting, here is the test failure
> (full properly formatted details at
>
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/broom.mixed-00check.html
> ).
>
>    ══ Failed tests
> ════════════════════════════════════════════════════════════════   ──
> Error ('test-alltibbles.R:57:21'): (code run outside of `test_that()`)
> ──────   Error in `.requirePackage(package)`: unable to find required
> package 'rstan'   Backtrace:        ▆     1. └─broom.mixed (local)
> testf("glance", z) at test-alltibbles.R:62:13     2.
> ├─testthat::expect_is(get(fn_str)(obj), "tbl_df") at
> test-alltibbles.R:57:21     3. │ └─testthat::quasi_label(enquo(object),
> label, arg = "object")     4. │ └─rlang::eval_bare(expr,
> quo_get_env(quo))     5. ├─get(fn_str)(obj)     6.
> └─broom.mixed:::glance.brmsfit(obj)     7.
> └─broom.mixed:::glance_stan(...)     8. ├─stats::sigma(x)     9.
> └─broom.mixed:::sigma.brmsfit(x)    10. ├─"sigma" %in%
> brms::variables(object)    11. ├─brms::variables(object)    12.
> └─brms:::variables.brmsfit(object)    13. └─methods (local)
> dimnames(x$fit)    14. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`,
> `<env>`)    15. └─methods:::.findInheritedMethods(classes, fdef, mtable)
>     16. └─methods::getClass(cl1, where = where, .Force = TRUE)    17.
> └─methods::getClassDef(Class, where)    18.
> └─methods:::.requirePackage(package)      [ FAIL 1 | WARN 4 | SKIP 1 |
> PASS 237 ]   Error: Test failures   Execution halted
>
>
>    This is in a test section where I loop over fitted examples from
> different modeling packages. *If* the relevant package is installed, I
> test the various methods defined in broom.mixed for extracting
> information from that kind of object.
>
>    This appears to be failing when testing objects from 'brms', because
> 'rstan' isn't available. However, I don't see how brms can be available
> when rstan isn't, since brms Imports: rstan?
>
>    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 ... ???
>
>    Any hints/insights/guesses/suggestions for further diagnostics are
> welcome.
>
>    cheers
>      Ben
>
>
>
>
> --
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> * E-mail is sent at my convenience; I don't expect replies outside of
> working hours.
>
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