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 <bbol...@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. > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
