windows CI breaking

[sebdalgarno]

seems to be an issue with vignette building

[aylapear]

Removed the vignettes and run the checks with just one each time and it appears that bbtutorial.Rmd is causing the issue.

* checking for file 'D:\a\bboutools\bboutools/DESCRIPTION' ... OK
* preparing 'bboutools':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error: --- re-building 'bbtutorial.Rmd' using rmarkdown
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted
Error: Process completed with exit code 1.
Run ## --------------------------------------------------------------------
Show testthat output
Run actions/upload-artifact@v4
Warning: No files were found with the provided path: D:/a/bboutools/bboutools/check. No artifacts will be uploaded.

As it ran fine with the other vignette bboumethds.Rmd

── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file 'D:\a\bboutools\bboutools/DESCRIPTION' ... OK
* preparing 'bboutools':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted 'LazyData' from DESCRIPTION
* building 'bboutools_0.0.0.9005.tar.gz'

[aylapear]

When vignette error didn't occur there was this weird error on windows so bb_fit_survival_ml() tests had to be skipped.

> library(testthat)
> library(bboutools)
Loading required package: nimble
nimble version 1.1.0 is loaded.
For more information on NIMBLE and a User Manual,
please visit https://r-nimble.org./

Note for advanced users who have written their own MCMC samplers:
  As of version 0.13.0, NIMBLE's protocol for handling posterior
  predictive nodes has changed in a way that could affect user-defined
  samplers in some situations. Please see Section 15.5.1 of the User Manual.

Attaching package: 'nimble'

The following object is masked from 'package:stats':

    simulate

> 
> test_check("bboutools")
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = bYear
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_bYear
Available Name 1 = AdultsFemales
Error, could not find name
Name = bYear
Available Name 1 = AdultsFemales
Error, could not find name
Name = lifted_eRecruitment_oBi_cB_times_AdultsFemales_oBi_cB_L23
Available Name 1 = AdultsFemales
Error, could not find name
Name = lifted_eRecruitment_oBi_cB_times_AdultsFemales_oBi_cB_L23
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_adult_female_proportion
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_adult_female_proportion
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_adult_female_proportion
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = logProb_sAnnual
Available Name 1 = AdultsFemales
Error, could not find name
Name = sAnnual
Available Name 1 = AdultsFemales

Error: Error: R CMD check found ERRORs
1 error ✖ | 0 warnings ✔ | 0 notes ✔
Execution halted
Error: Process completed with exit code 1.

[aylapear]

Update action to not build the vignette on windows as well

[aylapear]

We were unable to determine what was causing this issue and so for now R CMD Check on windows is set to not build vignette and skipping some tests on windows as well.