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HighlanderLab / SIMplyBee

SIMplyBee R package extends AlphaSimR for simulating honeybee populations and breeding programmes
http://www.simplybee.info/
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Merging the remaining changes to prepare the package for CRAN #581

Closed janaobsteter closed 2 weeks ago

gregorgorjanc commented 2 months ago

@janaobsteter I am seeing this R CMD check (via GitHub action) failing with

Quitting from lines 618-622 [colony_strength] (F_Quantitative_Genetics.Rmd)
[308](https://github.com/HighlanderLab/SIMplyBee/actions/runs/9970676222/job/27550092259?pr=581#step:5:310)
Error: Error: processing vignette 'F_Quantitative_Genetics.Rmd' failed with diagnostics:
[309](https://github.com/HighlanderLab/SIMplyBee/actions/runs/9970676222/job/27550092259?pr=581#step:5:311)
no slot of name "queen" for this object of class "MultiColony"
[310](https://github.com/HighlanderLab/SIMplyBee/actions/runs/9970676222/job/27550092259?pr=581#step:5:312)
--- failed re-building ‘F_Quantitative_Genetics.Rmd’
[311](https://github.com/HighlanderLab/SIMplyBee/actions/runs/9970676222/job/27550092259?pr=581#step:5:313)
--- re-building ‘G_Sampling_functions.Rmd’ using rmarkdown
[312](https://github.com/HighlanderLab/SIMplyBee/actions/runs/9970676222/job/27550092259?pr=581#step:5:314)
--- finished re-building ‘G_Sampling_functions.Rmd’
[313](https://github.com/HighlanderLab/SIMplyBee/actions/runs/9970676222/job/27550092259?pr=581#step:5:315)
--- re-building ‘Z_FAQ.Rmd’ using rmarkdown
[314](https://github.com/HighlanderLab/SIMplyBee/actions/runs/9970676222/job/27550092259?pr=581#step:5:316)
--- finished re-building ‘Z_FAQ.Rmd’
[315](https://github.com/HighlanderLab/SIMplyBee/actions/runs/9970676222/job/27550092259?pr=581#step:5:317)
SUMMARY: processing the following file failed:
[316](https://github.com/HighlanderLab/SIMplyBee/actions/runs/9970676222/job/27550092259?pr=581#step:5:318)
  ‘F_Quantitative_Genetics.Rmd’
[317](https://github.com/HighlanderLab/SIMplyBee/actions/runs/9970676222/job/27550092259?pr=581#step:5:319)
Error: Error: Vignette re-building failed.
janaobsteter commented 2 weeks ago

@gregorgorjanc , this is now the version accepted to CRAN. I've added all anchors to \links and removed the checks for AlphaSimR version since it now depends on the latest version with the correct handling of the misc slot.

Could you please merge this into HLab, then I can merge dev into main and I will also mark this as commit 0.4.0