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Merged
gregorgorjanc merged 10 commits into from
Aug 28, 2024
Merged

Merging the remaining changes to prepare the package for CRAN #581

gregorgorjanc merged 10 commits into from
Aug 28, 2024

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@janaobsteter
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@janaobsteter janaobsteter commented Jul 17, 2024

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janaobsteter commented Jul 17, 2024
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The factor in the "caste" was changed to "character", since the factor thing was making it slow and used memory. Also, I created generic functions to test whether we can improve the speed

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gregorgorjanc commented Jul 17, 2024

@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.

gregorgorjanc
gregorgorjanc reviewed Jul 17, 2024
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tests/testthat/test-L2_colony_functions.R Outdated
})


test_that("swarm1", {
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Do we need a test for buildUp1 too @janaobsteter ?

gregorgorjanc
gregorgorjanc reviewed Jul 17, 2024
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@janaobsteter looked over this - only one comment above and see the checks

gregorgorjanc
gregorgorjanc reviewed Aug 15, 2024
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@janaobsteter see comments above

gregorgorjanc
gregorgorjanc reviewed Aug 20, 2024
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@janaobsteter similar comments to last time;)

@janaobsteter janaobsteter changed the title Seeing the changes from my fork to HLab lab (remainder from the hackathon?) Merging the remaining changes to prepare the package for CRAN Aug 23, 2024
gregorgorjanc
gregorgorjanc reviewed Aug 23, 2024
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gregorgorjanc reviewed Aug 23, 2024
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R/Functions_L0_auxilary.R Outdated
@@ -1063,7 +1063,7 @@ getQueenYearOfBirth <- function(x, simParamBee = NULL) {
}
} else if (isColony(x)) {
if(packageVersion("AlphaSimR") > package_version("1.5.3")){
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@janaobsteter Best to just fix package version in DESCRIPTION and then we don't need this code duplication.

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gregorgorjanc reviewed Aug 23, 2024
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@janaobsteter looks good - needs minor tweaks and then we can merge

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janaobsteter commented Aug 28, 2024

@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

gregorgorjanc
gregorgorjanc approved these changes Aug 28, 2024
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LGTM @janaobsteter! Thanks for doing all this edits for the help page linking! That must have been annoying.

@gregorgorjanc gregorgorjanc merged commit 6a08666 into HighlanderLab:devel Aug 28, 2024
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