vignette fails to build on GHA

[bschilder]

Happens across all platforms:

Quitting from lines 69-76 (echoplot.Rmd) 
Error: Error: processing vignette 'echoplot.Rmd' failed with diagnostics:
Can't combine `..1$Method` <factor<2f980>> and `..4$Method` <ordered<4e1b3>>.

Different error, but similar situation to this issue: RajLabMSSM/echolocatoR#129

[bschilder]

Related:
https://stackoverflow.com/questions/66244056/error-cant-combine-1a-double-and-2a-factoree569

Seems this might be a version difference in how rows of different types are being bound by default. Unsure which package/function is causing this tho. Running update.packages(ask=F) to try and replicate this.

[bschilder]

Running update.packages(ask=F) to try and replicate this.

Now able to replicate the issue with: devtools::build_vignettes()

[bschilder]

Noticing other warnings:

Warning messages:
1: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation ideoms with `aes()`
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated. 
2: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

I think these warnings and the original error might be related to the integration of tidy with ggplot2:
https://cmdlinetips.com/2018/07/ggplot2-version-3-0-0-brings-tidy-evaluation-to-ggplot/

aes_string() was deprecated in ggplot2 3.0.0.

This makes zero sense to me why they're deprecating this. The new method they suggest to replace it with is fare more verbose and complicated. Will stick with the old method for now since it will be a long time before they remove aes_string.

Using size aesthetic for lines was deprecated in ggplot2 3.4.0.

I think this is happening within add_multitrack_lines with geom_vline.

Can't combine ..1$Method <factor<2f980>> and ..4$Method <ordered<4e1b3>>.

Occurs within the add_snp_labels subfunction.

Specifically, when the initial snp_plot is created, echodata::melt_finemapping_results does not order the "Method" factor levels in the same way echoplot does. Fixed by making echodata::melt_finemapping_results do this in a consistent way.

Found another issue within construct_snp_labels along the way.

if(remove_duplicates){
        labelSNPs <- labelSNPs |>
            dplyr::group_by(dplyr::vars(grouping_vars)) |>
            dplyr::arrange(rowID) |>
            dplyr::slice(dplyr::n())
    }

to

if(isTRUE(remove_duplicates)){
    labelSNPs$rowID <- seq_len(nrow(labelSNPs))
    # labelSNPs[,by=as.list(grouping_vars)]
    labelSNPs <- labelSNPs |>
        dplyr::group_by_at(.vars = grouping_vars) |> 
        dplyr::arrange(rowID) |>
        dplyr::slice_head(n = 1) |>
        data.table::data.table()
    labelSNPs$rowID <- NULL
}

[bschilder]

Addressing these things + this #11 fixed this issue ! Vignette runs all the way through now.