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update transformerList constructor according to the latest scales package change #393

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merged 3 commits into from
Jan 13, 2024

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mikejiang
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@mikejiang mikejiang commented Dec 5, 2023

To fix the bioconductor build failures
https://bioconductor.org/checkResults/3.18/bioc-LATEST/flowWorkspace/nebbiolo2-buildsrc.html

Error: processing vignette 'flowWorkspace-Introduction.Rmd' failed with diagnostics:
'trans' must be a list of transformer objects (generated by scales::trans_new method)

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@amcdavid amcdavid left a comment

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If this is really just that scales renamed their class from trans -> transform, and we don't depend on any other behavior of new scales, we could add a function

is_scales_transform = function(x) inherits(trans, "transform") || inherits(trans, "trans")

and replace all the is tests with this function. That way we can avoid the scales > 1.3.0 dependency. This will make it easier to bring this patch into internal version without having to upgrade scales, and a bit friendlier to other users of this package to avoid a hard version pin. What do you think?

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Yes I see what you mean, Open source cytolib/flowWorkspace code base already diverges quite significantly from internal repo though, Just want to quickly patch up to pass bioconductor builds (already pushed the patch to their current release and develop branches) and move on.
Feel free to submit a PR if you prefer to proposal, I am fine with either.

@djhammill
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djhammill commented Jan 5, 2024

@mikjiang, I agree with @amcdavid - we should try to support older versions of scales as well if possible. I've submitted a new PR (#397) to this branch with the required changes.

@mikejiang mikejiang merged commit 0137cfc into devel Jan 13, 2024
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3 participants