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@luhann
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@luhann luhann commented Oct 17, 2025

Hi,

Thanks for all the work you do on corncob.

I am busy attempting to implement TreeSummarizedExperiment support for corncob, in the process I noticed that tests were giving a warning due to the fact that plot.differentialTest was using geom_errorbarh which has been deprecated. This PR just updates the plot and all tests pass without issue now.

@svteichman
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@luhann Thank you for noting this issue and submitting a PR! We really appreciate when people submit their own patches to issues they find in our software! However, I'm seeing failing R-CMD-checks (which I think is due to orientation = "x"). I replaced that with orientation = "y" in PR #189 , which resolves the errors, and checked that this doesn't affect the outputs. Could you confirm that this makes sense to you, or if it doesn't let me know why you used orientation = "x"?

Thanks!
Sarah

@luhann
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luhann commented Oct 17, 2025

Yup, I just noticed that now, I had fixed the error after I noticed the vignettes not building but forgot to amend this commit with the fix. It's supposed to be orientation = "y", but if you've included it in #189 I can go ahead and close this.

@svteichman
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Ok great, I'll close this and then merge PR #189. Thanks!

@svteichman svteichman closed this Oct 17, 2025
@luhann luhann deleted the fix_test branch October 17, 2025 22:24
@adw96
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adw96 commented Oct 18, 2025

Seconding Sarah's thanks for this and especially for TreeSummarizedExperiment @luhann . We appreciate it very much.

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3 participants