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adw96 / DivNet

diversity estimation under ecological networks
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'glue::collapse' is deprecated. Use 'glue_collapse' instead. #18

Closed jvhagey closed 5 years ago

jvhagey commented 5 years ago

When running the following; simplifyBeta(dv_ps_locB, ps, "bray-curtis", "Sample_Type")

I get the following warning: Error: Unknown columns 282, 283, 284, 285, 286 and ... In addition: Warning message: 'glue::collapse' is deprecated. Use 'glue_collapse' instead. See help("Deprecated") and help("glue-deprecated").

While trying to sort out the "Error: Unknown columns 282, 283, 284, 285, 286 and ..." part of the error, which I think is a separate issue, I discovered that the glue package has a deprecated function. Version 1.2.0 of glue uses "collapse" and glue 1.3.0 uses "glue_collapse".

Don't know that its an urgent issue at the moment as the code still ran, but just FYI.

adw96 commented 5 years ago

Thanks so much for letting us know, Jill! @bryandmartin is travelling at the moment but I'll ask him to look into this when he is back next week.

@bryandmartin It looks like it should be an easy fix (renaming collapse to glue_collapse) but we will want to do some unit tests to make sure. If we don't have a unit test that captures this could you write one? Thanks!

bryandmartin commented 5 years ago

I think this is a phyloseq issue, and I tested it again and it is working for me. Are you still getting this issue @jvhagey ?

jvhagey commented 5 years ago

@adw96 @bryandmartin Sorry, for the late reply. The error message comes when using R 3.5.0, DivNet_0.3.0 and breakaway_4.6.7. After updating R to 3.5.2, DivNet_0.3.1 and breakaway_4.6.8 the error message isn't there so looks like its all good now.

adw96 commented 5 years ago

Thanks for getting back to us, Jill! Glad to see we've hopefully resolved the issue but let us know if you find it again! I will close this issue for now.