Guard NSE against S4Vectors parallelVectorNames() regression (#140) - #129
Closed
sa-lee wants to merge 1 commit into
Closed
Guard NSE against S4Vectors parallelVectorNames() regression (#140)#129sa-lee wants to merge 1 commit into
sa-lee wants to merge 1 commit into
Conversation
Collaborator
Author
|
Closing: fixed upstream in S4Vectors 8b236a8 (parallelVectorNames() now reads the class prototype instead of x[0L]). Verified the vanilla package passes the suite and builds the vignette on the patched S4Vectors, so the plyranges-side guard is unnecessary. Keeping the regression tests only. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fixes plyranges NSE on S4Vectors devel, where
parallelVectorNames()now lists metadata columns (Bioconductor/S4Vectors#140). This behaviour changes how mcols columns bind to the masking env i.e. named like functions (e.g.gc→base::gc();baseMean→ error), which breaksfilter/mutate/summarise/selectand the vignette build.overscope_env()(new) builds the core env from an mcols-stripped copy, then splices the correctly-bound metadata env back as parent.select_rng()core names.select.DeferredGenomicRanges()exclude names.Note: needs a DESCRIPTION version bump before release.