setDT() works on S4 slots (again), and := works in under-allocated S4 slots #6703
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MichaelChirico
changed the title
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #6703 +/- ##
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Coverage 98.61% 98.61%
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Files 79 79
Lines 14553 14561 +8
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+ Hits 14352 14360 +8
Misses 201 201 ☔ View full report in Codecov by Sentry. |
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Generated via commit eeeb61c Download link for the artifact containing the test results: ↓ atime-results.zip
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MichaelChirico
changed the title
tdhock
reviewed
Jan 6, 2025
| @@ -3048,6 +3052,9 @@ rleidv = function(x, cols=seq_along(x), prefix=NULL) { | |||
| is.name(e[[1L]]) && is.name(e[[2L]]) # e.g. V1:V2, but not min(V1):max(V2) or 1:max(V2) | |||
| } | |||
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| # for assignments like x[[1]][, a := 2] or setDT(x@DT) | |||
| .is_simple_extraction = function(e) e %iscall% c('$', '@', '[[') && is.name(e[[2L]]) | |||
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great thanks for adding this helper fun
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lgtm but I don't really use S4 very often... |
nor do i... basically relying on sandboxing, existing tests, and revdeps here. |
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Closes #6701 (and possibly #6575). Closes #6704.
Lumped together because of #6702 -- really this should be one small change fixing both places. After #6702 it will only be possible for a bug to affect both call sites of
.is_simple_extraction().I'm not totally clear what broke exactly -- something about the change to
.shallow()broke assignment back to an S4 slot.On a side note, I'm not totally clear this should be allowed in the first place -- it really bends S4 semantics IMO.
For example, if we try and pass a
data.tableto a class's slot which is declared asdata.frame, S4 will coerce it to data.frame:Glancing at the one downstream I debugged, personally I think they should change the code:
https://github.com/HimesGroup/snpsettest/blob/38d5b86217fcd9061e3714bf911eb4ffb36ea1b3/R/harmonize_sumstats.R#L83-L88
setDT()there is having global effects perhaps unintentionally. Something likesnps = as.data.table(x@snps)seems more appropriate.Anyway, that's a thought for another day.