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csoneson
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I think this was caused by a regression in S4Vectors, and seems to be fixed by Bioconductor/S4Vectors@8b236a8 and Bioconductor/S4Vectors@721733a. However, I don't see an issue with using [ instead of subset() either.
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The current unit tests on the Bioc builders are failing on all tested platforms, see for example:
https://bioconductor.org/checkResults/devel/bioc-LATEST/eisaR/kjohnson3-checksrc.html
I could not figure out why
subset(GRanges, type == "exon")suddenly fails, but found a simple workaround by using the bracket operator instead.At the same time, I fixed some additional notes.