[Bioc-devel] help with GENESIS failing build on kjohnson3

[Ivan Krylov]

Dear Stephanie Gogarten,

В Fri, 6 Mar 2026 16:22:27 -0800
Stephanie Gogarten <sdmorris using uw.edu> пишет:

> GENESIS is failing on the mac builder kjohnson3
> <https://bioconductor.org/checkResults/devel/bioc-LATEST/GENESIS/kjohnson3-buildsrc.html>
> with an error that I don't understand.

>> Error in `[.data.table`:
>> ! attempt access index 3/3 in VECTOR_ELT

>> 16. x[, `:=`("allele.index", seq_len(.N)), by = "variant.id"]
>> 17. data.table:::`[.data.table`(...)

The macOS builder 'kjohnson3' has data.table version 1.17.8 installed
[*]. The 1.17.x series was increasingly incompatible with R-devel,
which we only fixed in 1.18.0 (and then fixed again in 1.18.2.1). This
is one of those problems:
https://github.com/Rdatatable/data.table/issues/7486

Installing data.table 1.18.2.1 from CRAN on kjohnson3 should fix the
problem.

-- 
Best regards,
Ivan

[*]
https://bioconductor.org/checkResults/devel/bioc-LATEST/kjohnson3-R-instpkgs.html