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

3 messages · Stephanie Gogarten, Ivan Krylov, Shepherd, Lori

Original
Stephanie Gogarten
# 
Hi,

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. It is passing on linux, as well as
every system (including macOS) on R universe
<https://bioc.r-universe.dev/GENESIS#checktable>. I don't know how to
proceed here, as I can't reproduce the error. Can anyone offer guidance? Is
there a chance that passing the R universe builds will be sufficient for
inclusion in the next Bioonductor release?

thanks,
Stephanie Gogarten
Ivan Krylov
# 
Dear Stephanie Gogarten,

? Fri, 6 Mar 2026 16:22:27 -0800
Stephanie Gogarten <sdmorris at uw.edu> ?????:
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.
10 days later
Shepherd, Lori
# 
Kjohnson3 has the updated data.table.  The issue is the missing reverse dependencies.  It looks like its stemming from the error in gdsfmt, that prevents the other packages from being available. When gdsfmt is available this should resolve.



Lori Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263