GenomicRanges::union fails on R devel
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@guillaume-devailly-8722
Last seen 5 days ago
Toulouse, France

Hello,

I'm preparing for a new package submission to Bioconductor. I have some Continuous Integration through GitHub Action that are failing on R devel (4.2.0), but running fine on R release (4.1.1).

The issue seems to be with with GenomicRanges::union(), i.e. :

library(GenomicRanges)    
x <- GRanges("chr1", IRanges(c(2, 9) , c(7, 19)), strand=c("+", "-"))
y <- GRanges("chr1", IRanges(5, 10), strand="-") 
union(x, y)
#> Error in ..Internal(is.unsorted(x, FALSE)) : 
#>    2 arguments passed to .Internal(is.unsorted) which requires 3

What should/can I do about it? Should I proceed with my bioconductor submission? Wait a few days for the issue to be fixed by others?

Here's how to reproduce the issue, assuming you have docker:

docker run -e PASSWORD=password -p 8787:8787 --rm -ti rocker/tidyverse:devel

Then connect to http://localhost:8787 (login: rstudio: password: password) and:

remotes::install_bioc("GenomicRanges")
library(GenomicRanges)
x <- GRanges("chr1", IRanges(c(2, 9) , c(7, 19)), strand=c("+", "-"))
y <- GRanges("chr1", IRanges(5, 10), strand="-") 

union(x, y)
devel GenomicRanges • 359 views
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Mike Smith ★ 5.5k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg / de.NBI

Currently the Bioconductor devel branch uses the release version of R (R-4.1.x), so you don't need to worry about this issue for now. If you like using Docker for testing it might be worth using the Bioconductor Docker images that are built on rocker at https://hub.docker.com/r/bioconductor/bioconductor_docker You can use the devel tag for Bioconductor 3.14.

As an aside, package development questions are best submitted to the devel mailing list at https://stat.ethz.ch/mailman/listinfo/bioc-devel . You'll have to register there as part of the submission too.

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Great, thank you for the explanations!

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