Re: Conflict between R 4.5 and Bioc 3.20

[Dirk Eddelbuettel <edd@debian.org>]

On 17 April 2025 at 14:43, Charles Plessy wrote:
| I just noticed that r-base 4.5.0-1 cannot migrate to Trixie because it breaks
| Bioconductor 3.20, which was developed and tested upstream against R 4.4.3.

Are you really there is actual 'breakage' in any of the packages in 3.20?

While they were built under R 4.4.3 they continue to work with R 4.5.0 as there
is no API / ABI change.

You can easily test that under the r-base Docker container which already has
R 4.5.0 and points at testing/unstable as usual. I just ran 'apt update -qq;
apt install r-bioc-alabaster.sce' and it of course loads as expected. [1]

I also usually mix and match on my own box and don't immediately update to
new BioC there and never had issues. So I am not sure the situation is as
dire as you say.

Dirk

[1] Quick log

> search()
 [1] ".GlobalEnv"                   "package:alabaster.sce"       
 [3] "package:alabaster.base"       "package:SingleCellExperiment"
 [5] "package:SummarizedExperiment" "package:Biobase"             
 [7] "package:GenomicRanges"        "package:GenomeInfoDb"        
 [9] "package:IRanges"              "package:S4Vectors"           
[11] "package:BiocGenerics"         "package:stats4"              
[13] "package:MatrixGenerics"       "package:matrixStats"         
[15] "package:stats"                "package:graphics"            
[17] "package:grDevices"            "package:utils"               
[19] "package:datasets"             "package:methods"             
[21] "Autoloads"                    "package:base"                
> getRversion()
[1] ‘4.5.0’
> system("cat /etc/debian_version")
trixie/sid
> 


-- 
dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org