[Bioc-devel] Which version of R for a new package

Julien Wollbrett ju||en@wo||brett @end|ng |rom un||@ch
Wed Mar 13 09:51:25 CET 2019


I created a package and submitted it to Bioconductor but I have a build
Bioconductor 3.9 requires R version 3.6 and for the moment I only have
version 3.5.2 on my computer.
In the vignette of my package I use AnnotationHub 3.8 to load one fasta
file and one gtf file.
I have no error when I build the package in my computer but I have this
error when the package is build on Bioconductor


Isn't it possible to use AnnotationHub from Bioconductor 3.8 on a
package present in Bioconductor 3.9 ?
I also tried to use the AnnotationHub from Bioconcudtor 3.9 but I have
an other error :


This error is not verbose enough to help me to understand it.

the error comes from these lines :

BiocManager::install("AnnotationHub", version = "3.8")
ah <- AnnotationHub()
ah_annotations <- query(ah, c("GTF","Ensembl", "Caenorhabditis elegans",
annotation_object <- ah_annotations[["AH50789"]]
ah_transcriptomes <- query(ah, c("FaFile","Ensembl", "Caenorhabditis
elegans", "Caenorhabditis_elegans.WBcel235"))
path_to_transcriptome <- ah_transcriptomes[["AH49057"]]$path

The best idea is probably to donwload the same R version on my computer
than the one used to build packages in Bioconductor 3.9.
As far as I know the last stable version of R is the 3.5.3.
So could you tell me which beta version of R 3.6 is used in Bioconductor

It is the first package I submit to Bioconductor and I am a bit lost. So
any suggestion is welcome :-).

Thank you for your help.

Best regards,

Julien Wollbrett

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