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

[Shepherd, Lori]

We always check newly submitted packages against the latest or devel branch of Bioconductor as this will be the suite of packages that it needs to be compatible with for dependencies.  Depending on the time of year that branch is either the latest release version of R  or R devel.  We are currently using R-devel in preparation for their next release next month for R 3.6.

http://bioconductor.org/developers/how-to/useDevel/


So using R 3.6 is a requirement or at least it has to be compatible on our builders.



Next -  if the install.package code is in your R code, vignettes, examples, or test code.  Please remove it.  These are not encouraged directly in package code and are controlled with the dependencies lists in the DESCRIPTION and the NAMESPACE.  You should simple to the library call in the vignettes, example, or test code  and  the functions should be recognized in R code if they were specified in the NAMESPACE (or you can use the :: to indicate functions from another package).


Next -  Yes AnnotationHub resources from 3.8  should be available in 3.9.  The only reason they are generally not available is if they were deprecated, defunct, or replaced. In this case the file for

path_to_transcriptome <- ah_transcriptomes[["AH49057"]]$path

was marked as defunct because there were major updates to Rsamtools and the rzzip format that these files were in were no longer supported.  These were from older ensembl releases as well as we have not provided the FaFile format for a few years. There are updated resources as twobit and gtf files that hopefully will be sufficient. For ensembl 95 :


> query(ah,c("Ensembl", "Caenorhabditis elegans", "95"))
AnnotationHub with 7 records
# snapshotDate(): 2019-02-19
# $dataprovider: Ensembl
# $species: Caenorhabditis elegans
# $rdataclass: TwoBitFile, GRanges, EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH67916"]]'

            title
  AH67916 | Ensembl 95 EnsDb for Caenorhabditis elegans
  AH68081 | Caenorhabditis_elegans.WBcel235.cdna.all.2bit
  AH68082 | Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.2bit
  AH68083 | Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.2bit
  AH68084 | Caenorhabditis_elegans.WBcel235.ncrna.2bit
  AH68713 | Caenorhabditis_elegans.WBcel235.95.abinitio.gtf
  AH68714 | Caenorhabditis_elegans.WBcel235.95.gtf

You can always check the status of a record with recordStatus

> ah = AnnotationHub()

> recordStatus(ah, "AH49057")

   record  status
1 AH49057 Defunct

http://bioconductor.org/packages/devel/bioc/vignettes/AnnotationHub/inst/doc/AnnotationHub-HOWTO.html#ensembl-gtf-and-fasta-files-for-txdb-gene-models-and-sequence-queries



Please feel free to ask any additional questions.  It might also help to ask on your submission issue as your reviewer could also answer other questions as well.


Cheers,




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Julien Wollbrett <julien.wollbrett using unil.ch>
Sent: Wednesday, March 13, 2019 4:51:25 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] Which version of R for a new package

Hello,

I created a package and submitted it to Bioconductor but I have a build
error.
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

http://bioconductor.org/spb_reports/BgeeCall_buildreport_20190312133742.html

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 :

http://bioconductor.org/spb_reports/BgeeCall_buildreport_20190312124437.html

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

the error comes from these lines :

BiocManager::install("AnnotationHub", version = "3.8")
library(AnnotationHub)
ah <- AnnotationHub()
ah_annotations <- query(ah, c("GTF","Ensembl", "Caenorhabditis elegans",
"Caenorhabditis_elegans.WBcel235.84"))
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
3.9?

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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