repos argument not kept

[LiNk-NY]

I am using BiocManager for managing the installation of packages. I would like to make use of both bspm for CRAN packages and BiocManager for Bioconductor packages.

It seems that bspm::enable() shim does not keep the input's repos argument, seen at https://github.com/Enchufa2/bspm/blob/5d9f5f1b786807efa7c249dd81ddedd18579b33d/R/integration.R#L53 leading to the error below.

> BiocManager::repositories()
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest

                                                        BioCsoft 
                   "https://bioconductor.org/packages/3.16/bioc" 
                                                         BioCann 
        "https://bioconductor.org/packages/3.16/data/annotation" 
                                                         BioCexp 
        "https://bioconductor.org/packages/3.16/data/experiment" 
                                                   BioCworkflows 
              "https://bioconductor.org/packages/3.16/workflows" 
                                                       BioCbooks 
                  "https://bioconductor.org/packages/3.16/books" 
                                                            CRAN 
"https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" 
> install.packages("BSgenome", repos = BiocManager::repositories())
[truncated]
Available system packages...

Error in dbs[bins, "Version"] : subscript out of bounds

[Enchufa2]

Thanks for the report. Could you please try the fix in the fix/51 branch?

[Enchufa2]

This is with @eddelbuettel's r2u docker image:

> install.packages("BSgenome", repos = BiocManager::repositories())
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org

Available system packages as root...

  There are binary versions available but the source versions are later:
                 binary source
BSgenome         1.66.1 1.66.2
GenomeInfoDb     1.34.4 1.34.6
GenomicRanges    1.50.1 1.50.2
GenomeInfoDbData  1.2.8  1.2.9
BiocParallel     1.32.4 1.32.5

Do you want to install later versions from sources? (Yes/no/cancel)

[Enchufa2]

If no further issues, I'll merge #52 and roll a patch release to CRAN.

[LiNk-NY]

Thanks for the quick fix @Enchufa2 It looks good!

I'm not sure why I get a different version of BSgenome under the binary column. Is this due to the version of R that I am using (R 4.2.1)?

 There are binary versions available but the source versions are later:
                        binary    source
BSgenome                1.62.0    1.66.2

With the container (using R 4.2.2) I can see the versions that you have above.

Note. For binary generation, it would be best to use the packages that are restricted and defined by BiocManager so to avoid 'old' binaries in the binary column shown here (which is incompatible with R 4.2.1; it's an R 4.1.0 package).

[Enchufa2]

What's your OS version and what repo are you using for the binaries? That's probably the difference.

[LiNk-NY]

I am using:

$ lsb_release -a
Distributor ID: Ubuntu
Description:    Ubuntu 22.04.1 LTS
Release:    22.04
Codename:   jammy

> dbb <- bspm::available_sys()
> dbb[rownames(dbb) == "bsgenome", ]
   Package    Version Repository 
"bsgenome"   "1.62.0"   "Ubuntu" 

> packageVersion("bspm")
[1] '0.4.0.1'

I guess I'm using these repos in:

sources.list.d/

deb https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu/ jammy main

sources.list

deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/

[Enchufa2]

The repo is the difference then. The docker image above uses r2u instead.