[Bioc-devel] BiocManager and local Bioconductor mirror

[Martin Morgan]

I'm not sure why this does not work.

The key is BiocManager::repositories(), which determines the repositories where R looks for packages. R choose the first repository where it finds the package (maybe of equivalent version, not exactly sure...). The first argument to repositories() can be a site repository, so

> BiocManager::repositories("https://ima.repo")
                                        site_repository
                                     "https://ima.repo"
                                               BioCsoft
           "https://bioconductor.org/packages/3.9/bioc"
...

The Bioc repositories themselves are based on getOption("BioC_mirror") and getOption("repos"), so 

> options(BioC_mirror = "https://a.mirror.org")
> BiocManager::repositories()
                                           BioCsoft
           "https://a.mirror.org/packages/3.9/bioc"
                                            BioCann
"https://a.mirror.org/packages/3.9/data/annotation"
...

These can be file paths; we are just delegating to install.packages().

It sounds like this doesn't work, somehow for you. Can you elaborate?

Martin

On 11/8/18, 6:13 AM, "Bioc-devel on behalf of Rainer Johannes" <bioc-devel-bounces using r-project.org on behalf of Johannes.Rainer using eurac.edu> wrote:

    Dear all,
    
    I like the new BiocManager package with its new possibilities to install specific versions of Bioconductor - but what I miss is the possibility to specify a local Bioconductor mirror from which to install packages. 
    Our calculation clusters don't have direct internet access, so I am mirroring CRAN and Bioconductor to local folders that are accessible by the cluster. Previously, with BiocInstaller and biocLite.R, I could install packages from these simply setting options(repos = "<path to local CRAN dir>") and options(BioC_mirror = "<path to local BioC dir>"). Now, with BiocManager this does no longer work. Is it possible to specify a local mirror for BiocManager? And if not - would it be possible to add this possibility?
    
    thanks!
    
    jo
    
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