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[Bioc-devel] BiocManager and local Bioconductor mirror

3 messages · Rainer Johannes, Martin Morgan

Original
Rainer Johannes
# 
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
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
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
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 at r-project.org on behalf of Johannes.Rainer at 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
    
    _______________________________________________
    Bioc-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/bioc-devel
Martin Morgan
# 
Let's continue this on github at https://github.com/Bioconductor/BiocManager/issues/31
?On 11/8/18, 6:31 AM, "Martin Morgan" <mtmorgan.bioc at gmail.com> wrote:
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 at r-project.org on behalf of Johannes.Rainer at 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
        
        _______________________________________________
        Bioc-devel at r-project.org mailing list
        https://stat.ethz.ch/mailman/listinfo/bioc-devel