Let's continue this on github at
https://github.com/Bioconductor/BiocManager/issues/31
On 11/8/18, 6:31 AM, "Martin Morgan" <mtmorgan.b...@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-boun...@r-project.org on behalf of johannes.rai...@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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