[Bioc-devel] Would it make sense for BiocManager::install to cache downloaded packages?

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Wed Nov 4 19:52:24 CET 2020

FWIW BiocManager::install() really delegates to install.packages(). The packages are downloaded to 'destdir=' as documented on ?install.packages -- typically file.path(tempdir(), "downloaded_packages") -- and one path to  troubleshooting installs is to tackle the problematic installation(s) using `install.packages(pkgs_in_downloaded_packages, repos = NULL)`, where pkgs_in_downloaded_packages are the packages that have failed to install on first pass.

It does seem like this would be a reasonable feature for base R, that we could inherit, so one could ask on R-devel or submit a bug report / feature request (e.g., via `bug.report()`).


On 11/4/20, 1:19 PM, "Bioc-devel on behalf of Vincent Carey" <bioc-devel-bounces using r-project.org on behalf of stvjc using channing.harvard.edu> wrote:

    I certainly have run into this situation with R generally.  It seems like a
    patch to
    install.packages would be the best approach to introduce this
    functionality.  I wonder
    if Henrik Bengtsson or Dirk Eddelbuettel have pondered this.

    In any case, I am sympathetic with the suggestion but I believe this has to
    be done
    and tested outside the core developer team -- resources are too scant, and
    event of concern seems relatively rare.  But maybe I overestimate the

    On Wed, Nov 4, 2020 at 12:19 PM Keith Hughitt <keith.hughitt using gmail.com>

    > Sometimes I will go to update a machine / do a clean Bioconductor install
    > and a large number of packages will need to be downloaded.
    > If something goes wrong during the installation, which is not uncommon in
    > cases where the number of packages being installed is large, then the
    > process has to be restarted and the packages re-downloaded all-over again.
    > Often, it may take some trial-and-error to fix the problem preventing the
    > install from completing, the result of which is that you may end up
    > re-downloading 50+ packages several times.
    > Would it perhaps make sense for BiocManager to download packages/checksums
    > to somewhere like "~/.cache/bioc/pkg" so that they could be re-used during
    > future installs?
    > Obviously, it would be good for BiocManger to have some ability to suggest
    > old packages for removal (e.g. outdated/haven't been used in a long time)
    > to avoid filling up people's hard-drives.
    > Another possibility would be to build on top of the work done by renv,
    > which already has a very nice caching system.
    > In any case, it seems like it would be something (relatively)
    > straight-forward to implement that would save a lot of bandwidth and time
    > for users.
    > Just a thought..
    > Keith
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