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()`). Martin On 11/4/20, 1:19 PM, "Bioc-devel on behalf of Vincent Carey" <[email protected] on behalf of [email protected]> 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 the event of concern seems relatively rare. But maybe I overestimate the burden. On Wed, Nov 4, 2020 at 12:19 PM Keith Hughitt <[email protected]> wrote: > 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 old packages for removal (e.g. outdated/haven't been used in a long time) 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
