another helpful element -- to have an option to warn early on if the available space in R_TMPDIR value is not sufficiently large
not sure how to do that portably but perhaps there is a way On Wed, Nov 4, 2020 at 1:52 PM Martin Morgan <mtmorgan.b...@gmail.com> wrote: > 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" < > bioc-devel-boun...@r-project.org on behalf of st...@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 > the > event of concern seems relatively rare. But maybe I overestimate the > burden. > > On Wed, Nov 4, 2020 at 12:19 PM Keith Hughitt <keith.hugh...@gmail.com > > > 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]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > The information in this e-mail is intended only for the > ...{{dropped:18}} > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel