I'd be interested to hear views on how and when Ubuntu users should upgrade to R 3.5.0. I made the upgrade a few days ago but reverted because of issues installing packages such as rJava, which I installed on the system with r-cran-rjava. Also any advice on how to do a clean uninstall of the previous version before making the leap greatly appreciated. Thank you. Robin [[alternative HTML version deleted]]
Hi Robin, Thanks for asking here rather than on Twitter. I am old-school and think this is a better place / more searchable / more easy to expand. On 2 May 2018 at 09:35, Robin Lovelace wrote: | I'd be interested to hear views on how and when Ubuntu users should upgrade | to R 3.5.0. | | I made the upgrade a few days ago but reverted because of issues installing | packages such as rJava, which I installed on the system with r-cran-rjava. | | Also any advice on how to do a clean uninstall of the previous version | before making the leap greatly appreciated. I guess it all depends. You really need to ensure you have no old r-cran-* packages with binary code left as that code would not load. So if in doubt, don't upgrade. Check your system, do 'dpkg -l | grep r-cran' (and/or r-bioc). Use 'apt cache policy r-cran-abc' to check on a (hypothetical) package abc. (We have RcppAPT to query apt from R too.) For Ubuntu, we opted for some flexibility by NOT imposing the r-api-3* tags. If you want, and know what you are doing, you _can_ upgrade now, use what is available as binaries (r-recommended plus some more) and then complement with local installation into /usr/local/lib/R/site-packages to complete your system. It is what I do as I tend to install a lot from CRAN directly. For Debian, we do not have that option. An upgrade will only be available once everything has been rebuilt for r-api-3.5, or else all old packages will get uninstalled -- which may not be what one wants. I would be happy to hear what others think. Jeroen already voiced his support for also making Ubuntu 'harder' to upgrade by adding the tag. I am still on the fence on that -- to me, having the flexibility seems worth the risk of shooting one's foot off -- but I may be in the minority. As a start, we can probably collect the names of a few 'harder to install' packages that should go to the new repo sooner rather than later. rJava may be one, maybe some of the database interfaces too. Maybe RQuantLib just because it is huge. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Many thanks Dirk, kind-of makes sense and I think my 'hold your horses' attitude is probably safest for now. Two follow-up questions: - Roughly how long will it be until "everything has been rebuilt"? - Could this seemingly new project help manage external deps: https://github.com/r-hub/sysreqsdb ? On Wed, May 2, 2018 at 1:23 PM, Dirk Eddelbuettel <edd at debian.org> wrote:> > Hi Robin, > > Thanks for asking here rather than on Twitter. I am old-school and think > this > is a better place / more searchable / more easy to expand. > > On 2 May 2018 at 09:35, Robin Lovelace wrote: > | I'd be interested to hear views on how and when Ubuntu users should > upgrade > | to R 3.5.0. > | > | I made the upgrade a few days ago but reverted because of issues > installing > | packages such as rJava, which I installed on the system with > r-cran-rjava. > | > | Also any advice on how to do a clean uninstall of the previous version > | before making the leap greatly appreciated. > > I guess it all depends. You really need to ensure you have no old r-cran-* > packages with binary code left as that code would not load. > > So if in doubt, don't upgrade. > > Check your system, do 'dpkg -l | grep r-cran' (and/or r-bioc). Use 'apt > cache policy r-cran-abc' to check on a (hypothetical) package abc. (We > have > RcppAPT to query apt from R too.) > > For Ubuntu, we opted for some flexibility by NOT imposing the r-api-3* > tags. If you want, and know what you are doing, you _can_ upgrade now, use > what is available as binaries (r-recommended plus some more) and then > complement with local installation into /usr/local/lib/R/site-packages to > complete your system. It is what I do as I tend to install a lot from CRAN > directly. > > For Debian, we do not have that option. An upgrade will only be available > once everything has been rebuilt for r-api-3.5, or else all old packages > will > get uninstalled -- which may not be what one wants. > > I would be happy to hear what others think. Jeroen already voiced his > support for also making Ubuntu 'harder' to upgrade by adding the tag. I am > still on the fence on that -- to me, having the flexibility seems worth the > risk of shooting one's foot off -- but I may be in the minority. > > As a start, we can probably collect the names of a few 'harder to install' > packages that should go to the new repo sooner rather than later. rJava may > be one, maybe some of the database interfaces too. Maybe RQuantLib just > because it is huge. > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >[[alternative HTML version deleted]]
On Wed, May 2, 2018 at 10:35 AM, Robin Lovelace <rob00x at gmail.com> wrote:> I'd be interested to hear views on how and when Ubuntu users should upgrade > to R 3.5.0. > I made the upgrade a few days ago but reverted because of issues installing > packages such as rJava, which I installed on the system with r-cran-rjava.My strategy will be to jump to R 3.5 when I upgrade my servers to Ubuntu Bionic in a few weeks (will probably do a clean install). Currently c2d4u has pretty great coverage of CRAN binaries for Xenial (and Trusty) so I will stick with Xenial + R 3.4 for now.>From activity on launchpad it looks like c2d4u-3.5 is currentlyfocussing on Ubuntu Bionic, which is great because that will give us a clean path forward. Hopefully in a few weeks from now, most r-cran packages will be there so we can upgrade to Bionic and R3.5 at the same time.> Also any advice on how to do a clean uninstall of the previous version > before making the leap greatly appreciated.Due to the missing api tags, I think it will be very difficult to automatically determine which r-cran packages you can keep. If you really need to upgrade you probably want to purge r-cran-* and r-base-* and reinstall from the new ppa.
On 3 May 2018 at 13:21, Jeroen Ooms wrote: | On Wed, May 2, 2018 at 10:35 AM, Robin Lovelace <rob00x at gmail.com> wrote: | > I'd be interested to hear views on how and when Ubuntu users should upgrade | > to R 3.5.0. | > I made the upgrade a few days ago but reverted because of issues installing | > packages such as rJava, which I installed on the system with r-cran-rjava. | | My strategy will be to jump to R 3.5 when I upgrade my servers to | Ubuntu Bionic in a few weeks (will probably do a clean install). | Currently c2d4u has pretty great coverage of CRAN binaries for Xenial | (and Trusty) so I will stick with Xenial + R 3.4 for now. | | >From activity on launchpad it looks like c2d4u-3.5 is currently | focussing on Ubuntu Bionic, which is great because that will give us a | clean path forward. Hopefully in a few weeks from now, most r-cran | packages will be there so we can upgrade to Bionic and R3.5 at the | same time. c2d4u3.5 looks great! But for Travis we will also need trusty aka 14.04 :-/ | > Also any advice on how to do a clean uninstall of the previous version | > before making the leap greatly appreciated. | | Due to the missing api tags, I think it will be very difficult to | automatically determine which r-cran packages you can keep. If you | really need to upgrade you probably want to purge r-cran-* and | r-base-* and reinstall from the new ppa. Maybe the interfaces to the package systems can help: ie update.packages() has 'checkbuilt' option may be useful. On the Linux side I added a few queries to the RcppAPT package, so it can tell you which packages depend on older R versions like 3.4.* (or older). Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org