On Sun, May 13, 2018 at 9:30 AM, Dirk Eddelbuettel <e...@debian.org> wrote:
> > On 13 May 2018 at 09:03, Bill Harris wrote: > | > | safest way to go. Does something like this make sense: > | > | > | 1. aptitude safe-upgrade should be safe: there won't be any 3.5.0 > Debian > | packages coming through until the environment is ready for them to > come > | through (which most likely means that base R and other Stretch R > packages > | are upgraded to 3.5.0?).. > > Unsure. > > You did not specify if you look only at Debian distro repositories, or if > you > include the backports managed by Johannes (which should be safe he plays > along with the r-api-3.5 tag). > Here is my complete sources.list: # # deb cdrom:[Official Debian GNU/Linux Live 9.1.0 gnome 2017-07-23T04:21]/ stretch main #deb cdrom:[Official Debian GNU/Linux Live 9.1.0 gnome 2017-07-23T04:21]/ stretch main deb http://ftp.us.debian.org/debian/ stretch main non-free contrib deb-src http://ftp.us.debian.org/debian/ stretch main non-free contrib deb http://security.debian.org/debian-security stretch/updates main contrib non-free deb-src http://security.debian.org/debian-security stretch/updates main contrib non-free # stretch-updates, previously known as 'volatile' deb http://ftp.us.debian.org/debian/ stretch-updates main contrib non-free deb-src http://ftp.us.debian.org/debian/ stretch-updates main contrib non-free ## R https://cran.r-project.org/ ## deb https://cran.cnr.berkeley.edu/bin/linux/debian stretch-cran34/ deb http://cran.wustl.edu/bin/linux/debian stretch-cran34/ I'll be glad to take advice. > > | 2. update.packages() inside R is /not/ safe, because it could pick up > | problematic packages from CRAN that aren't under your control. > > I actually take the opposite view. > > I am comfortable compiling from source, so this mode happens to be my > default. I use the littler scripts install.r and update.r _all the time_ to > install / update. > > I think I reasoned through to that once, and then I forgot. so install.packages() and update.packages() is safe; aptitude safe-upgrade may or may not be safe, depending upon what you see in my sources-list. Right? > | 3. install.packages() inside R is /not/ safe, for the same reason. > > That seems to be the same as 2. so ... > > | 4. A prominent note will be posted here, when these two restrictions > are > | removed. > | > | Are those true statements? Would steps 2 and 3 work if the packages > don't > | require compiled C++ code? If so, is there a way to tell which packages > | are at risk without memorizing what seems like a very long list? > | > | If we (think we) need a new package we don't currently have installed, > are > | we out of luck until 3.5.0 is officially released in Stretch? > > Again, "pure Debian" or "Debian plus CRAN repos" ? > In addition to what you see in my sources.list, I've also installed a few packages from github or similat (hydromad comes to mind). Perhaps the CRAN package that might test all this the most is rstan. I'm okay if a small number of github packages--or any packages, for that matter--fail; I just would rather not do something that makes a /lot/ of extra work if I could avoid it. > > | Is there a place where an official summary of the state of the R system > on > | Stretch is maintained? > | > | I've tried to scan this list, but I may well have missed the answers to > my > | questions about Stretch. > > We're volunteers so something may always fall short somewhere. > Documentation > is always a good candidate. Contributions are always welcome. > > I'll keep that in mind. > Thanks, Bill [[alternative HTML version deleted]] _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
