R-3.5.0 is installed here. When I tried to update installed packages errors were reported when their dependencies were built under a prior version of R. Reading ?update.packages() I did not see an option that would automatically update dependences built under an earlier version of R. Is there such an option that I missed? Alternatively, is there a function I can run that will rebuild all installed packages after I upgrade R versions? Regards, Rich
update.packages() after updating R version
5 messages · Rich Shepard, Bert Gunter, Duncan Murdoch
Is this warning in ?update.packages relevant? "Take care when using dependencies (passed to install.packages <http://127.0.0.1:17277/help/library/utils/help/install.packages>) with update.packages, for it is unclear where new dependencies should be installed. The current implementation will only allow it if all the packages to be updated are in a single library, when that library will be used." -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Sat, May 26, 2018 at 4:24 PM, Rich Shepard <rshepard at appl-ecosys.com> wrote:
R-3.5.0 is installed here. When I tried to update installed packages errors were reported when their dependencies were built under a prior version of R. Reading ?update.packages() I did not see an option that would automatically update dependences built under an earlier version of R. Is there such an option that I missed? Alternatively, is there a function I can run that will rebuild all installed packages after I upgrade R versions? Regards, Rich
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posti ng-guide.html and provide commented, minimal, self-contained, reproducible code.
On Sat, 26 May 2018, Bert Gunter wrote:
Is this warning in ?update.packages relevant?
Bert,
Short answer: no.
I have only a single R library here: /usr/lib/R/library.
I've tried 'install.packages("<pkgname>", dependencies = TRUE) and still
need to follow the dependencies chain down, re-install, then back up.
Thanks,
Rich
On 26/05/2018 7:24 PM, Rich Shepard wrote:
R-3.5.0 is installed here. When I tried to update installed packages
errors were reported when their dependencies were built under a prior
version of R.
Reading ?update.packages() I did not see an option that would
automatically update dependences built under an earlier version of R. Is
there such an option that I missed?
I think you want update.packages(ask = FALSE, checkBuilt = TRUE) to automatically update all packages and their dependencies. With the default checkBuilt=FALSE, R just sees whether a dependency is a high enough version number. But packages installed under R x.y.z are not usable in R x.y+1.w. Duncan Murdoch
Alternatively, is there a function I can run that will rebuild all installed packages after I upgrade R versions? Regards, Rich
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
On Sat, 26 May 2018, Duncan Murdoch wrote:
I think you want update.packages(ask = FALSE, checkBuilt = TRUE) to automatically update all packages and their dependencies. With the default checkBuilt=FALSE, R just sees whether a dependency is a high enough version number. But packages installed under R x.y.z are not usable in R x.y+1.w.
Duncan, Mea culpa! I knew of the 'ask' option but for some reason the 'checkBuilt' option did not register when I scanned the list. Yes, using the two is doing the job. There are many packages from earlier versions now being brought current. Many thanks, Rich