R help - May 2018 - update.packages() after updating R version

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

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.
>
	[[alternative HTML version deleted]]

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