R help - Apr 2020 - Automating package updates after major version change

After upgrading from -3.6.2 to -4.0.0 I ran 'update.packages()' and
spent
time rebuilding dependencies, too. Is there a script or method that
automates package updates after a major version change in R?

My web searches on this topic found tips for only regular package updates
without rebuilding multiple dependencies.

TIA,

Rich

?install.packages  (argument dependencies)
which is explicitly  pointed to by ?update.packages

"Warning

Take care when using dependencies (passed to 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 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 Sun, Apr 26, 2020 at 9:00 AM Rich Shepard <rshepard at appl-ecosys.com>
wrote:
>
> After upgrading from -3.6.2 to -4.0.0 I ran 'update.packages()' and
spent
> time rebuilding dependencies, too. Is there a script or method that
> automates package updates after a major version change in R?
>
> My web searches on this topic found tips for only regular package updates
> without rebuilding multiple dependencies.
>
> TIA,
>
> 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 Sun, 26 Apr 2020, Bert Gunter wrote:
> ?install.packages  (argument dependencies)
> which is explicitly  pointed to by ?update.packages
>
> "Warning
>
> Take care when using dependencies (passed to 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,

Thank you. I'll read both help pages to better understand applying them to
unknown dependencies. Here, they're all in one library as I'm the only
user.

Regards,

Rich

Not so coincidentally, I just worked thru this for myself.

I did want to rebuild and reinstall everything, but as automatically
as possible, although in a way that let me see what happened and what
went wrong.

http://numberwright.com/2020/04/clean-and-new/

There are several things to consider: CRAN packages (easy), GitHub
packages (less easy), and random other packages (require manual
intervention).

I'm sure there are other possible workflows.

Sarah

On Sun, Apr 26, 2020 at 12:00 PM Rich Shepard <rshepard at
appl-ecosys.com> wrote:
>
> After upgrading from -3.6.2 to -4.0.0 I ran 'update.packages()' and
spent
> time rebuilding dependencies, too. Is there a script or method that
> automates package updates after a major version change in R?
>
> My web searches on this topic found tips for only regular package updates
> without rebuilding multiple dependencies.
>
> TIA,
>
> Rich
>

-- 
Sarah Goslee (she/her)
http://www.numberwright.com

A package on github called yamlpack appears to do a lot of the work
involved. I can't vouch for it personally.

https://github.com/combiz/yamlpack

On Sun, Apr 26, 2020 at 1:12 PM Sarah Goslee <sarah.goslee at gmail.com>
wrote:
> Not so coincidentally, I just worked thru this for myself.
>
> I did want to rebuild and reinstall everything, but as automatically
> as possible, although in a way that let me see what happened and what
> went wrong.
>
> http://numberwright.com/2020/04/clean-and-new/
>
> There are several things to consider: CRAN packages (easy), GitHub
> packages (less easy), and random other packages (require manual
> intervention).
>
> I'm sure there are other possible workflows.
>
> Sarah
>
> On Sun, Apr 26, 2020 at 12:00 PM Rich Shepard <rshepard at
appl-ecosys.com>
> wrote:
> >
> > After upgrading from -3.6.2 to -4.0.0 I ran
'update.packages()' and spent
> > time rebuilding dependencies, too. Is there a script or method that
> > automates package updates after a major version change in R?
> >
> > My web searches on this topic found tips for only regular package
updates
> > without rebuilding multiple dependencies.
> >
> > TIA,
> >
> > Rich
> >
>
>
> --
> Sarah Goslee (she/her)
> http://www.numberwright.com
>
> ______________________________________________
> 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.
>

-- 
Patrick S. Malone, Ph.D., Malone Quantitative
NEW Service Models: http://malonequantitative.com

He/Him/His

	[[alternative HTML version deleted]]

On Sun, 26 Apr 2020, Sarah Goslee wrote:
> Not so coincidentally, I just worked thru this for myself.
Thanks, Sarah.

Stay well,

Rich

On Sun, 26 Apr 2020, Sarah Goslee wrote:
> Not so coincidentally, I just worked thru this for myself.
> http://numberwright.com/2020/04/clean-and-new/
Sarah,

This isn't working for me on Slackware-14.2/x86_64. My R library is in
/usr/lib64/R/library/ and I copied the contents to a text file, one package
per line.

Using the filename, packagelist, as an argument to install.packages()
fails:
> install.packages(packagelist)
Error in install.packages(packagelist) : object 'packagelist' not found

Adding quotes didn't help.

Creating a script, newversionupdate.R, containing the line,
install.packages(packagelist)

and sourcing it also failed.

What might I be doing incorrectly?

Regards,

Rich