[R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04

[Neal Fultz]

In the past, I've extracted the pre-built debian packages into the user's
personal folder, instead of installing them via apt. It worked (but it was
not fun), and was pretty manual.  That might interact a bit better with
some of the third party tools for dealing with dependencies in shiny apps,
compared to system-wide installs; ymmv.

On Wed, Aug 9, 2023 at 8:00 AM Thomas Petzoldt <
thomas.petzoldt using tu-dresden.de> wrote:

> Hi Dirk,
>
> thank you very much dirk for the quick response. I was aware that
> r-package-devel may not be the optimal place ;-) but hoped to address
> the right audience between r-devel and r-help.
>
> Many thanks also for the suggestions, especially r2u and sorry for
> confusing the name of Michael.
>
> Thomas
>
> Am 09.08.2023 um 16:41 schrieb Dirk Eddelbuettel:
> > On 9 August 2023 at 16:26, Thomas Petzoldt wrote:
> > | I am running a couple of  shiny servers with several apps that are
> based
> > | around own CRAN packages. It worked stable for years, but due to the
> > | growing number of packages, the compile time for regular manual package
> > | installation and updates became inconvenient.
> > |
> > | Therefore, I have been very happy to use pre-compiled packages from the
> > | c2d4u repository: deb
> > | https://ppa.launchpadcontent.net/c2d4u.team/c2d4u4.0+/ubuntu/ jammy
> main
> >
> > These days you also have r2u which has all of CRAN ie 20k binaries
> (each, for
> > two Ubuntu flavors). See  https://eddelbuettel.github.io/r2u
> >
> > | This is indeed a great service, thanks to Dirk Edelbuettel, mark Rutter
> >
> > That would be Michael Rutter.
> >
> > | and the complete team! The downside is, that now the r-cran-* binaries
> > | are installed automatically, together with the system update. I
> > | experienced now repeated cases that crashed some of the shiny apps,
> > | mainly due to conflicts between the binary packages and other packages
> > | installed from sources.
> >
> > If you use r2u (as I do on a laptop, an ec2 server, all my CI testing for
> > work and testing for months now) you get all packages and do not need to
> > mix.  Try r2u, it's good.
> >
> > | My question: what is best practise, to disallow automatic updates for
> > | all r-cran-* packages? Uncommenting the complete package source in the
> > | apt/sources.list.d/cd4u...list file? Fiddling around with
> > | /etc/apt/preferences ?
> > |
> > | The ideal approach would be to put a plain textfile of all installed
> > | r-cran packages somewhere to the system, where packages that are to be
> > | upgraded (or oppositely: pinned) are just commented or outcommented.
> >
> > That is very Debian / Ubuntu specific question.  Can I ask you to bring
> it to
> > the dedicated list r-sig-debian ?
> >
> >  From the top of my head I can think of setting package status 'hold' (a
> > simpler per-package approach) or setting specific apt pinning values to
> not
> > alter packages from specific repos, see the manual pages.
> >
> > But please ask on r-sig-debian. This list is for generic R packaging
> questions.
> >
> > Thanks, Dirk
>
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