Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04
On 11 August 2023 at 07:54, Thomas Petzoldt wrote: | After moving this discussion to R-SIG-Debian | (https://stat.ethz.ch/pipermail/r-sig-debian/2023-August/thread.html), | Dirk Eddelbuettel suggested five different approaches. | | I made indeed a snapshot (a local copy) of the complete "site-library" | folder to another place of the file system (e.g. | "site-library-snapshot"). In the .Renviron file of the shiny user, the | environment variable R_LIBS_USER then points to this location. The base | packages from "library" are conservative, so I decided to use them from | the original position. | | Finally, an rmarkdown script provided by the shiny-server can report the | value of .libPaths() and versions and locations of installed packages: | | installed.packages()[,2:3] | | This works well, except for a package that contained relative symbolic | links to the file system. Perfect, and thanks for reporting back. One other exception would be 'bad' packages with a hard code installation path (via rpath or install_name_tool) but luckily CRAN outlaws that so it should be rare (but 'been there, done that' and had to fix a package or two of mine). In short, 'should work most of the time as described here'. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04
On 10.08.2023 at 17:56 Neal Fultz wrote: 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. Thank you for the suggestion. My implemented approach works indeed similar to this. After moving this discussion to R-SIG-Debian (https://stat.ethz.ch/pipermail/r-sig-debian/2023-August/thread.html), Dirk Eddelbuettel suggested five different approaches. I made indeed a snapshot (a local copy) of the complete "site-library" folder to another place of the file system (e.g. "site-library-snapshot"). In the .Renviron file of the shiny user, the environment variable R_LIBS_USER then points to this location. The base packages from "library" are conservative, so I decided to use them from the original position. Finally, an rmarkdown script provided by the shiny-server can report the value of .libPaths() and versions and locations of installed packages: installed.packages()[,2:3] This works well, except for a package that contained relative symbolic links to the file system. Thomas __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04
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.petzo...@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 > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04
Hi Thomas, On 9 August 2023 at 17:00, Thomas Petzoldt wrote: | 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. I have one more idea but I'll wait for you to post on r-sig-debian. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04
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 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04
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 -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
