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
[R-pkg-devel] preventing auto-update of R and c2d4u r-cran-* packages on Ubuntu 22.04
Hi, 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 This is indeed a great service, thanks to Dirk Edelbuettel, mark 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. 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. Thanks in advance, Thomas __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
