search for: r2u

I can understand why it changes the game. It would be sweet if we could do something like r2u for Debian, but for now > we can't. Switching between Debian and Ubuntu is not that onerous though. Do you mind clarifying what you do here? Do you operate Ubuntu when working in R? Or do you somehow operate Ubuntu to manage R packages and dependencies, and then switch back into Debian to...

...rom-source fails for lack of a (for compilation from source) needed -dev packages. Which is why _reliable_ and _complete_ provision of binaries is such a game changer. I have been at this for 20+ years (as it was that long ago that injected the first few r-cran-* packages into Debian). And having r2u is a complete gamechanger. I can drop into a random code repository (as today for work), run my `installDeps.r` helper to install everything, or in the demo for you just do `install.r interflex` (or, if one prefers run it as an R command via eg a simple `Rscript -e 'install.packages("inte...

The r2u repository [1] has been providing CRAN packages as Ubuntu binaries (with *full* and *complete* dependency resolution) since last May. It is being served from a well-connect Internet2 mirror thanks to the University of Illinois making it *fast*. By relying on the bspm package [2], it can access th...

I started using r2u (see https://eddelbuettel.github.io/r2u) recently and thought I was having a problem in that I was getting out-of-date versions of packages. I made enquiries of Dirk Eddelbuettel about this, and he enlightened me as to what the problem really was. I was seeing old versions of packages that were s...

...'xyz' is not available for package ''abc" * removing '/home/............/4.3/abc' Warning in install.packages : installation of package 'abc' had non-zero exit status. ok, AFAIU, wanting to manage R dependencies as easily as possible suggests using Ubuntu with r2u instead of Debian. Be my guest to evaluate this interpretation. Johan Den tirs. 6. jun. 2023 kl. 19.58 skrev Dirk Eddelbuettel <edd at debian.org>: > > On 6 June 2023 at 19:37, Johan Andresen wrote: > | I'd like input on how to install interflex > | <https://github.co...

...tories in my sources.list disagreeing about versions required.? That's not so urgent an issue for me that I wont just wait to see if it sorts itself out.? In my experience such collisions sometimes do. However, it prompted me to some questions: 1) Is this telling me it's time I went to r2u which does seem a "very good thing"?? Any reason NOT to change? 2) I read https://eddelbuettel.github.io/r2u/, not for the first time, and it looks simple, even I should? be able to do that.? Any gotchas?? See #3: 3) but it says things I don't really understand about the R versio...

I was delighted I with how fast (faster than a tickled toddler giggles) r2u scarfed packages I. up my Pop!_OS (Ubuntu in party attire tuned for System76). But, despite 40 years as my own sys admin (classic fool for a client?), I bolluxed up, ending up with an install chain that was inferior to compiling from source, despite having to occasionally track down system dependen...

...se be welcome to refer me to guidelines/a manual for doing so if you can imagine it happening. Johan Den ons. 7. jun. 2023 kl. 08.37 skrev Johan Andresen < johan.andresen at gmail.com>: > I can understand why it changes the game. > > It would be sweet if we could do something like r2u for Debian, but for now >> we can't. Switching between Debian and Ubuntu is not that onerous though. > > > Do you mind clarifying what you do here? Do you operate Ubuntu when > working in R? Or do you somehow operate Ubuntu to manage R packages and > dependencies, and then...

On 8 July 2024 at 19:32, marcoblanchette at icloud.com wrote: | Oh, again, sorry for the spam but the problem Lauren is seeing is when she is | trying to sign the key. Installing gnugpg usually takes care of that problem. I am not sure about that. For jammy, my current (and used) rocker/r2u:jammy Dockerfile is https://github.com/rocker-org/r2u/blob/master/jammy/Dockerfile and it does what Laurent want (plus a bit more: r2u setup) but I have been traveling since she first emailed me and have not run it to confirm. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

This is definitely tangential to the list: I'm on Ubuntu (22.04.2 LTS) not Debian and I'm sure this is about issues in the Ubuntu package management on my machine, R is only revealing them. The original subject line came from me wondering if my going over to the r2u repository would solve the problem.? However, as I think Dirk said, that's only really likely to be answered by trying it and I would rather see if I can understand what has gone wrong before I do anything radical. I am also hoping that having this, partially OTT thread on the list may help as...

...any of us put volunteer time into this trying to make things 'possible' and preferably 'easy' but we don't always get there. That said, I have shown multiple times over the last few years that the simple _one statement call_ of `install.packages("tidyverse")` works in r2u as demonstrated in a Docker container for r2u. I just 'taped' a fresh demo installing 103 binary packages in twenty seconds from this one command. [1] Myself, and many others, take advantage of that day in, day out on Ubuntu systems for direct work, for work in CI, for work on cloud instan...

On 26 March 2023 at 18:30, Dirk Eddelbuettel wrote: | Over the last few months I have provided multiple 'demos' as animated gifs | showing how for example `system.time(install.package("tinyverse"))` installs | all these packages and all their dependencies in under twenty seconds (!!). Classic typo as Josh kindly pointed out over DM:

...of packages may be needed. A demo is included below, it is reproducible in a container. We find the easiest/fastest reproduction is by saving the code snippet below in the current directory as eg 'matrixIssue.R' and have it run in a container as docker run --rm -ti -v `pwd`:/mnt rocker/r2u Rscript /mnt/matrixIssue.R This runs in under two minutes, first installing the older Matrix, next installs SeuratObject, and then by removing the older Matrix making the (already installed) current Matrix version the default. This simulates a package update for Matrix. Which, as the final snipp...

...t should install packages to somewhere inside | ~/.local by default. Use of ~/.local is a fairly recent convention (relative to the time R has been around, which is now decades) and one which R supports already eg in the (rather useful) portable config directories: > tools::R_user_dir("r2u") [1] "/home/edd/.local/share/R/r2u" > Your best bet really to govern your .libPaths from your Rprofile.site and Renviron.site rather than asking a few million R users to adjust from past practice. Also: personal preferences differ. I think of Linux as multi-tenant and ex...

Oh, again, sorry for the spam but the problem Lauren is seeing is when she is trying to sign the key. Installing gnugpg usually takes care of that problem. From: marcoblanchette at icloud.com <marcoblanchette at icloud.com> Date: Monday, July 8, 2024 at 12:26?PM To: Dirk Eddelbuettel <edd at debian.org> Cc: Gerber, Lauren J <lauren.gerber at helsinki.fi>, r-sig-debian at

...r Image On 8 July 2024 at 19:32, marcoblanchette at icloud.com wrote: | Oh, again, sorry for the spam but the problem Lauren is seeing is when she is | trying to sign the key. Installing gnugpg usually takes care of that problem. I am not sure about that. For jammy, my current (and used) rocker/r2u:jammy Dockerfile is https://github.com/rocker-org/r2u/blob/master/jammy/Dockerfile and it does what Laurent want (plus a bit more: r2u setup) but I have been traveling since she first emailed me and have not run it to confirm. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org...

Hello, Are there any plans to add R packages for Ubuntu on other architectures in addition to amd64? We are looking for s390x packages as the version from the distro's package manger is 4.2.2. I'm happy to help in any way I can. Thank you. Regards, Vivian Kong Linux on IBM Z Open Source Ecosystem IBM Canada Toronto Lab [[alternative HTML version deleted]]

Hi, I see R by default installs packages in ~/R. I know I can change the default directory with R_LIBS_USER, but software shouldn't be polluting the home directory. For example both python and node install packages to ~/.local/lib, ruby to ~/.local/share. They don't install to for example ~/node. R should do the same: it should install packages to somewhere inside ~/.local by default.

...where inside > | ~/.local by default. > > Use of ~/.local is a fairly recent convention (relative to the time R has > been around, which is now decades) and one which R supports already eg in the > (rather useful) portable config directories: > > > tools::R_user_dir("r2u") > [1] "/home/edd/.local/share/R/r2u" > > > > Your best bet really to govern your .libPaths from your Rprofile.site and > Renviron.site rather than asking a few million R users to adjust from past > practice. > > Also: personal preferences differ. I...

Don't you have to load BiocManager before using it? -----Original Message----- From: R-SIG-Debian <r-sig-debian-bounces at r-project.org> On Behalf Of Gerber, Lauren J Sent: Tuesday, October 15, 2024 9:15 AM To: r-sig-debian at r-project.org Cc: dirk at eddelbuettel.com Subject: Re: [R-sig-Debian] R Package: 'ggbreak' in Dockerfile Hi All, Does anyone have experience