My machine runs Fedora 32. I have installed “R version 3.6.3” through dnf.
R version 4.0.0 has been released on 2020-04-24, so I would like to upgrade.
Two questions: (1) is it possible to install an appropriate R’s repository so as to upgrade as soon as possible and safely through dnf? or, (2) do I have to wait for Fedora project to check the latest R release before being able to upgrade through dnf?
I have already checked Fedora Packaging Guidelines for R libraries - Fedora Project Wiki and https://cran.r-project.org/doc/manuals/r-patched/R-admin.pdf.
Thank you very much
There was a PR to update R to version 4.0.0 a couple of days ago, apparently it will find its way to Fedora shortly. Unless you urgently need something not found in 3.6.3, it’s best to wait and not mix and match stuff.
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I am also waiting for this update. Hopefully it will come very soon.
I’m too waiting for R 4.0 rpm to be released for Fedora. Could I install rpm released for OpenSuse?
Any timeline for the update of GNU R on Fedora 32?
We are still waiting for R 4.0.0. Is it normal? Do we have to do something? Thanks for the update.
R v.4 has been in rawhide for over a month now and it’s currently at 4.0.2.
Given that R v4 is in many ways incompatible with older versions, it would be against our Updates policy to introduce breaking changes in a stable release, so I don’t think that F32 will be getting R v4 after all.
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You could try the following:
Download the rpms of R (v.4.0.x) from Koji (R-4.0.2-1.fc33 | Build Info | koji) and install it using dnf.
It may or may not work but worth a try…
Looks like R with all its modules is about 15,000 packages, so not so easy to maintain and build, see here: iucar/cran Copr (Builds only for F31?)
Repo file for F32 is here: https://copr.fedorainfracloud.org/coprs/iucar/cran/repo/fedora-32/iucar-cran-fedora-32.repo
Maybe easier to use this: Docker ?
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R 4 is being built in a side tag for F32; it will be some time before all builds are complete.
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does that mean we will see R 4.0.0 in F32?
The update is now in testing, though it may take some time to reach mirrors. Please test and leave feedback.
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I understand that it feels like v4 is incompatible with older versions, but the problem is on Fedora 32, R 3.6.x is virtually not usable. I’m unable to install many bioconductor packages and I’m struggling cause there seems to be no way to solve this issue but install R 4.0, which can’t be done in Fedora.
This has always been the case with R. When it updates, many bioconductor packages stop supporting the previous R versions. This makes it really important for the distro to give a way to update R to the latest version.
On Ubuntu there’s a PPA that helps you get the latest version. It exists because it’s absolutely needed. So while you’d worry that the new version breaks things, it’s actually that the old version breaks things when it comes to R.
I don’t think I’ll be able to explain any better as I don’t have the technical know how. If you were to use R the way data scientists and bioinformaticians use it, you’d realize.
This is not the first time we’re facing this issue. At every Fedora update, R is basically unusable for a while. I’m so tired of this, I’m not sure what to do.
I’m kicking myself now for having updated to 32.
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Hi @luckybarrel, and welcome to the Community. If you have a moment, please have a look at the #start-here category.
As @qulogic mentioned, R 4.0.2 is already in the testing repositories and will hit the main repos soon. Follow the link for instructions on how to get the update immediately.
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Don’t Bioconductor 3.10 packages work with R 3.6.x?
Eliott has submitted the update to R 4.0.2 for F32, you can upgrade to it right now using the --enablerepo=updates-testing dnf flag.
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Thank you so much! Will this update everything to testing or only R?
So using
sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2020-4c0ce71810
will only update R right?
Yes, some Bioconductor packages are not getting installed. The ones I’ve had issues with were Rsubread, DEP. Every time it’s some different bioconductor package which can’t get installed.
This really needs a better solution as updating Fedora is hit or miss for R. I thought I did wait long enough to upgrade, but no.
(And for clarification: With R update the problem of installing exists even on the previous Fedora version, it’s just that I’d already have the R package installed so my work is not disrupted)
Thanks for the link. I did go through it all, but did not understand it well. Thanks for clarifying. Also, I needed to make a larger point of how this is always an issue…
It will update all the packages included in that particular batch, not the whole system.
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Thanks again for the clarification.
R version 4.0.2 is now in the main (updates) repo.
How are others planning their upgrade? Since the packages need to be reinstalled with R v4, I plan to use installed.packages() to save a list of them, upgrade R, then install the list of packages for R v4.
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