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Updating to R 4.5.1 on Ubuntu Plucky

6 messages · Simone Blomberg, Dirk Eddelbuettel

Original
Simone Blomberg
# 
Hi,

When I do apt update I get the following output:

simoneb at laptop:~$ sudo apt update
Hit:1 https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/ InRelease
Hit:2 http://au.archive.ubuntu.com/ubuntu plucky InRelease
Hit:3 http://security.ubuntu.com/ubuntu plucky-security InRelease
Hit:4 http://archive.ubuntu.com/ubuntu plucky-proposed InRelease
All packages are up to date.
Notice: Missing Signed-By in the sources.list(5) entry for 'https://cloud.r-project.org/bin/linux/ubuntu'

Should I be disturbed by the Missing Signed-By? If so, is there a way to fix it?

Thanks,

Simone.



Dr. Simone Blomberg, BSc (Hons), PhD, MAppStat, (she/her) Why it matters.<https://medium.com/gender-inclusivit/why-i-put-pronouns-on-my-email-signature-and-linkedin-profile-and-you-should-too-d3dc942c8743>

Associate Professor | School of the Environment
The University of Queensland | St. Lucia | Queensland 4072 | Australia
email: S.Blomberg1_at_uq.edu.au

Honorary Associate Professor | Division of Ecology and Evolution

Research School of Biology | Australian National University


UQ ALLY Supporting the diversity of sexuality, sex characteristics and gender identity at UQ.

Policies:

1.  I will NOT analyse your data for you.
2.  Your deadline is your problem.


If you can't stand algebra, stay out of evolutionary biology. - John Maynard Smith.



NEW UPDATED PREPRINT JUST OUT. PLEASE DISTRIBUTE TO YOUR NETWORKS:

https://www.biorxiv.org/content/10.1101/2024.10.26.620394v2
Dirk Eddelbuettel
#
On 15 June 2025 at 23:45, Simone Blomberg via R-SIG-Debian wrote:
| When I do apt update I get the following output:
| 
| simoneb at laptop:~$ sudo apt update
| Hit:1 https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/ InRelease
[...]
| Notice: Missing Signed-By in the sources.list(5) entry for 'https://cloud.r-project.org/bin/linux/ubuntu'
| 
| Should I be disturbed by the Missing Signed-By? If so, is there a way to fix it?

That is covered in the README.md at

  https://cloud.r-project.org/bin/linux/ubuntu/
  
where Michael and I explain how to

  a) add the apt repo for the ubuntu mirror at CRAN and
  b) how to add a key for it.

There are scripted solutions too as eg each and every CI run using this repo
does it too. One way is (based on my r-ci setup)

  wget -q -O- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
     sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

but it's late on a Sunday here so I am not double-checking this against the
README.md which I did double and triple-checked when we updated it.

You did not share with us what you did you saying more is tricky.  (Also
while I uploaded the R 4.5.1 package to Debian on Friday I do not yet see a
4.5.1 Ubuntu package so Michael may not have gotten to it. All these steps
are done by colunteers so you should factor that into your expectations of
the timeliness of the service.

Best, Dirk
Simone Blomberg
# 
Hi Dirk,

Thanks for your help. I really appreciate it! I followed the instructions for installation that are on CRAN. It may be just that Michael hasn't updated the .deb packages yet. I'll wait and see. The handling of the apt sources list has changed a bit in the last couple of Ubuntu releases. I thought maybe that was causing a problem. Also, I should probably RTFM. ?

Thanks again for all your efforts,

Simone.


Dr. Simone Blomberg, BSc (Hons), PhD, MAppStat, (she/her) Why it matters.<https://medium.com/gender-inclusivit/why-i-put-pronouns-on-my-email-signature-and-linkedin-profile-and-you-should-too-d3dc942c8743>

Associate Professor | School of the Environment
The University of Queensland | St. Lucia | Queensland 4072 | Australia
email: S.Blomberg1_at_uq.edu.au

Honorary Associate Professor | Division of Ecology and Evolution

Research School of Biology | Australian National University


UQ ALLY Supporting the diversity of sexuality, sex characteristics and gender identity at UQ.

Policies:

1.  I will NOT analyse your data for you.
2.  Your deadline is your problem.


If you can't stand algebra, stay out of evolutionary biology. - John Maynard Smith.



NEW UPDATED PREPRINT JUST OUT. PLEASE DISTRIBUTE TO YOUR NETWORKS:

https://www.biorxiv.org/content/10.1101/2024.10.26.620394v2
Dirk Eddelbuettel
# 
Hi Simone,
On 16 June 2025 at 03:45, Simone Blomberg wrote:
| Thanks for your help. I really appreciate it! I followed the instructions for
| installation that are on CRAN. It may be just that Michael hasn't updated the
| .deb packages yet. I'll wait and see. The handling of the apt sources list has
| changed a bit in the last couple of Ubuntu releases. I thought maybe that was
| causing a problem. Also, I should probably RTFM. ?

There are two distinct issues here, and you are conflating them. Treating
them separately makes it easier.

One is that indeed as of right now we have no R 4.5.1 for Ubuntu at CRAN.
Michael will get to it, he always has. (I did my part on the Debian bits he
uses, now we wait.) You can use rocker/r-base aka r-base with 4.5.1 now, as
you can for Debian unstable/testing.

Two is that apt input format changed from .list to .sources, and also changes
how security keys are reported / required -- all following some time after
22.04. I think that hit me for 24.04 but my repos (i.e. r2u) do the right
thing now, as do the machines I run. How to set that up on your end is more
of a generic Ubuntu question you could google (and sorry I do this to you but
I don't have a link handy as I said it is coming up to 23h on a Sunday
here). My scripts (for r2u, for r-ci, ... ) do the right thing, you can find
it there too. I have no issue either on this machine (still 24.10 nor on
another updated to 25.04).

I am sure you can sort this out over one fresh hot cup of coffee or tea. If
and when you do feel would you mind sending the notes to this thread?

Thanks, Dirk
Simone Blomberg
# 
Two steps:

sudo curl -fsSL https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | gpg --dearmor | sudo tee /etc/apt/keyrings/cran.gpg > /dev/null

This downloads the key, turns it in to a binary in the correct format, then writes the key in the keyring.

Then I edited my R .sources file ( in directory: /etc/apt/sources.list.d)  and pasted in the following in the Signed By: field.

/etc/apt/keyrings/cran.gpg

So now my R .sources file looks like this:

Types: deb
URIs: https://cloud.r-project.org/bin/linux/ubuntu/
Suites: noble-cran40/
Components:
Signed-By: /etc/apt/keyrings/cran.gpg

then sudo apt update and the Missing Signed-By notice is gone. Now just have to wait for Michael to give us R 4.5.1!

And I didn't even need to make a cup of coffee! Will do that now...

Thanks Dirk and everyone for making R available on Linux, and specifically Ubuntu.

Cheers,

Simone.



Dr. Simone Blomberg, BSc (Hons), PhD, MAppStat, (she/her) Why it matters.<https://medium.com/gender-inclusivit/why-i-put-pronouns-on-my-email-signature-and-linkedin-profile-and-you-should-too-d3dc942c8743>

Associate Professor | School of the Environment
The University of Queensland | St. Lucia | Queensland 4072 | Australia
email: S.Blomberg1_at_uq.edu.au

Honorary Associate Professor | Division of Ecology and Evolution

Research School of Biology | Australian National University


UQ ALLY Supporting the diversity of sexuality, sex characteristics and gender identity at UQ.

Policies:

1.  I will NOT analyse your data for you.
2.  Your deadline is your problem.


If you can't stand algebra, stay out of evolutionary biology. - John Maynard Smith.



NEW UPDATED PREPRINT JUST OUT. PLEASE DISTRIBUTE TO YOUR NETWORKS:

https://www.biorxiv.org/content/10.1101/2024.10.26.620394v2
Dirk Eddelbuettel
# 
Simone,
On 16 June 2025 at 04:36, Simone Blomberg wrote:
| Two steps:
| 
| sudo curl -fsSL https://cloud.r-project.org/bin/linux/ubuntu/
| marutter_pubkey.asc | gpg --dearmor | sudo tee /etc/apt/keyrings/cran.gpg > /
| dev/null
| 
| This downloads the key, turns it in to a binary in the correct format, then
| writes the key in the keyring.
| 
| Then I edited my R .sources file ( in directory: /etc/apt/sources.list.d)  and
| pasted in the following in the Signed By: field.
| 
| /etc/apt/keyrings/cran.gpg
| 
| So now my R .sources file looks like this:
| 
| Types: deb
| URIs: https://cloud.r-project.org/bin/linux/ubuntu/
| Suites: noble-cran40/
| Components: 
| Signed-By: /etc/apt/keyrings/cran.gpg
| 
| then sudo apt update and the Missing Signed-By notice is gone.

Yes, thanks, the above looks spot on and may be needed on everything newer
than 24.04.  On Debian systems I now also get a note about a '.list to
.sources' converter but that may not add the key. I have not tried this
helper. 

| Now just have to wait for Michael to give us R 4.5.1!

Indeed. 
| 
| And I didn't even need to make a cup of coffee! Will do that now...

Well I have one now :)  

Cheers, Dirk