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installation problem for R 4.0 on Debian buster

8 messages · Mark van der Loo, Johannes Ranke, Dirk Eddelbuettel

Original
Mark van der Loo
# 
Hi all,

I just spun up a fresh Debian Buster instance, then I added:

deb http://cloud.r-project.org/bin/linux/debian buster-cran40/

to /etc/apt/sources.list. I also ran the apt-key command as described here:
https://cran.r-project.org/bin/linux/debian/#secure-apt

So far so good, now when I do the following, I get no joy:

$ sudo apt-get install r-base

Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 r-base : Depends: r-recommended (= 4.0.0-1~bustercran.0) but it is not
going to be installed
E: Unable to correct problems, you have held broken packages.


However, when I use the buster-cran-35 deb line, all works fine. So there
seems to be something going on with buster-cran-40. Is this correct, or am
I missing something?

Thanks,
Mark
Dirk Eddelbuettel
#
On 5 June 2020 at 00:31, Mark van der Loo wrote:
| Hi all,
| 
| I just spun up a fresh Debian Buster instance, then I added:
| 
| deb http://cloud.r-project.org/bin/linux/debian buster-cran40/
| 
| to /etc/apt/sources.list. I also ran the apt-key command as described here:
| https://cran.r-project.org/bin/linux/debian/#secure-apt
| 
| So far so good, now when I do the following, I get no joy:
| 
| $ sudo apt-get install r-base
| 
| Reading package lists... Done
| Building dependency tree
| Reading state information... Done
| Some packages could not be installed. This may mean that you have
| requested an impossible situation or if you are using the unstable
| distribution that some required packages have not yet been created
| or been moved out of Incoming.
| The following information may help to resolve the situation:
| 
| The following packages have unmet dependencies:
|  r-base : Depends: r-recommended (= 4.0.0-1~bustercran.0) but it is not
| going to be installed
| E: Unable to correct problems, you have held broken packages.
| 
| 
| However, when I use the buster-cran-35 deb line, all works fine. So there
| seems to be something going on with buster-cran-40. Is this correct, or am
| I missing something?

You run one command to install r-base. It tells that it wants to (but can't)
install r-recommended.

To have the system tell you more and why, add r-recommended:

  $ sudo apt-get install r-base r-recommended

Keep adding packages while it complains. After maybe five or so steps you
should. It is often because _one_ of the libraries brought in by the 'new'
package conflict. That can happen with backports.  (And it is one of the
reasons I like 'testing' better but hey personal tastes and preferences
cannot be debated...)

Dirk
Johannes Ranke
# 
Hi Mark,

Am Freitag, 5. Juni 2020, 00:31:34 CEST schrieb Mark van der Loo:
OK, then you need to keep reading. Instead of simply installing R 4.0.0 you 
need to remove the packages depending on r-api-35 as detailed in

https://cran.r-project.org/bin/linux/debian/#debian-bullseye-testing

The reason is that the backported r-cran-* packages have a lower version 
number than the r-cran-* packages in the Debian archive, but the packages in 
the Debian archive depend on r-api-35 while the new backport provides r-
api-40.

Also, you will need to rebuild all locally installed packages as detailed on 
the CRAN Debian page.

Greetings,

Johannes
Dirk Eddelbuettel
#
On 5 June 2020 at 08:52, Johannes Ranke wrote:
| Hi Mark,
| 
| Am Freitag, 5. Juni 2020, 00:31:34 CEST schrieb Mark van der Loo:
| > Hi all,
| > 
| > I just spun up a fresh Debian Buster instance, then I added:
| > 
| > deb http://cloud.r-project.org/bin/linux/debian buster-cran40/
| > 
| > to /etc/apt/sources.list. I also ran the apt-key command as described here:
| > https://cran.r-project.org/bin/linux/debian/#secure-apt
| > 
| > So far so good, 
| 
| OK, then you need to keep reading. Instead of simply installing R 4.0.0 you 
| need to remove the packages depending on r-api-35 as detailed in
| 
| https://cran.r-project.org/bin/linux/debian/#debian-bullseye-testing
| 
| The reason is that the backported r-cran-* packages have a lower version 
| number than the r-cran-* packages in the Debian archive, but the packages in 
| the Debian archive depend on r-api-35 while the new backport provides r-
| api-40.

That sounds ... suboptimal. And I am not sure I understand why that would be.
Can you explain?  Are they behind a version?  If so, why?

Also, apt-pinning can help here.  You can give a repo a higher-than-default
priority. Maybe that would be applicable here?

Dirk
 
| Also, you will need to rebuild all locally installed packages as detailed on 
| the CRAN Debian page.
| 
| Greetings,
| 
| Johannes 
| 
| > now when I do the following, I get no joy:
| > 
| > $ sudo apt-get install r-base
| > 
| > Reading package lists... Done
| > Building dependency tree
| > Reading state information... Done
| > Some packages could not be installed. This may mean that you have
| > requested an impossible situation or if you are using the unstable
| > distribution that some required packages have not yet been created
| > or been moved out of Incoming.
| > The following information may help to resolve the situation:
| > 
| > The following packages have unmet dependencies:
| >  r-base : Depends: r-recommended (= 4.0.0-1~bustercran.0) but it is not
| > going to be installed
| > E: Unable to correct problems, you have held broken packages.
| > 
| > 
| > However, when I use the buster-cran-35 deb line, all works fine. So there
| > seems to be something going on with buster-cran-40. Is this correct, or am
| > I missing something?
| > 
| > Thanks,
| > Mark
| > 
| > 	[[alternative HTML version deleted]]
| > 
| > _______________________________________________
| > R-SIG-Debian mailing list
| > R-SIG-Debian at r-project.org
| > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Johannes Ranke
# 
Hey Dirk,

Am Freitag, 5. Juni 2020, 20:07:22 CEST schrieb Dirk Eddelbuettel:
yes, absolutely, thanks for the hint! The backport of R 4.0.0 for bullseye is 
not needed any more. I just updated the page, so it will by synced to CRAN 
soon.

Cheers,

Johannes
Johannes Ranke
# 
Am Freitag, 5. Juni 2020, 20:04:48 CEST schrieb Dirk Eddelbuettel:
Sorry Mark, it was me who did not read as much as I should - you are on a 
fresh buster system, so no need to remove r-api-35 packages...

Also, I think I have run into the same problem (r-recommended uninstallable) 
when checking the situation on buster in a chroot.
OK, for buster I updated the backports of the recommended packages. I think 
things are fine now (pending CRAN syncs), i.e. the backport to buster including 
the recommended packages should be installable using

apt install -t buster-cran40 r-base

If you have buster packages depending on r-api-35 installed, these will be 
removed by the above command (just tested in my buster chroot).

Cheers,

Johannes
Mark van der Loo
# 
Johannes, Dirk,

thanks for keeping discussing this. I can confirm it works now. Thank you
for the solution.
Absolutely no problem. I'm happy it's solved. In case ppl are curious why I
use Buster: it's the latest Debian currently offered by my cloud provider.

Cheers,
Mark




On Sat, Jun 6, 2020 at 1:25 AM Johannes Ranke <johannes.ranke at jrwb.de>
wrote: