R SIG Debian - Jun 2020 - installation problem for R 4.0 on Debian buster

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

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

Am Freitag, 5. Juni 2020, 20:04:48 CEST schrieb 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
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.
> | 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?
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
> 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, Dirk,

thanks for keeping discussing this. I can confirm it works now. Thank you
for the solution.
> 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...
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:
> Am Freitag, 5. Juni 2020, 20:04:48 CEST schrieb 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
>
> 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.
>
> > | 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?
>
> 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
>
> > 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
>
>
>
>
	[[alternative HTML version deleted]]