R SIG Debian - Aug 2023 - Is r2u at 3.4.1? [branch about handling package collisions under Ubuntu/Debian]

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 I doubt if I'll be the last to hit this sort of package management
nightmare.? Some of the issues clearly are pure OS issues but the impact
for me is definitely on R.

On 16/08/2023 00:06, Dirk Eddelbuettel wrote:
> Hi Chris,
>
> Thanks for posting here, and sorry I missed it for two days due to sorting
> mailing list traffic into folders and clearly not glancing at all of them.
Don't think I said before how much I appreciate you responding at all.
> On 13 August 2023 at 09:12, Chris Evans wrote:
> | I am putting this here as it may be of general and not just my own
> | interest.? I am currently running 4.3.1 on Ubuntu 22.04.2 LTS but am
> | hitting an issue that the magick package won't update because
> | libmagick++-dev won't update because, presumably, of two repositories
in
> | my sources.list disagreeing about versions required.? That's not so
>
> That can happen, and pinning can help. I would suggest to look at
'apt-cache
> polict nameofthepackagehere'. (See below for concrete example.)
So I try this.

root at Clevo2:/media/chris/Clevo_SSD2/Data/MyR/R/distill_blog/test2/_posts# 
apt-cache policy libmagick++-dev
libmagick++-dev:
 ? Installed: (none)
 ? Candidate: 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2
 ? Version table:
 ???? 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2 500
 ??????? 500 https://esm.ubuntu.com/apps/ubuntu jammy-apps-security/main 
amd64 Packages
 ??????? 500 https://esm.ubuntu.com/apps/ubuntu jammy-apps-security/main 
i386 Packages
 ???? 8:6.9.11.60+dfsg-1.3build2 500
 ??????? 500 http://mirror.infomaniak.ch/ubuntu jammy/universe amd64 
Packages
 ??????? 500 http://mirror.infomaniak.ch/ubuntu jammy/universe i386 Packages

And the key problems remains this (actually, it's got a bit worse):

root at Clevo2:/media/chris/Clevo_SSD2/Data/MyR/R/distill_blog/test2/_posts# 
apt-get install libmagick++-dev
Reading package lists... Done
Building dependency tree... Done
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.
 ?libcairo2-dev : Depends: libfontconfig1-dev (>= 2.2.95)
 ???????????????? Depends: libfreetype6-dev (>= 2.1.10)
 ?libglib2.0-dev : Depends: libglib2.0-0 (= 2.72.4-0ubuntu1) but 
2.72.4-0ubuntu2.2 is to be installed
 ????????????????? Depends: libglib2.0-bin (= 2.72.4-0ubuntu1)
 ????????????????? Depends: libglib2.0-dev-bin (= 2.72.4-0ubuntu1)
 ?libmagickcore-6.q16-dev : Depends: libfreetype6-dev
 ?libwmf-dev : Depends: libfreetype-dev but it is not installable
E: Unable to correct problems, you have held broken packages.

Which brings me to Dirk's on the nail question:
> (Also: how come there are two libmagick++-dev, ie why do you have a 2nd
one,
> ie do you know which additional repo you turned on?)
Exactly!!! The weird thing is is that it was weeks back that I added a 
repo., or
I think I did, probably more than one about handling gpx files in 
Ubuntu/Debian.

But that was weeks before this started and as you see from that 
apt-cache policy
(if I understand it correctly), the repos involved seem to be the 
mainstream ones.
That's true when I do apt-cache policy on any of the packages that are 
being
complained about.

aptitude doesn't help and dpkg --get-selections | grep hold returns 
nothing (literally)
and none of the other things I could find on the web about these sorts 
of collisions
helped ... and I can't see that others have this problem (apart from 
some very old
reports for Ubuntu 14 and 16!)

Are there any more suggestions?? Are there good Debian/Ubuntu places 
where I should
be putting this?? If so, any advice about how to word it?!

Are there frightening radical steps I should take next?!

... and back to the human
>
> Cheers, Dirk
Cheers indeed.
>
> | Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor,
> | University of Roehampton, London, UK.
>
> Nice. I got to workshop-keynote once in Guayaquil and regret not making
over
> to Quito.
Ah, I'm the reverse.? Ecuador seems to be sliding into a frightening 
narcogang
dominated state that previously it had always avoided.? I guess that puts my
problems in perspective.
>
-- 
Chris Evans (he/him)
Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor, 
University of Roehampton, London, UK.
Work web site: https://www.psyctc.org/psyctc/
CORE site: http://www.coresystemtrust.org.uk/
Personal site: https://www.psyctc.org/pelerinage2016/

Chris,

This got a little long so I'll chop a few things down.

On 22 August 2023 at 19:38, Chris Evans wrote:
| On 16/08/2023 00:06, Dirk Eddelbuettel wrote:
| >
| > That can happen, and pinning can help. I would suggest to look at
'apt-cache
| > polict nameofthepackagehere'. (See below for concrete example.)
| 
| So I try this.
| 
| root at Clevo2:/media/chris/Clevo_SSD2/Data/MyR/R/distill_blog/test2/_posts# 
| apt-cache policy libmagick++-dev
| libmagick++-dev:
|  ? Installed: (none)
|  ? Candidate: 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2
|  ? Version table:
|  ???? 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2 500
|  ??????? 500 https://esm.ubuntu.com/apps/ubuntu jammy-apps-security/main 
| amd64 Packages
|  ??????? 500 https://esm.ubuntu.com/apps/ubuntu jammy-apps-security/main 
| i386 Packages
|  ???? 8:6.9.11.60+dfsg-1.3build2 500
|  ??????? 500 http://mirror.infomaniak.ch/ubuntu jammy/universe amd64 
| Packages
|  ??????? 500 http://mirror.infomaniak.ch/ubuntu jammy/universe i386 Packages

This shows you two sources supplying libmagick++-dev: one from esm.ubuntu.com
security updates. That is fine.  The other is an add-on repo, just like r2u.

But we cannot limitlessly combine those. r2u assume "everything else"
comes
from the standard repos and tries to (and succeeds, generally) in working
with it. So here, for now, I would point at mirror.infomaniak.ch/ubuntu as a
likely source of your troubles.

| And the key problems remains this (actually, it's got a bit worse):
| 
| root at Clevo2:/media/chris/Clevo_SSD2/Data/MyR/R/distill_blog/test2/_posts# 
| apt-get install libmagick++-dev
| Reading package lists... Done
| Building dependency tree... Done
| 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.
|  ?libcairo2-dev : Depends: libfontconfig1-dev (>= 2.2.95)
|  ???????????????? Depends: libfreetype6-dev (>= 2.1.10)
|  ?libglib2.0-dev : Depends: libglib2.0-0 (= 2.72.4-0ubuntu1) but 
| 2.72.4-0ubuntu2.2 is to be installed
|  ????????????????? Depends: libglib2.0-bin (= 2.72.4-0ubuntu1)
|  ????????????????? Depends: libglib2.0-dev-bin (= 2.72.4-0ubuntu1)
|  ?libmagickcore-6.q16-dev : Depends: libfreetype6-dev
|  ?libwmf-dev : Depends: libfreetype-dev but it is not installable
| E: Unable to correct problems, you have held broken packages.

At that point I generally try to packages it lists on the left (ie
libcairo2-dev, ?libglib2.0-dev, ?libmagickcore-6.q16-dev, libwmf-dev) and try
individual 'apt install PACKAGEHERE' to see what errors that implies.
With a
bit experience you gain from trying this you generally can work out what is
wrong and make amends.

I should add that none of this so far has anything to do with r2u. This is
just mixing repo.

So let's try to see if we can get your libmagick++-dev issue resolved and
take it from there.

Cheers, Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

On Tue, 22 Aug 2023 19:38:57 +0200
Chris Evans <chrishold at psyctc.org> wrote:
>  ???? 8:6.9.11.60+dfsg-1.3build2 500
>  ??????? 500 http://mirror.infomaniak.ch/ubuntu jammy/universe amd64 
> Packages
Interesting. mirror.infomaniak.ch seems to be a full mirror of Ubuntu
repos, but https://packages.ubuntu.com/jammy/libmagick++-dev says that
the current version of the package is
8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3, not 8:6.9.11.60+dfsg-1.3build2. On
the other hand, I do see the 8:6.9.11.60+dfsg-1.3build2 version in the
changelog [*], it's just a bit older.

I think that your sources.list is missing the security updates repo,
which seems to be separate from the main repo:

deb http://security.ubuntu.com/ubuntu jammy-security main universe

-- 
Best regards,
Ivan

[*]
http://changelogs.ubuntu.com/changelogs/pool/universe/i/imagemagick/imagemagick_6.9.11.60+dfsg-1.3ubuntu0.22.04.3/changelog