R SIG Debian - Jun 2024 - Issue with pkgconf when upgrading to 4.4.1

Hi all,

I am running Ubuntu 20.04.6 (focal) (yes, planning to upgrade soon) and just
updated to 4.4.1. However, the process did not quite go as smoothly. 'sudo
apt upgrade' ran but 'r-base-dev' was not updated because of a
dependency issue:

[08:57] ? wviechtb at wv-x5 ? ~/ ? sudo apt upgrade r-base-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... 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-dev : Depends: pkgconf but it is not going to be installed
E: Broken packages

I was brave/foolish enough to just plow ahead:

[08:58] ? wviechtb at wv-x5 ? ~/ ? sudo apt install pkgconf
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
  libpkgconf3
The following packages will be REMOVED:
  pkg-config
The following NEW packages will be installed:
  libpkgconf3 pkgconf
0 upgraded, 2 newly installed, 1 to remove and 1 not upgraded.
Need to get 61.9 kB of archives.
After this operation, 39.9 kB of additional disk space will be used.
Do you want to continue? [Y/n]
Get:1 http://de.archive.ubuntu.com/ubuntu focal/universe amd64 libpkgconf3 amd64
1.6.3-5 [28.5 kB]
Get:2 http://de.archive.ubuntu.com/ubuntu focal/universe amd64 pkgconf amd64
1.6.3-5 [33.4 kB]
Fetched 61.9 kB in 10s (6,106 B/s)
Selecting previously unselected package libpkgconf3:amd64.
(Reading database ... 579412 files and directories currently installed.)
Preparing to unpack .../libpkgconf3_1.6.3-5_amd64.deb ...
Unpacking libpkgconf3:amd64 (1.6.3-5) ...
dpkg: pkg-config: dependency problems, but removing anyway as you requested:
 r-base-dev depends on pkg-config.
 libmkl-dev:amd64 depends on pkg-config.
 libmagickwand-6.q16-dev:amd64 depends on pkg-config.
 libmagickcore-6.q16-dev:amd64 depends on pkg-config.
 libmagick++-6.q16-dev:amd64 depends on pkg-config.
 libglib2.0-dev:amd64 depends on pkg-config.
 libfontconfig1-dev:amd64 depends on pkg-config.
 libextutils-pkgconfig-perl depends on pkg-config.
 libdap-dev:amd64 depends on pkg-config; however:
  Package pkg-config is to be removed.

(Reading database ... 579417 files and directories currently installed.)
Removing pkg-config (0.29.1-0ubuntu4) ...
Selecting previously unselected package pkgconf.
(Reading database ... 579403 files and directories currently installed.)
Preparing to unpack .../pkgconf_1.6.3-5_amd64.deb ...
Adding 'diversion of /usr/bin/pkg-config to /usr/bin/pkg-config.real by
pkgconf'
Adding 'diversion of /usr/share/aclocal/pkg.m4 to
/usr/share/aclocal/pkg.real.m4 by pkgconf'
Adding 'diversion of /usr/share/man/man1/pkg-config.1.gz to
/usr/share/man/man1/pkg-config.real.1.gz by pkgconf'
Adding 'diversion of /usr/share/pkg-config-crosswrapper to
/usr/share/pkg-config-crosswrapper.real by pkgconf'
Unpacking pkgconf (1.6.3-5) ...
Setting up libpkgconf3:amd64 (1.6.3-5) ...
Setting up pkgconf (1.6.3-5) ...
Processing triggers for man-db (2.9.1-1) ...
Processing triggers for libc-bin (2.31-0ubuntu9.16) ...

After which 'sudo apt upgrade r-base-dev' ran. As far as I can tell, I
haven't totally borked my system (yet), and R 4.4.1 runs just fine, plus I
am not getting any further complaints from apt. But the process probably
isn't quite as intended.

Reporting this here after this came up on Mastodon by another user who ran into
the same issue:

https://emacs.ch/@pglpm/112664623789549089

and Dirk's suggestion to post this here.

Best,
Wolfgang

On 23 June 2024 at 16:39, Viechtbauer, Wolfgang (NP) wrote:
| Hi all,
| 
| I am running Ubuntu 20.04.6 (focal) (yes, planning to upgrade soon) and just
updated to 4.4.1. However, the process did not quite go as smoothly. 'sudo
apt upgrade' ran but 'r-base-dev' was not updated because of a
dependency issue:
| 
| [08:57] ? wviechtb at wv-x5 ? ~/ ? sudo apt upgrade r-base-dev
| Reading package lists... Done
| Building dependency tree
| Reading state information... Done
| Calculating upgrade... 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-dev : Depends: pkgconf but it is not going to be installed
| E: Broken packages
| 
| I was brave/foolish enough to just plow ahead:
| 
| [08:58] ? wviechtb at wv-x5 ? ~/ ? sudo apt install pkgconf
| Reading package lists... Done
| Building dependency tree
| Reading state information... Done
| The following additional packages will be installed:
|   libpkgconf3
| The following packages will be REMOVED:
|   pkg-config
| The following NEW packages will be installed:
|   libpkgconf3 pkgconf
| 0 upgraded, 2 newly installed, 1 to remove and 1 not upgraded.
| Need to get 61.9 kB of archives.
| After this operation, 39.9 kB of additional disk space will be used.
| Do you want to continue? [Y/n]
| Get:1 http://de.archive.ubuntu.com/ubuntu focal/universe amd64 libpkgconf3
amd64 1.6.3-5 [28.5 kB]
| Get:2 http://de.archive.ubuntu.com/ubuntu focal/universe amd64 pkgconf amd64
1.6.3-5 [33.4 kB]
| Fetched 61.9 kB in 10s (6,106 B/s)
| Selecting previously unselected package libpkgconf3:amd64.
| (Reading database ... 579412 files and directories currently installed.)
| Preparing to unpack .../libpkgconf3_1.6.3-5_amd64.deb ...
| Unpacking libpkgconf3:amd64 (1.6.3-5) ...
| dpkg: pkg-config: dependency problems, but removing anyway as you requested:
|  r-base-dev depends on pkg-config.
|  libmkl-dev:amd64 depends on pkg-config.
|  libmagickwand-6.q16-dev:amd64 depends on pkg-config.
|  libmagickcore-6.q16-dev:amd64 depends on pkg-config.
|  libmagick++-6.q16-dev:amd64 depends on pkg-config.
|  libglib2.0-dev:amd64 depends on pkg-config.
|  libfontconfig1-dev:amd64 depends on pkg-config.
|  libextutils-pkgconfig-perl depends on pkg-config.
|  libdap-dev:amd64 depends on pkg-config; however:
|   Package pkg-config is to be removed.
| 
| (Reading database ... 579417 files and directories currently installed.)
| Removing pkg-config (0.29.1-0ubuntu4) ...
| Selecting previously unselected package pkgconf.
| (Reading database ... 579403 files and directories currently installed.)
| Preparing to unpack .../pkgconf_1.6.3-5_amd64.deb ...
| Adding 'diversion of /usr/bin/pkg-config to /usr/bin/pkg-config.real by
pkgconf'
| Adding 'diversion of /usr/share/aclocal/pkg.m4 to
/usr/share/aclocal/pkg.real.m4 by pkgconf'
| Adding 'diversion of /usr/share/man/man1/pkg-config.1.gz to
/usr/share/man/man1/pkg-config.real.1.gz by pkgconf'
| Adding 'diversion of /usr/share/pkg-config-crosswrapper to
/usr/share/pkg-config-crosswrapper.real by pkgconf'
| Unpacking pkgconf (1.6.3-5) ...
| Setting up libpkgconf3:amd64 (1.6.3-5) ...
| Setting up pkgconf (1.6.3-5) ...
| Processing triggers for man-db (2.9.1-1) ...
| Processing triggers for libc-bin (2.31-0ubuntu9.16) ...
| 
| After which 'sudo apt upgrade r-base-dev' ran. As far as I can tell, I
haven't totally borked my system (yet), and R 4.4.1 runs just fine, plus I
am not getting any further complaints from apt. But the process probably
isn't quite as intended.
| 
| Reporting this here after this came up on Mastodon by another user who ran
into the same issue:
| 
| https://emacs.ch/@pglpm/112664623789549089
| 
| and Dirk's suggestion to post this here.

This is mostly likely 'merely' a change coming from the other end
(i.e. Debian unstable/testing where I did what [1] shows) and which is out of
sync on a four years older (!!) release like focal until a) someone tells us
and/or b) someone sends us a tested / improved build recipe.

Most likely Michael (once he is back from a short trip) can just make an sed
call to adjust the debian/control file gets from my (current, Debian
unstable/testing) sources for these backports; switching pkgconf back to
pkg-config may be all it takes.

For what it is worth, I built also a 'local' build on 23.10 and it had
no
issues. Focal is older, you value its stability but there will an occassional
'tax' to pay on these deltas.

Thanks for reporting it though. These things can only be improved if we're
aware.

Dirk

[1] The corresponding debian/changelog was

r-base (4.4.0-2) unstable; urgency=medium

  * debian/control: Add libdeflate-dev to Depends of r-base-dev (Closes:
#1069842)
  * debian/control: Change pkg-config to pkgconf in Depends of r-base-dev
[lintian]

 -- Dirk Eddelbuettel <edd at debian.org>  Fri, 26 Apr 2024 08:46:14 -0500


| Best,
| Wolfgang
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| R-SIG-Debian at r-project.org
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-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org