[R-sig-Debian] Issue with pkgconf when upgrading to 4.4.1

[Viechtbauer, Wolfgang (NP)]

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 using 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 using 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