This is a recently installed Debian bookworm system, initially using the
package from debian experimental (guix 1.3.0-3, built with guile 3.0),
and "guix pull" up to a recent guix master:

vagrant@vagranttdgxbookworm:~$ guix describe
Generation 7    Oct 28 2021 11:04:25    (current)
  guix 0e6470b
    repository URL: /home/vagrant/src/guix
    branch: master
    commit: 0e6470b47f00470c213fbf20bddc5bcf1e2f8e2a


Most things seem to work fine, but noticed an oddity with guix shell:

vagrant@vagranttdgxbookworm:~$ guix shell --pure --check --development guix guix git less

guix shell: checking the environment variables visible from shell
'/bin/bash'...
guix shell: warning: variable 'PKG_CONFIG_PATH' is missing from shell
environment
hint: One or more environment variables have a different value in the
shell than the one we set.  This means that you may find yourself
running code in an environment different from the one you asked Guix to
prepare.

This usually indicates that your shell startup files are unexpectedly
modifying those environment variables.  For example, if you
are using Bash, make sure that environment variables are set or modified
in `~/.bash_profile' and _not_ in `~/.bashrc'.  For more
information on Bash startup files, run:

     info "(bash) Bash Startup Files"

Alternatively, you can avoid the problem by passing the `--container' or
`-C' option.  That will give you a fully isolated
environment running in a "container", immune to the issue described
above.

vagrant@vagranttdgxbookworm:~$ guix shell --pure --development guix guix git less

vagrant@vagranttdgxbookworm:~$ echo $PKG_CONFIG_PATH
/gnu/store/9vk59alg27y0cp1za91nfdjiy718cn1f-profile/lib/pkgconfig


So, --check seems to think the environment variable is missing but
running without --check the variable is defined...

I don't see anything obviously relevent in /etc/profile/ or
/etc/profile.d/guix.sh or /etc/profile.d/bash-completions.sh or
~/.profile or ~/.bashrc ... just used the defaults that shipped in
Debian.


live well,
  vagrant