Hi,

I also observed this bug and reported it as 53355.  I tried to search
for bugs, but I didn't find this bug report until Ludo mentioned it.  I
think it's probably the same bug, so I've merged them.

Ludovic Courtès <ludo@gnu.org> writes:

> It looks like the shell-check machinery is misdiagnosing things, as
> Vagrant reported in <https://issues.guix.gnu.org/51466> (is this on
> Debian too?).

Yes, it's also Debian.  Debian Bullseye.  I've also verified that
similar behavior occurs on Fedora, although the problematic env vars are
different.  I tried fiddling with SHELL like Vagrant did, but I couldn't
make the error go away like he did.  Maybe I did something differently.

> Could you try the debugging tricks I proposed there?

Sure thing!  Thank you for taking the time to make the patch, even
though it was simple.  Here is the result on my Debian Bullseye ppc64el
system:

--8<---------------cut here---------------start------------->8---
[0] [env] marusich@suzaku:~/guix-master
$ ./pre-inst-env guix shell --check --pure --development guix
guix shell: checking the environment variables visible from shell '/bin/sh'...

;;; (dropped "env || /usr/bin/env || set; echo GUIX-CHECK-DONE; read x; exit" #<vlist ()>)

;;; (variable "$ LIBRARY_PATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/lib" "$ LIBRARY_PATH")

;;; (variable "C_INCLUDE_PATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/include" "C_INCLUDE_PATH")

;;; (variable "USER=marusich" "USER")

;;; (variable "GUIX_LOCPATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/lib/locale" "GUIX_LOCPATH")

;;; (variable "HOME=/home/marusich" "HOME")

;;; (variable "GUILE_LOAD_COMPILED_PATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/lib/guile/3.0/site-ccache:/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/share/guile/site/3.0" "GUILE_LOAD_COMPILED_PATH")

;;; (variable "CPLUS_INCLUDE_PATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/include/c++:/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/include" "CPLUS_INCLUDE_PATH")

;;; (variable "INFOPATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/share/info" "INFOPATH")

;;; (variable "LOGNAME=marusich" "LOGNAME")

;;; (variable "PKG_CONFIG_PATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/lib/pkgconfig" "PKG_CONFIG_PATH")

;;; (variable "TERM=screen.xterm-256color" "TERM")

;;; (variable "ACLOCAL_PATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/share/aclocal" "ACLOCAL_PATH")

;;; (variable "PATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/bin:/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/sbin" "PATH")

;;; (variable "GUIX_ENVIRONMENT=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile" "GUIX_ENVIRONMENT")

;;; (variable "GUILE_LOAD_PATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/share/guile/site/3.0" "GUILE_LOAD_PATH")

;;; (variable "PWD=/home/marusich/guix-master" "PWD")
guix shell: warning: variable 'LIBRARY_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.

[1] [env] marusich@suzaku:~/guix-master
$
--8<---------------cut here---------------end--------------->8---

The presence of the "$" in front of LIBRARY_PATH seems suspicious:

  ;;; (variable "$ LIBRARY_PATH=/gnu/store/hvcq6yjfjjc7060pq09zm1rj02mivg4h-profile/lib" "$ LIBRARY_PATH")

I'm not sure why the "$" is being added.  I tried various things to
remove it.  I tried explicitly setting PS1 to an empty string in my
~/.bashrc.  I also tried setting it explicitly to an empty string in
/etc/profile.  Maybe if we can figure out where that "$ " prefix is
coming from, we can resolve this issue?

-- 
Chris

PGP: https://savannah.gnu.org/people/viewgpg.php?user_id=106836