>From what I can tell this situation I landed in doesn't involve any bugs and won't happen to a normal user, but for the sake of documenting it for developers, here goes:
I have $XDG_CONFIG_HOME/guix/latest point to a git repository so I can update it swiftly. In the repo, a ./guix/config.scm is generated from ./guix/config.scm.in sometimes, I guess on ./configure; I haven't tried to figure out exactly when but certainly not every time I run 'make'. That config.scm will contain absolute paths to gzip, bzip2, and some other things. If you used a Guix environment to build, those will be /gnu/store/... paths. When you update things and garbage-collect, those store items might get removed, since $XDG_CONFIG_HOME/guix/latest/guix/config.scm is not a GC root (rightly so, as far as I understand). And thus, guix commands will start failing, saying they can't find /gnu/store/.../bin/bzip2 or whatever. That sums up the problem description. Fixing it might be tricky if you need to use 'guix environment' to run ./configure or whatever to fix the config.scm, since you possibly first need to fix the issue to be able to use 'guix environment' (it will work only if no calls are made to the missing /gnu/store/... executables). Manually fixing the config.scm is easy, fortunately. Just change the absolute /gnu/store/... paths which point at non-existing store items to point to existing store items. Taylan
