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From: Konrad Hinsen <konrad.hinsen@fastmail.net>
To: Tomas Volf <~@wolfsden.cz>
Cc: Guix Devel <guix-devel@gnu.org>
Subject: Re: Symlinks in "guix pack" and "guix shell"
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References: <m1o7d41o7m.fsf@fastmail.net> <ZbeJiqAlqGJTbxu3@ws>
Date: Mon, 29 Jan 2024 14:23:24 +0100
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Hi Tomas,

Thanks for your reply!

> I think the relevant part is whether some certificate package is installe=
d (via
> propagated inputs) or not.  If I explicitly add nss-certs to the command =
above,
> it starts to work:

Sorry, I forgot to add that I always have nss-certs among my packages
when I try this symlink. Otherwise I get an error message as well.

> Could you please share some examples where you get no error, but it has no
> effect?  Maybe they really are bugs (and should be reported).

Here is my most recent experiment:

$ guix time-machine --url=3Dhttps://codeberg.org/khinsen/guix.git --commit=
=3D615023ddc9407f27ec7c04060fb520a4cbb3b03f  --disable-authentication -- pa=
ck -S /etc/ssl=3Detc/ssl -S /etc/protocols=3Detc/protocols --format=3Dsquas=
hfs --save-provenance snakemake bash git git-annex coreutils wget python ns=
s-certs net-base
guix time-machine: warning: channel authentication disabled
guix pack: warning: ambiguous package specification `python'
guix pack: warning: choosing python@3.10.7 from gnu/packages/python.scm:610=
:2
/gnu/store/psq0bqcsnbk7p5w1m2771mlilyikicp6-snakemake-bash-git-git-annex-co=
reutils-squashfs-pack.gz.squashfs

$ singularity exec /gnu/store/psq0bqcsnbk7p5w1m2771mlilyikicp6-snakemake-ba=
sh-git-git-annex-coreutils-squashfs-pack.gz.squashfs bash
WARNING: passwd file doesn't exist in container, not updating
WARNING: group file doesn't exist in container, not updating
Singularity> ls /etc
hosts  localtime  resolv.conf
Singularity> exit

Neither /etc/ssl nor /etc/protocols are present in the container.

On the other hand, the same packages exported for Docker:

$ guix time-machine --url=3Dhttps://codeberg.org/khinsen/guix.git --commit=
=3D615023ddc9407f27ec7c04060fb520a4cbb3b03f  --disable-authentication -- pa=
ck -S /etc/ssl=3Detc/ssl -S /etc/protocols=3Detc/protocols --format=3Ddocke=
r --save-provenance snakemake bash git git-annex coreutils wget python nss-=
certs net-base
guix time-machine: warning: channel authentication disabled
guix pack: warning: ambiguous package specification `python'
guix pack: warning: choosing python@3.10.7 from gnu/packages/python.scm:432=
:2
/gnu/store/90ylyh60vvi2inqg9i8wlcfbv8m2px89-snakemake-bash-git-git-annex-co=
reutils-docker-pack.tar.gz

$ docker load -i /gnu/store/90ylyh60vvi2inqg9i8wlcfbv8m2px89-snakemake-bash=
-git-git-annex-coreutils-docker-pack.tar.gz
Loaded image: snakemake-bash-git-git-annex-coreutils:latest

$ docker run -it snakemake-bash-git-git-annex-coreutils:latest bash
bash-5.1# ls /etc
ls /etc
hostname  hosts  mtab  protocols  resolv.conf  ssl

Both links are present.

Finally, "guix shell" now works (I hadn't tried for a few months):

$ guix time-machine --url=3Dhttps://codeberg.org/khinsen/guix.git --commit=
=3D615023ddc9407f27ec7c04060fb520a4cbb3b03f  --disable-authentication -- sh=
ell -C -N -S /etc/ssl=3Detc/ssl -S /etc/protocols=3Detc/protocols snakemake=
 bash git git-annex coreutils wget python nss-certs net-base
guix time-machine: warning: channel authentication disabled
guix shell: warning: ambiguous package specification `python'
guix shell: warning: choosing python@3.10.7 from gnu/packages/python.scm:43=
2:2
[env]$ ls /etc
group  hosts  nsswitch.conf  passwd  protocols	resolv.conf  services  ssl

For this example, the only failure is for "pack =E2=80=93format=3Dsquashfs".
But the very same command line applied to a different commit (a few
weeks earlier) worked fine.

In case you wonder why I use a personal fork of Guix: For Singularity
export to be usable, I need a patch that is on core-updates
(https://git.savannah.gnu.org/cgit/guix.git/commit/?h=3Dcore-updates&id=3Dd=
8875d76555faf1a11f6838312bfe4b7f6121d2c). In
the meantime, I added a graft version of this patch to my personal fork.

Finally, I cleaned up the output of the above commands by removing the
usual messages from the build process, keeping only the messages that
are specific to my example.

Cheers,
  Konrad.