guix guix-science channels : built incompatibilties

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2 participants
  • Andreas Enge
  • Arnaud Mounier
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Arnaud Mounier
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A
A
Arnaud Mounier wrote on 18 Aug 06:48 -0700
(address . bug-guix@gnu.org)
83ff8736-d00a-42da-b992-2114a160f24f@ube.fr
Hi,
I recently install Guix on a GNU/Linux Debian Bookworm on a separate
partion /gnu. I upgrade to Debian Trixie right now and after that I try
to upgrade my Guix foreign distro install.
What I have done, after Trixie update :
1. $> sudo -i guix pull
2. $> guix pull
after that I want to update packages ($>guix package -u) but I can't yet.
The first "guix pull" work fine but not the second one.
I'm asking if it's the right way to update guix within a foreign distro.
Here is the result of the "guix pull" with my user :
Toggle quote (22 lines)
> ❯ guix pull
> Mise à jour du canal « guix-science » depuis le dépôt Git « https://codeberg.org/guix-science/guix-science.git »...
> Mise à jour du canal « guix » depuis le dépôt Git « https://git.guix.gnu.org/guix.git »...
> Construction depuis ces canaux :
> guix-sciencehttps://codeberg.org/guix-science/guix-science.git 7bbff91
> guix https://git.guix.gnu.org/guix.git ef6b7bf
> Computing Guix derivation for 'x86_64-linux'... |warning: 'youtube-dl' is deprecated, use 'yt-dlp' instead
> /
> substitute: mise à jour des substituts depuis « https://ci.guix.gnu.org »... 100.0 %
> La dérivation suivante sera compilée :
> /gnu/store/iidk170dicniy40czi9ldvzqm1slziff-profile.drv
>
> construction du cache des paquets…
> -builder for `/gnu/store/hn41v25h4b1bmy9jihxhr00smaizg8vy-guix-package-cache.drv' failed to produce output path `/gnu/store/3lkzw6msnry9cwlbvazjss27af37fn34-guix-package-cache'
> la compilation de /gnu/store/hn41v25h4b1bmy9jihxhr00smaizg8vy-guix-package-cache.drv a échoué
> conseil : Cela indique généralement un bogue dans l'un des canaux que vous tirez (pull), ou une incompatibilité entre eux. Vous pouvez consulter le log généré et rapporter le problème aux développeurs du canal.
>
> Les canaux que vous tirez sont : guix-science guix.
>
> Vous trouverez le journal de compilation dans « /var/log/guix/drvs/hn/41v25h4b1bmy9jihxhr00smaizg8vy-guix-package-cache.drv.gz ».
> cannot build derivation `/gnu/store/iidk170dicniy40czi9ldvzqm1slziff-profile.drv': 1 dependencies couldn't be built
> guix pull: erreur : build of `/gnu/store/iidk170dicniy40czi9ldvzqm1slziff-profile.drv' failed
And the backtrace :
Toggle quote (41 lines)
> ❯ zcat /var/log/guix/drvs/hn/41v25h4b1bmy9jihxhr00smaizg8vy-guix-package-cache.drv.gz
> (repl-version 0 1 1)
> Generating package cache for '/gnu/store/jy4cpng62x8kqjb3py2iw0zvl7w1cjca-profile'...
>
> Backtrace:
> In guix/repl.scm:
> 141:4 19 (machine-repl _ _)
> 126:7 18 (_)
> In ice-9/boot-9.scm:
> 1747:15 17 (with-exception-handler #<procedure 7fffedf75f90 at ic…> …)
> 1752:10 16 (with-exception-handler _ _ #:unwind? _ # _)
> In guix/repl.scm:
> 99:21 15 (_)
> In unknown file:
> 14 (_ #<procedure 7fffedf70960 at guix/repl.scm:100:25 ()> …)
> 13 (primitive-load "/gnu/store/r5jydxgp5y16n0l7zi1znf5d1nj…")
> In ice-9/boot-9.scm:
> 1752:10 12 (with-exception-handler _ _ #:unwind? _ # _)
> In gnu/packages.scm:
> 466:11 11 (generate-package-cache _)
> In srfi/srfi-1.scm:
> 460:18 10 (fold #<procedure expand-cache expr> _ _)
> In gnu/packages.scm:
> 426:37 9 (expand-cache . _)
> In guix/packages.scm:
> 1444:17 8 (supported-package? #<package python-jupyterlab@4.3.4 …> …)
> In guix/memoization.scm:
> 101:0 7 (_ #<hash-table 7ffff78187a0 23941/28099> #<package py…> …)
> In guix/packages.scm:
> 1422:39 6 (_)
> 1692:16 5 (package->bag _ _ _ #:graft? _)
> 1796:47 4 (thunk)
> In guix-science/packages/jupyter.scm:
> 105:11 3 (native-inputs #<package python-jupyterlab@4.3.4 guix-s…>)
> In ice-9/boot-9.scm:
> 1685:16 2 (raise-exception _ #:continuable? _)
> 1780:13 1 (_ #<&compound-exception components: (#<&undefined-vari…>)
> In unknown file:
> 0 (backtrace #<undefined>)
>
> (exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (nss-certs-for-test)) (value #f))
Thank's a lot,
arnome
--
« Quand les hommes considèrent certaines situations comme réelles, elles
sont réelles dans leur conséquence. »
Le théorème de Thomas.
..: Arnaud Mounier • Informaticien :..
UMR 6298 ARTEHIS - Archéologie, Terre, Histoire et Sociétés
Bâtiment Sciences Gabriel
6, Boulevard Gabriel
21000 Dijon
Téléphone : 0 380 393 622
A
A
Andreas Enge wrote on 18 Aug 08:10 -0700
(name . Arnaud Mounier)(address . arnaud.mounier@ube.fr)(address . 79263-done@debbugs.gnu.org)
aKNCYEayZFxGMVCM@jurong
Hello,

and thanks for your report!

This is also handled on codeberg, and actually an issue with the
guix-science channel:
after we made a change in Guix.

This should be fixed now, and you should be able to do a
"guix pull" again.

Andreas
Closed
A
A
Arnaud Mounier wrote on 18 Aug 23:43 -0700
(name . Andreas Enge)(address . andreas@enge.fr)(address . 79263-done@debbugs.gnu.org)
d65305ca-5cac-4416-8dd8-8871e64aba03@ube.fr
Hello Andreas,
Many thanks for this prompt reaction. It works fine now, and the pull
and package update commands ended successfully. You can close this bug.
I still have one question on the update process of Guix on a foreign
distro. Here's what I attempted to do:
1. <user@fd>$> sudo -i guix pull
2. <user@fd>$> guix pull
3. <user@fd>$> guix package -u
Is it the right way to do it, or do I just need the last 2 commands?
Should I add a point between 1 and 2 with this command?
<user>$>sudo -i guix package -u
Please excuse me if it's not the right way to ask this kind of unrelated
bug question. If so, do you know where I can ask it?
Regards,
arnome
Le 18/08/2025 à 17:10, Andreas Enge a écrit :
Toggle quote (14 lines)
> Hello,
>
> and thanks for your report!
>
> This is also handled on codeberg, and actually an issue with the
> guix-science channel:
> https://codeberg.org/guix-science/guix-science/issues/157
> after we made a change in Guix.
>
> This should be fixed now, and you should be able to do a
> "guix pull" again.
>
> Andreas
>
--
« Quand les hommes considèrent certaines situations comme réelles, elles
sont réelles dans leur conséquence. »
Le théorème de Thomas.
..: Arnaud Mounier • Informaticien :..
UMR 6298 ARTEHIS - Archéologie, Terre, Histoire et Sociétés
Bâtiment Sciences Gabriel
6, Boulevard Gabriel
21000 Dijon
Téléphone : 0 380 393 622
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