guix pull fails while Migrating profile generations

guix pull fails while Migrating profile generations

[Henk Katerberg]

On my GuixSD system:

# guix pull
Migrating profile generations to '/var/guix/profiles/per-user/root'...
guix pull: error: symlink: File exists: "/var/guix/profiles/per-user/root/current-guix-1-link"

# ls -al /var/guix/profiles/per-user/root
total 8
drwxr-xr-x 2 root root 4096 Oct 24 13:31 ./
drwxrwxrwt 4 root root 4096 Oct 19 13:13 ../
lrwxrwxrwx 1 root root   19 Oct 24 13:31 current-guix -> current-guix-6-link
lrwxrwxrwx 1 root root   51 Oct 23 10:47 current-guix-1-link -> /gnu/store/qdw75jq1ca2yn5v2p2shsqzynx9kb4ry-profile
lrwxrwxrwx 1 root root   51 Oct 23 10:47 current-guix-2-link -> /gnu/store/vq18fwd8h9c551iwjf2wdqdjiw7v6ga6-profile
lrwxrwxrwx 1 root root   51 Oct 23 10:47 current-guix-3-link -> /gnu/store/09c5qi053swrdsr4ydcm0f3xwpr3chl2-profile
lrwxrwxrwx 1 root root   51 Oct 23 10:49 current-guix-4-link -> /gnu/store/9lpay121z4r07m76fqq75a31njgdcysp-profile
lrwxrwxrwx 1 root root   51 Oct 24 09:17 current-guix-5-link -> /gnu/store/hi11y3myi2590ca7vkhilx12l6gd277s-profile
lrwxrwxrwx 1 root root   51 Oct 24 13:31 current-guix-6-link -> /gnu/store/dc6d6ycff573s8rln1sks02nghccgwfx-profile


I tried booting into an older generation of the system, but the current-guix-?-link symlinks are still there. Even in the first generation of the system guix pull now fails. Apparently due to its inability to create symlinks that are already there.

I tried removing the symlinks, but that did not resolve the issue.

What can I do to recover?

Regards,
Henk

Re: guix pull fails while Migrating profile generations

[Ludovic Courtès]

Hello,

Henk Katerberg <henk.katerberg@verum.com> skribis:

> # guix pull
> Migrating profile generations to '/var/guix/profiles/per-user/root'...
> guix pull: error: symlink: File exists: "/var/guix/profiles/per-user/root/current-guix-1-link"
>
> # ls -al /var/guix/profiles/per-user/root
> total 8
> drwxr-xr-x 2 root root 4096 Oct 24 13:31 ./
> drwxrwxrwt 4 root root 4096 Oct 19 13:13 ../
> lrwxrwxrwx 1 root root   19 Oct 24 13:31 current-guix -> current-guix-6-link
> lrwxrwxrwx 1 root root   51 Oct 23 10:47 current-guix-1-link -> /gnu/store/qdw75jq1ca2yn5v2p2shsqzynx9kb4ry-profile
> lrwxrwxrwx 1 root root   51 Oct 23 10:47 current-guix-2-link -> /gnu/store/vq18fwd8h9c551iwjf2wdqdjiw7v6ga6-profile
> lrwxrwxrwx 1 root root   51 Oct 23 10:47 current-guix-3-link -> /gnu/store/09c5qi053swrdsr4ydcm0f3xwpr3chl2-profile
> lrwxrwxrwx 1 root root   51 Oct 23 10:49 current-guix-4-link -> /gnu/store/9lpay121z4r07m76fqq75a31njgdcysp-profile
> lrwxrwxrwx 1 root root   51 Oct 24 09:17 current-guix-5-link -> /gnu/store/hi11y3myi2590ca7vkhilx12l6gd277s-profile
> lrwxrwxrwx 1 root root   51 Oct 24 13:31 current-guix-6-link -> /gnu/store/dc6d6ycff573s8rln1sks02nghccgwfx-profile

It seems that everything was migrated and is OK, but
~/.config/guix/current still points to the “old” target no?

Could you make sure you have something similar to this:

  $ readlink ~/.config/guix/current
  /var/guix/profiles/per-user/ludo/current-guix

?

HTH!

Ludo’.

RE: guix pull fails while Migrating profile generations

[Henk Katerberg]

Hi Ludo,

root@stoeptegel ~/.config/guix# ls -al
total 8
drwxr-xr-x 2 root root 4096 Nov  6 08:55 ./
drwxr-xr-x 3 root root 4096 Oct 19 13:33 ../
lrwxrwxrwx 1 root root   33 Oct 25 09:16 current -> /root/.config/guix/current-1-link


I have since performed the following steps:
  cd /var/guix/profiles/per-user/root
  rm current-guix-1-link
  rm current-guix-2-link
  rm current-guix-3-link
  rm current-guix-4-link
  rm current-guix-5-link
  rm current-guix-6-link
  rm current-guix 
  /run/current-system/profile/bin/guix pull

That pull no longer complained and seems to have been successfull:

root@stoeptegel ~/.config/guix# ls -al
total 8
drwxr-xr-x 2 root root 4096 Nov  6 09:01 ./
drwxr-xr-x 3 root root 4096 Oct 19 13:33 ../
lrwxrwxrwx 1 root root   45 Nov  6 09:01 current -> /var/guix/profiles/per-user/root/current-guix

root@stoeptegel ~# ls -al /var/guix/profiles/per-user/root
total 8
drwxr-xr-x 2 root root 4096 Nov  6 10:57 ./
drwxrwxrwt 5 root root 4096 Nov  6 08:54 ../
lrwxrwxrwx 1 root root   19 Nov  6 09:59 current-guix -> current-guix-2-link
lrwxrwxrwx 1 root root   51 Nov  6 09:59 current-guix-2-link -> /gnu/store/17mlp6dhc65mpqrm2x0w7p45znqxcfhs-profile

The machine is currently performing a guix system reconfigure. So, I think I've recovered.

Unfortunately, I have no way of reproducing the erroneous situation. I have experienced the problem on two distinct GuixSD installations and got there throught normal guix commands (no manual tinkering).


Regards,
Henk

________________________________________
From: Ludovic Courtès [ludo@gnu.org]
Sent: Tuesday, November 6, 2018 11:29 AM
To: Henk Katerberg
Cc: help-guix@gnu.org
Subject: Re: guix pull fails while Migrating profile generations

Hello,

Henk Katerberg <henk.katerberg@verum.com> skribis:

> # guix pull
> Migrating profile generations to '/var/guix/profiles/per-user/root'...
> guix pull: error: symlink: File exists: "/var/guix/profiles/per-user/root/current-guix-1-link"
>
> # ls -al /var/guix/profiles/per-user/root
> total 8
> drwxr-xr-x 2 root root 4096 Oct 24 13:31 ./
> drwxrwxrwt 4 root root 4096 Oct 19 13:13 ../
> lrwxrwxrwx 1 root root   19 Oct 24 13:31 current-guix -> current-guix-6-link
> lrwxrwxrwx 1 root root   51 Oct 23 10:47 current-guix-1-link -> /gnu/store/qdw75jq1ca2yn5v2p2shsqzynx9kb4ry-profile
> lrwxrwxrwx 1 root root   51 Oct 23 10:47 current-guix-2-link -> /gnu/store/vq18fwd8h9c551iwjf2wdqdjiw7v6ga6-profile
> lrwxrwxrwx 1 root root   51 Oct 23 10:47 current-guix-3-link -> /gnu/store/09c5qi053swrdsr4ydcm0f3xwpr3chl2-profile
> lrwxrwxrwx 1 root root   51 Oct 23 10:49 current-guix-4-link -> /gnu/store/9lpay121z4r07m76fqq75a31njgdcysp-profile
> lrwxrwxrwx 1 root root   51 Oct 24 09:17 current-guix-5-link -> /gnu/store/hi11y3myi2590ca7vkhilx12l6gd277s-profile
> lrwxrwxrwx 1 root root   51 Oct 24 13:31 current-guix-6-link -> /gnu/store/dc6d6ycff573s8rln1sks02nghccgwfx-profile

It seems that everything was migrated and is OK, but
~/.config/guix/current still points to the “old” target no?

Could you make sure you have something similar to this:

  $ readlink ~/.config/guix/current
  /var/guix/profiles/per-user/ludo/current-guix

?

HTH!

Ludo’.

Re: guix pull fails while Migrating profile generations

[Thorsten Wilms]

Hi!

On Ubuntu, starting from
"guix pull: error: symlink: File exists: ..."

I manually removed/changed/created symlinks and had guix working again.

A few `guix pull` and `sudo guix pull` later:

---
~: guix pull
guile: warning: failed to install locale
hint: Consider installing the `glibc-utf8-locales' or `glibc-locales' 
package and defining `GUIX_LOCPATH', along these lines:

      guix package -i glibc-utf8-locales
      export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"

See the "Application Setup" section in the manual, for more info.


Migrating profile generations to '/var/guix/profiles/per-user/thorwil'...
guix pull: error: symlink: File exists: 
"/var/guix/profiles/per-user/thorwil/current-guix"
---

(glibc-utf8-locales is installed and 
GUIX_LOCPATH=/home/thorwil/.guix-profile/lib/locale is set, but that's 
another topic)


Now:
---
~: readlink ~/.config/guix/current
current-1-link
---

current-1-link doesn't exist!


I'm breathing manually now. I would appreciate an overview of what is 
supposed to sit where and where it is supposed to point to. I may have 
gotten something wrong ... but then again, guix working and failing 
again shortly after isn't exactly the outcome I'd expect in that case.


Sidenote: I wanted to try pulling as root and then choosing the same 
commit as user, as recently suggested:

---
~: sudo guix describe
(...)
guix: describe: command not found
---

Plain `guix describe` did work, until this linking business went wrong 
again.

---
~: sudo guix --version
=> 0.15.0-2.8bbb79c
---

-- 
Thorsten Wilms

thorwil's design for free software:
http://thorwil.wordpress.com/

Overview of Guix pull symlinks and thoroughly test it

[swedebugia]

[-- Attachment #1: Type: text/plain, Size: 2108 bytes --]

Hi

Reading (again) about somebody being bit by the pull-bull ;-) (below)

Is there an overview of guix directories and symlinks?

Anyone got any ideas of how to thoroughly test this pull-beast to make 
it less brittle and erroneous?

Cheers

swedebugia


-------- Forwarded Message --------
Subject: 	Re: guix pull fails while Migrating profile generations
Date: 	Tue, 6 Nov 2018 20:33:54 +0100
From: 	Thorsten Wilms <t_w_@freenet.de>
Reply-To: 	t_w_@freenet.de
To: 	help-guix@gnu.org



Hi!

On Ubuntu, starting from
"guix pull: error: symlink: File exists: ..."

I manually removed/changed/created symlinks and had guix working again.

A few `guix pull` and `sudo guix pull` later:

---
~: guix pull
guile: warning: failed to install locale
hint: Consider installing the `glibc-utf8-locales' or `glibc-locales' 
package and defining `GUIX_LOCPATH', along these lines:

guix package -i glibc-utf8-locales
export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale"

See the "Application Setup" section in the manual, for more info.


Migrating profile generations to '/var/guix/profiles/per-user/thorwil'...
guix pull: error: symlink: File exists: 
"/var/guix/profiles/per-user/thorwil/current-guix"
---

(glibc-utf8-locales is installed and 
GUIX_LOCPATH=/home/thorwil/.guix-profile/lib/locale is set, but that's 
another topic)


Now:
---
~: readlink ~/.config/guix/current
current-1-link
---

current-1-link doesn't exist!


I'm breathing manually now. I would appreciate an overview of what is 
supposed to sit where and where it is supposed to point to. I may have 
gotten something wrong ... but then again, guix working and failing 
again shortly after isn't exactly the outcome I'd expect in that case.


Sidenote: I wanted to try pulling as root and then choosing the same 
commit as user, as recently suggested:

---
~: sudo guix describe
(...)
guix: describe: command not found
---

Plain `guix describe` did work, until this linking business went wrong 
again.

---
~: sudo guix --version
=> 0.15.0-2.8bbb79c
---

-- 
Thorsten Wilms

thorwil's design for free software:
http://thorwil.wordpress.com/


[-- Attachment #2: Type: text/html, Size: 4326 bytes --]

Re: guix pull fails while Migrating profile generations

[Thorsten Wilms]

On 06/11/2018 20.33, Thorsten Wilms wrote:

> A few `guix pull` and `sudo guix pull` later:
> 
> ---
> ~: guix pull

> Migrating profile generations to '/var/guix/profiles/per-user/thorwil'...
> guix pull: error: symlink: File exists: 
> "/var/guix/profiles/per-user/thorwil/current-guix"
> ---

Since guix is working again, it seems this was about the change from
export 
PATH="/home/thorwil/.guix-profile/bin:/home/thorwil/.guix-profile/sbin${PATH:+:}$PATH"
to
export PATH="/home/thorwil/.config/guix/current/bin${PATH:+:}$PATH"

I edited .profile, but didn't consider to bring that change to the 
current terminal. Sorry about the noise.


-- 
Thorsten Wilms

thorwil's design for free software:
http://thorwil.wordpress.com/

Re: guix pull fails while Migrating profile generations

[Thorsten Wilms]

On 07/11/2018 16.04, Thorsten Wilms wrote:
> Since guix is working again, it seems this was about the change from
> export 
> PATH="/home/thorwil/.guix-profile/bin:/home/thorwil/.guix-profile/sbin${PATH:+:}$PATH" 
> 
> to
> export PATH="/home/thorwil/.config/guix/current/bin${PATH:+:}$PATH"

Wrong once more. One reboot later, it happens again:

~: guix pull
(...)
Migrating profile generations to '/var/guix/profiles/per-user/thorwil'...
guix pull: error: symlink: File exists: 
"/var/guix/profiles/per-user/thorwil/current-guix-3-link"


So I haven't got the slightest clue what got it back to working the last 
time.


-- 
Thorsten Wilms

thorwil's design for free software:
http://thorwil.wordpress.com/

Re: guix pull fails while Migrating profile generations

[Ludovic Courtès]

Hi,

Thorsten Wilms <t_w_@freenet.de> skribis:

> On 07/11/2018 16.04, Thorsten Wilms wrote:
>> Since guix is working again, it seems this was about the change from
>> export
>> PATH="/home/thorwil/.guix-profile/bin:/home/thorwil/.guix-profile/sbin${PATH:+:}$PATH" 
>>
>> to
>> export PATH="/home/thorwil/.config/guix/current/bin${PATH:+:}$PATH"
>
> Wrong once more. One reboot later, it happens again:
>
> ~: guix pull
> (...)
> Migrating profile generations to '/var/guix/profiles/per-user/thorwil'...
> guix pull: error: symlink: File exists:
> "/var/guix/profiles/per-user/thorwil/current-guix-3-link"

Could you try this:

  rm ~/.config/guix/current
  ln -s /var/guix/profiles/per-user/thorwil/current-guix \
        ~/.config/guix/current

and then:

  guix pull -l 1w

?

HTH,
Ludo’.

Re: guix pull fails while Migrating profile generations

[Thorsten Wilms]

On 09/11/2018 17.37, Ludovic Courtès wrote:
> Could you try this:
> 
>    rm ~/.config/guix/current
>    ln -s /var/guix/profiles/per-user/thorwil/current-guix \
>          ~/.config/guix/current

I did that 2 or 3 `guix pull` ago and the error didn't appear again since.


> and then:
> 
>    guix pull -l 1w
> 
> ?

Generation 1	Nov 07 2018 21:45:53
   guix b31e156
     repository URL: https://git.savannah.gnu.org/git/guix.git
     branch: master
     commit: b31e1561611ebe4916890183b24e6e13cb83bf59
Generation 2	Nov 07 2018 22:09:09
   guix ea68b3f
     repository URL: https://git.savannah.gnu.org/git/guix.git
     branch: master
     commit: ea68b3f6527cf4a02c554cf3f6f446e30f4940f6
   2 packages upgraded: mash@2.1, minced@0.3.2
Generation 3	Nov 08 2018 11:03:36
   guix 8fa9ace
     repository URL: https://git.savannah.gnu.org/git/guix.git
     branch: master
     commit: 8fa9ace1d6022ff2dca4618d1c7b22dc4be28b86
   2 new packages: python-pyelftools, spread-sheet-widget
   12 packages upgraded: java-ngs@2.9.3, ncbi-vdb@2.9.3, ngs-sdk@2.9.3, 
preseq@2.0.3, pspp@1.2.0,
     python-ilinkedlist@0.3.1, raxml@8.2.12, ritornello@2.0.1, 
seqtk@1.3, sra-tools@2.9.3, tadbit@0.2.0,
     vsearch@2.9.1
Generation 4	Nov 09 2018 18:40:29	(current)
   guix 06bc7b8
     repository URL: https://git.savannah.gnu.org/git/guix.git
     branch: master
     commit: 06bc7b82f7c6cb623911867f55b58b3316d3ddfc
   14 new packages: emacs-clang-format, emacs-gtk-look, fstrcmp, 
r-aggregation, r-arm, r-destiny,
     r-feature, r-h5, r-ks, r-misc3d, r-multicool, r-rgl, r-savr, xmlrpc-c
   7 packages upgraded: crossguid@0.0-2.fef89a4, 
guile-newt@0-1.4eaa3cf84, kodi@18.0b5,
     r-minimal@3.5.1, r@3.5.1, rmath-standalone@3.5.1, wxmaxima@18.10.1


-- 
Thorsten Wilms

thorwil's design for free software:
http://thorwil.wordpress.com/