bug#58988: guix pull stopped to work on my GuixSD

bug#58988: guix pull stopped to work on my GuixSD

[guixuser]

Hello, in the last days I cant sucessfully use "guix pull" anymore, the 
command always fails showing a stack trace and a big sequences of zeros. 
I first asked help on #guix at irc.libera.chat, I tried "sudo -i guix 
pull", also tried "guix gc --verify=contents,repair" but unfortunately I 
still with the same results when trying guix pull.

Here is the output I get when issuing "guix pull"

$ guix pull                                                              
                                                                          
                             [470/472]
Atualizando canal "guix" a partir do repositório Git 
"https://git.savannah.gnu.org/git/guix.git"...
Compilando a partir deste canal:
   guix      https://git.savannah.gnu.org/git/guix.git   e26b529
Backtrace:
In ice-9/boot-9.scm:
   1752:10 19 (with-exception-handler _ _ #:unwind? _ # _)
In guix/store.scm:
    659:37 18 (thunk)
In guix/status.scm:
     815:4 17 (call-with-status-report _ _)
In guix/store.scm:
    1321:3 16 (_)
    1298:8 15 (call-with-build-handler #<procedure 7fe3b3dbc900 at g…> …)
In guix/build/syscalls.scm:
    1425:3 14 (_)
    1392:4 13 (call-with-file-lock/no-wait _ #<procedure 7fe3a9cbcde…> …)
In guix/store.scm:
   2168:25 12 (run-with-store #<store-connection 256.99 7fe3b3da9e10> …)
In guix/scripts/pull.scm:
     452:2 11 (_ _)
In guix/channels.scm:
     891:2 10 (_ _)
In guix/monads.scm:
     471:9  9 (_ _)
In guix/store.scm:
   1996:13  8 (_ #<store-connection 256.99 7fe3b3da9e10>)
In guix/channels.scm:
    682:20  7 (build-from-source #<<channel-instance> channel: #<<ch…> …)
In ice-9/boot-9.scm:
    2836:4  6 (save-module-excursion #<procedure 7fe3a0b12520 at guix…>)
In guix/channels.scm:
    689:25  5 (_)
In unknown file:
            4 (primitive-load "/gnu/store/cpc4zc2cn4sslr043lxf5virg7p…")
In ice-9/eval.scm:
    223:20  3 (proc #<directory (guile-user) 7fe3bc68dc80>)
In unknown file:
            2 (%resolve-variable (7 . #) #<directory (guile-user) 7fe…>)
In ice-9/boot-9.scm:
   1685:16  1 (raise-exception _ #:continuable? _)
   1685:16  0 (raise-exception _ #:continuable? _)

ice-9/boot-9.scm:1685:16: In procedure raise-exception:
erro: 
#{\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x
0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;
\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x
....
0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;}#: 
variável não vinculada

bug#58988: Adding more verbose information

[guixuser]

I still learning about guile and guix, I found I way to provide the 
complete output of stacktrace, I first loaded guix in a interactive 
session with "pull" as the unique argument as follows, and applied 
(main), and after the exceptions I used ,bt command.

$ guile -l $(which guix) -- pull
GNU Guile 3.0.8
Copyright (C) 1995-2021 Free Software Foundation, Inc.

Guile comes with ABSOLUTELY NO WARRANTY; for details type `,show w'.
This program is free software, and you are welcome to redistribute it
under certain conditions; type `,show c' for details.

Enter `,help' for help.
scheme@(guile-user)> (main)
Atualizando canal "guix" a partir do repositório Git 
"https://git.savannah.gnu.org/git/guix.git"...
Compilando a partir deste canal:
   guix      https://git.savannah.gnu.org/git/guix.git   e3280ae
ice-9/boot-9.scm:1685:16: In procedure raise-exception:
erro: 
#{\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x
...

Entering a new prompt.  Type `,bt' for a backtrace or `,q' to continue.
scheme@(guile-user) [1]> ,bt
In guix/ui.scm:
    2238:7 24 (run-guix . _)
   2201:10 23 (run-guix-command _ . _)
In ice-9/boot-9.scm:
   1752:10 22 (with-exception-handler _ _ #:unwind? _ #:unwind-for-type 
_)
   1747:15 21 (with-exception-handler #<procedure 7f4d1f502c90 at 
ice-9/boot-9.scm:1831:7 (exn)> _ #:unwind? _ #:unwind-for-type _)
   1752:10 20 (with-exception-handler _ _ #:unwind? _ #:unwind-for-type 
_)
In guix/store.scm:
    659:37 19 (thunk)
In guix/status.scm:
     815:4 18 (call-with-status-report _ _)
In guix/store.scm:
    1321:3 17 (_)
    1298:8 16 (call-with-build-handler #<procedure 7f4d1f502480 at 
guix/ui.scm:1170:2 (continue store things mode)> _)
In guix/build/syscalls.scm:
    1425:3 15 (_)
    1392:4 14 (call-with-file-lock/no-wait _ #<procedure 7f4cfbddadb0 at 
guix/scripts/pull.scm:890:21 ()> _)
In guix/store.scm:
   2168:25 13 (run-with-store #<store-connection 256.99 7f4d1f3f5a50> 
#<procedure 7f4cfbdddf60 at guix/scripts/pull.scm:452:2 (state)> 
#:guile-for-build _ #:system _ #:target _)
In guix/scripts/pull.scm:
     452:2 12 (_ _)
In guix/channels.scm:
     891:2 11 (_ _)
In guix/monads.scm:
     471:9 10 (_ _)
In guix/store.scm:
   1996:13  9 (_ #<store-connection 256.99 7f4d1f3f5a50>)
In guix/channels.scm:
    682:20  8 (build-from-source #<<channel-instance> channel: 
#<<channel> name: guix url: "https://git.savannah.gnu.org/git/guix.git" 
branch: "master" commit: #f introduction: #<<channel-in…> …)
In ice-9/boot-9.scm:
    2836:4  7 (save-module-excursion #<procedure 7f4d1433f7a0 at 
guix/channels.scm:683:20 ()>)
In guix/channels.scm:
    689:25  6 (_)
In unknown file:
            5 (primitive-load 
"/gnu/store/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae/build-aux/build-self.scm")
In ice-9/eval.scm:
    223:20  4 (proc #<directory (guile-user) 7f4d1f460c80>)
In unknown file:
            3 (%resolve-variable (7 . #) #<directory (guile-user) 
7f4d1f460c80>)
In ice-9/boot-9.scm:
   1685:16  2 (raise-exception _ #:continuable? _)
   1685:16  1 (raise-exception _ #:continuable? _)
   1685:16  0 (raise-exception _ #:continuable? _)

bug#58988: How Can I restore a file inside /gnu/store/ ?

[guixuser]

I think I tracked the problem but I still dont know how to fix this, the 
file used just before the exceptions being triggered which is 
'buid-self.scm' just have a bunch of 0's, I need to fix this file but 
/gnu/store/ is read only, How can I restore this file?

~$ hexdump 
/gnu/store/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae/build-aux/build-self.scm
0000000 0000 0000 0000 0000 0000 0000 0000 0000
*
0005930 0000 0000 0000 0000 0000
0005939

bug#58988: How Can I restore a file inside /gnu/store/ ?

[Tobias Geerinckx-Rice via Bug reports for GNU Guix]

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Heyo,

Adding some notable info that user_ shared on IRC:

> user2@host ~$ sudo guix build --repair 
> /gnu/store/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae
> Senha: 
> substitute: atualizando substitutos de 
> "https://ci.guix.gnu.org"... 100.0%
> substituindo 
> /gnu/store/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae...
> baixando de 
> https://ci.guix.gnu.org/nar/lzip/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae 
> ...
>
> guix-e3280ae               792KiB/s 00:21 | 16.1MiB transferred

guixuser@airmail.cc 写道：
> I need to fix this file but
> /gnu/store/ is read only, How can I restore this file?

Well, ‘sudo guix gc --verify=contents,repair’, or ‘guix build 
--repair’.

Since neither worked: if you've ‘guix pull’ed before, you should 
have some previous profiles as

  /var/guix/profiles/per-user/$USER/current-guix-*

If so: see if pulling any of those works, e.g.,

  $ /var/guix/profiles/per-user/$USER/current-guix-1-link/bin/guix 
  pull

Kind regards,

T G-R

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bug#58988: How Can I restore a file inside /gnu/store/ ?

[guixuser]

On 2022-11-04 10:18, Tobias Geerinckx-Rice wrote:
> Heyo,
> 
> Adding some notable info that user_ shared on IRC:
> 
>> user2@host ~$ sudo guix build --repair 
>> /gnu/store/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae
>> Senha: substitute: atualizando substitutos de 
>> "https://ci.guix.gnu.org"... 100.0%
>> substituindo 
>> /gnu/store/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae...
>> baixando de 
>> https://ci.guix.gnu.org/nar/lzip/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae 
>> ...
>> 
>> guix-e3280ae               792KiB/s 00:21 | 16.1MiB transferred
> 
> guixuser@airmail.cc 写道：
>> I need to fix this file but
>> /gnu/store/ is read only, How can I restore this file?
> 
> Well, ‘sudo guix gc --verify=contents,repair’, or ‘guix build 
> --repair’.
> 
> Since neither worked: if you've ‘guix pull’ed before, you should have
> some previous profiles as
> 
>  /var/guix/profiles/per-user/$USER/current-guix-*
> 
> If so: see if pulling any of those works, e.g.,
> 
>  $ /var/guix/profiles/per-user/$USER/current-guix-1-link/bin/guix  pull
> 
> Kind regards,
> 
> T G-R

Thanks for the input, but I still dont get it working I tried few 
differente profiles here, but they all still referencing the corrupted 
file, as an example I trie the following:

$  /var/guix/profiles/per-user/user/guix-profile-685-link/bin/guix pull  
                                                                          
                            [471/1977]
Atualizando canal "guix" a partir do repositório Git 
"https://git.savannah.gnu.org/git/guix.git"...
Autenticando canal "guix", commits de 9edb3f6 a 04f8295 (1 novos 
commits)...
Compilando a partir deste canal:
   guix      https://git.savannah.gnu.org/git/guix.git   04f8295
Backtrace:
In ice-9/boot-9.scm:
   1752:10 19 (with-exception-handler _ _ #:unwind? _ # _)
In guix/store.scm:
    659:37 18 (thunk)
In guix/status.scm:
     815:4 17 (call-with-status-report _ _)
In guix/store.scm:
    1321:3 16 (_)
    1298:8 15 (call-with-build-handler #<procedure 7ff172bd8a20 at g…> …)
In guix/build/syscalls.scm:
    1425:3 14 (_)
    1392:4 13 (call-with-file-lock/no-wait _ #<procedure 7ff172ef236…> …)
In guix/store.scm:
   2168:25 12 (run-with-store #<store-connection 256.99 7ff172b9f730> …)
In guix/scripts/pull.scm:
     452:2 11 (_ _)
In guix/channels.scm:
     891:2 10 (_ _)
In guix/monads.scm:
     471:9  9 (_ _)
In guix/store.scm:
   1996:13  8 (_ #<store-connection 256.99 7ff172b9f730>)
In guix/channels.scm:
    682:20  7 (build-from-source #<<channel-instance> channel: #<<ch…> …)
In ice-9/boot-9.scm:
    2836:4  6 (save-module-excursion #<procedure 7ff17513ce20 at guix…>)
In guix/channels.scm:
    689:25  5 (_)
In unknown file:
            4 (primitive-load "/gnu/store/vg5b37za8np63s03g98b8rw60h3…")
In ice-9/eval.scm:
    223:20  3 (proc #<directory (guile-user) 7ff177312c80>)
In unknown file:
            2 (%resolve-variable (7 . #) #<directory (guile-user) 7ff…>)
In ice-9/boot-9.scm:
   1685:16  1 (raise-exception _ #:continuable? _)
   1685:16  0 (raise-exception _ #:continuable? _)

ice-9/boot-9.scm:1685:16: In procedure raise-exception:
erro: 
#{\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\x0;\
....

bug#58988: How Can I restore a file inside /gnu/store/ ?

[guixuser]

On 2022-11-04 10:18, Tobias Geerinckx-Rice wrote:
> Heyo,
> 
> Adding some notable info that user_ shared on IRC:
> 
>> user2@host ~$ sudo guix build --repair 
>> /gnu/store/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae
>> Senha: substitute: atualizando substitutos de 
>> "https://ci.guix.gnu.org"... 100.0%
>> substituindo 
>> /gnu/store/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae...
>> baixando de 
>> https://ci.guix.gnu.org/nar/lzip/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae 
>> ...
>> 
>> guix-e3280ae               792KiB/s 00:21 | 16.1MiB transferred
> 
> guixuser@airmail.cc 写道：
>> I need to fix this file but
>> /gnu/store/ is read only, How can I restore this file?
> 
> Well, ‘sudo guix gc --verify=contents,repair’, or ‘guix build 
> --repair’.
> 
> Since neither worked: if you've ‘guix pull’ed before, you should have
> some previous profiles as
> 
>  /var/guix/profiles/per-user/$USER/current-guix-*
> 
> If so: see if pulling any of those works, e.g.,
> 
>  $ /var/guix/profiles/per-user/$USER/current-guix-1-link/bin/guix  pull
> 
> Kind regards,
> 
> T G-R

After trying "guix pull" with all "guix-<N>-link/bin/guix" files, I 
suspected that all 'build-self.scm' in my /gnu/store/ are corrupted, to 
confirm this I performed a find taking md5sum, and got the following 
output which confirm the corruption, Now I need to know if there is a 
way to manually fix this file, I know that touching /gnu/store/ is a bad 
idea, but since all those files are corrupted I cant see other way to 
fix my problem.

output:

$ find /gnu/store/ -name build-self.scm -exec md5sum {} \;
578dfd3e0a9384241db46b8e62340334  
/gnu/store/4m5pyspndkxzbq4vdyvidj9w0sckww8n-guix-c6d9492/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/59ff5s88yi480gi4rhws6lwk9gbxpz59-guix-314b436/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/65dcad1dnr354szvszg8y1hywclrml1b-guix-67a2049/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/vg5b37za8np63s03g98b8rw60h3vv2am-guix-04f8295/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/cd1858l8nawifai86wkj6df7rffw5c16-guix-34e6c5d/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/cpc4zc2cn4sslr043lxf5virg7pamj1n-guix-e26b529/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/iqmi836vjlyjdqqxyxax3z1yll4fh7pr-guix-86ec52f/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/ghmkh782rccb6l72k36f0qyayxlmaih7-guix-759d365/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/wc5i3nqg0z0rzkfab4swsyqpvj6fzb0f-guix-16d4ded/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/vqcnr5xx5m1g3wz9l2hvqmmxsf68fgyf-guix-3a84b4e/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/84vryc461kzcqk3ziyi8w800rndwz291-guix-1682aba/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/08h2958kbz7v2y9s4a97zgpd02avg6h6-guix-08f2a06/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/6ikw4m2hmwnp56iwlhhlai665qv78cn1-guix-4dfaddf/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/pakkv44927w98d965rhpdig6vk21hrn8-guix-d85c254/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/k1x5m8dhwwz5qiycgc96xwsw09r70jyw-guix-973dc45/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/r6j6whnjxvbay4r8yw54gcslwpzzq9bg-guix-754f260/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/541vb5bj1vichpwz24vba2bj8hgxclpm-guix-72a41c4/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/i6k6mx1s72vfqx27bybcpb1cf6cs8fvw-guix-7ecd85e/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/s9hjqjgwh9wmrx13vz542mnw66dl8ngx-guix-e0b414f/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/nxw9fhqjbwr9rdjza80d2r4aknb0qprw-guix-49e1a3a/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/yjllxib1fm3zqkwmr5j4lpxhz3zqsjjz-guix-e3280ae/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/1my1nch1kpymk85yf1469hf55d84k7q3-guix-3d8c243/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/y6j8bxwn9wi1c8lp41qs6d1xr5ps75di-guix-cd0d27f/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/v7z0c5c15k737i4041gp7q4ppd3fny7z-guix-270eb27/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/rxz8byngcmsq095f6j79n5wyw917f0nd-guix-1ea1fa9/build-aux/build-self.scm
578dfd3e0a9384241db46b8e62340334  
/gnu/store/m0g57k94wslg5zlz4b1apzl34mzk4dkp-guix-bebbf35/build-aux/build-self.scm

bug#58988: Solved

[guixuser]

Hello Guix, it turns out that after checking all my 'build-self.scm' in 
my /gnu/store was corrupted with 0's, I just tried the most direct 
approach, remounting /gnu/store as 'rw' and copying the original file 
from savannah, so it just worked, 'guix pull' it working again and after 
I pulled all went fine again.

Thanks you all.

bug#58988: guix pull stopped to work on my GuixSD

[Maxime Devos]

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retitle 58988 guix pull stopped to work on my Guix System
thanks

Small name correction for the record -- GuixSD is an old name.

Greetings,
Maxime.

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