nix-collect-garbage: error getting outputs of ... database disk image is malformed

I started getting these errors and I can no longer collect garbage.

# nix-collect-garbage 
finding garbage collector roots...
deleting garbage...
deleting '...'
...
deleting '...'
error: error getting outputs of ‘/nix/store/3zhh42kb125zmxi9kfqn6c6xxbzvggi2-gtk2-engines.deb.drv’: database disk image is malformed
0 store paths deleted, 0.00 MiB freed

The error is not always for the same file. Attached are 3 example drv files for which the error occurs.
errors.zip

I ran nix-store --verify --check-contents --repair and it succeeded without finding any issue.

Can you try

sqlite3 /nix/var/nix/db/db.sqlite 'pragma integrity_check'

This should print ok.

Hi,
I actually already worked around this issue (by deleting the GC root that was pulling in the problematic drvs and manually deleting these drvs, don't know if the latter was necessary). So while I don't know what this test would have done before I did that, now it does say ok.

> sqlite3 /nix/var/nix/db/db.sqlite 'pragma integrity_check' 
*** in database main ***
Page 957: btreeInitPage() returns error code 11
Page 13391: btreeInitPage() returns error code 11
Page 6178: btreeInitPage() returns error code 11
Page 10204: btreeInitPage() returns error code 11
Page 7794: btreeInitPage() returns error code 11
Error: database disk image is malformed

I'll try the solution the original reporter used -- track down the derivations responsible and evict them.

It wasn't possible. This fixed the issue:

# cd /nix/var/nix/db
# nix-shell -p sqlite

[nix-shell:/nix/var/nix/db]# sqlite3 db.sqlite ".backup 'db.bak.sqlite' "

[nix-shell:/nix/var/nix/db]# sqlite3 db.sqlite 
SQLite version 3.24.0 2018-06-04 19:24:41
Enter ".help" for usage hints.
sqlite> .output db.sql
sqlite> .dump
sqlite> 

[nix-shell:/nix/var/nix/db]# sqlite3 db.new.sqlite < db.sql

[nix-shell:/nix/var/nix/db]# mv db.new.sqlite db.sqlite

I was hoping that simply using the backup would be good enough, but it retained the corruption. It was necessary to make a textual export and rebuild the database.

It wasn't possible. This fixed the issue:
# nix-shell -p sqlite

[nix-shell:/nix/var/nix/db]# sqlite3 db.sqlite ".backup 'db.bak.sqlite' "

[nix-shell:/nix/var/nix/db]# sqlite3 db.sqlite 
SQLite version 3.24.0 2018-06-04 19:24:41
Enter ".help" for usage hints.
sqlite> .output db.sql
sqlite> .dump
sqlite> 

[nix-shell:/nix/var/nix/db]# sqlite3 db.new.sqlite < db.sql

[nix-shell:/nix/var/nix/db]# mv db.new.sqlite db.sqlite
I was hoping that simply using the backup would be good enough, but it retained the corruption. It was necessary to make a textual export and rebuild the database.

At first I forgot the cd /nix/var/nix/db step before running that but that fixed it indeed.

Oh yes! Sorry for not being explicit. Edited my previous comment to include the cd step.

This issue could be closed. I also experienced corruption but that was related to running out of disk space on /nix (future folx, make sure you check this!)

I marked this as stale due to inactivity. → More info

I closed this issue due to inactivity. → More info

@573

I'm still seeing this. Note that I had to change the actual .sql file produced by @573's answer. I had to remove BEGIN TRANSACTION and ROLLBACK, save the file, and then apply it. This took ages to complete, and then led me to issue 2218 which I could fix with @sondnm's solution there.

@pmiddend

I'm also seeing this, @pmiddend I kept the BEGIN TRANSACTION and changed the ROLLBACK to COMMIT in the dumped db.sql, then sqlite3 newdb.sqlite <db.sql ran pretty fast, and after moving newdb.sqlite to the location, it seems to fix my problem.

This issue has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/an-easier-way-to-repair-corrupted-nix-db/35915/1

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nix-collect-garbage: error getting outputs of ... database disk image is malformed #1353

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nix-collect-garbage: error getting outputs of ... database disk image is malformed #1353

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ambrop72 commented on Apr 22, 2017

edolstra commented on Apr 24, 2017

ambrop72 commented on Apr 24, 2017

sjmackenzie commented on Nov 23, 2018

clacke commented on Nov 23, 2018

clacke commented on Nov 23, 2018

573 commented on Apr 4, 2019

clacke commented on Apr 4, 2019

ghuntley commented on Sep 6, 2020

stale commented on Mar 5, 2021

stale commented on Apr 21, 2022

pmiddend commented on Aug 28, 2023

blurgyy commented on Aug 30, 2023

nixos-discourse commented on Nov 23, 2023

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