Bug 1669824

I don't think it's selinux related (restorecon).
It's more likely a corrupted sqlite database
and you fixed it by dump & restore.
Running out of space in / looks like the root cause.
System can get into an undefined state pretty easily.

If yous still have it, could you attach the broken
/var/lib/dnf/history.sqlite file to this bug?
If it's too big or if you don't want to attach it to a public bugzilla,
you can either email me (dmach) the file or link to it.

I have just re-checked that this is the broken version of the `history.sqlite` file and uploaded it here:

https://uni-bonn.sciebo.de/s/2IyonVck9y2leGp

The link should be good until 2019-12-31.

I ran:
PRAGMA integrity_check;
row 50351 missing from index rpm_name
row 52357 missing from index rpm_name
row 52739 missing from index rpm_name
row 56528 missing from index rpm_name
row 61235 missing from index rpm_name
row 67482 missing from index rpm_name

To fix that, I ran:
REINDEX;

This might help us to recover from this state.
Still not sure what the root cause is.

We need to read through https://www.sqlite.org/howtocorrupt.html
and make sure we don't do any of those steps in libdnf or in combination with PackageKit.

Data point: encountered the same issue with a different error message

SQLite version 3.26.0 2018-12-01 12:34:55
Enter ".help" for usage hints.
sqlite> PRAGMA integrity_check;
*** in database main ***
On tree page 2887 cell 223: invalid page number 21365001
Multiple uses for byte 2492 of page 2887
Error: database disk image is malformed
sqlite> 

dumping and undumping fixed the issue

I encountered the same issue and the reason was probably full filesystem on /.

I solved it by dump/restore of /usr/lib/dnf/history.sqlite.

Just hit this on f30, I've not knowingly filled up my /

[dg@major ~]$ sudo dnf remove v8-devel
terminate called after throwing an instance of 'SQLite3::LibException'
  what():  Step: database disk image is malformed in

        SELECT
            ti.action as action,
            ti.reason as reason
        FROM
            trans_item ti
        JOIN
            trans t ON ti.trans_id = t.id
        JOIN
            rpm i USING (item_id)
        WHERE
            t.state = 1
            /* see comment in TransactionItem.hpp - TransactionItemAction */
            AND ti.action not in (3, 5, 7, 10)
            AND i.name = 'grub2-pc-modules'
            AND i.arch = 'noarch'
        ORDER BY
            ti.trans_id DESC
        LIMIT 1
    
Aborted

Hit me also on F30 during update of packages

INSERT OR REPLACE INTO item_replaced_by VALUES (30730, 30729)

Removed all files

rm -rf /var/cache/dnf/* /var/lib/dnf/* /var/lib/yum/*

and run again

dnf update

This solved the issue

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@Ben I'm having the same issue right now in fedora 34, I run dnf update after installation and got this error, now every time I tried to install or run an update shows this error:

Total                                                                                                                                   246 kB/s | 1.3 MB     00:05     
Running transaction check
error: SELECT DISTINCT key FROM 'Requirename' ORDER BY key: 11: database disk image is malformed
...

  Installing       : newt-0.52.21-9.fc34.x86_64                                                                                                                     2/5 
error: INSERT INTO 'Requirename' VALUES(?, ?, ?): 11: database disk image is malformed
error: INSERT INTO 'Requirename' VALUES(?, ?, ?): 11: database disk image is malformed
error: INSERT INTO 'Requirename' VALUES(?, ?, ?): 11: database disk image is malformed
error: INSERT INTO 'Requirename' VALUES(?, ?, ?): 11: database disk image is malformed

----------------------------
dnf log file shows:

  File "/usr/lib/python3.9/site-packages/dnf/cli/main.py", line 130, in cli_run
    ret = resolving(cli, base)
  File "/usr/lib/python3.9/site-packages/dnf/cli/main.py", line 176, in resolving
    base.do_transaction(display=displays)
  File "/usr/lib/python3.9/site-packages/dnf/cli/cli.py", line 264, in do_transaction
    raise dnf.exceptions.Error(_('Transaction failed'))
dnf.exceptions.Error: Transaction failed
2021-06-07T09:48:31+0100 CRITICAL Error: Transaction failed

José,
the issue you have is a different one than this bug.
It is most likely related to RPM database rather than anything in DNF.
If you have more details than what you have reported or ideally a reproducer, could you file a new bug on RPM?