Getting "error: db5-error(5) from dbenv->open - In/Out-error"

[Jon Ingason]

I just installed Fedora 26 Beta 1.4 Gnome Workstation from
Fedora-Server-netinst-x86_64-26_Beta-1.4.iso. Then I did "sudo dnf
update" in terminal window:

$ sudo dnf update --refresh
Fedora 26 - x86_64 - Test Updates               5.4 MB/s |  23 MB
00:04
Senaste kontroll av utgång av metadata: för 0:00:00 sedan den ons 14 jun
2017 19
:16:47.
Beroenden upplösta.
================================================================================
 Paket            Arkitektur  Version                Förråd
 Storlk
================================================================================
Uppgraderar:
 libdb            x86_64      5.3.28-22.fc26         updates-testing
 749 k
 libdb-utils      x86_64      5.3.28-22.fc26         updates-testing
 137 k

Transaktionssammanfattning
================================================================================
Uppgradera  2 Paket

Total storlek att hämta: 887 k
Är detta ok [j/N]: j
Hämtar paket:
(1/2): libdb-utils-5.3.28-22.fc26.x86_64.rpm    1.7 MB/s | 137 kB
00:00
(2/2): libdb-5.3.28-22.fc26.x86_64.rpm          4.0 MB/s | 749 kB
00:00
--------------------------------------------------------------------------------
Totalt                                          691 kB/s | 887 kB     00:01
varning:
/var/cache/dnf/updates-testing-b081e891bd0bf8fd/packages/libdb-5.3.28-2
2.fc26.x86_64.rpm: Huvud V3 RSA/SHA256 Signature, nyckel-ID 64dab85d: NOKEY
Importing GPG key 0x64DAB85D:
 Userid     : "Fedora 26 Primary (26)
<fedora-26-primary(a)fedoraproject.org&gt;&quot;
 Fingerprint: E641 850B 77DF 4353 78D1 D7E2 812A 6B4B 64DA B85D
 From       : /etc/pki/rpm-gpg/RPM-GPG-KEY-fedora-26-x86_64
Är detta ok [j/N]: j
Nyckelimport lyckades
Kör transaktionskontroll
Transaktionskontrollen lyckades.
Kör transaktionstest
Transaktionstesten lyckades.
Kör transaktionen
  Förbereder   :
   1/1
  Uppgraderar  : libdb-5.3.28-22.fc26.x86_64
   1/4
  Kör skript   : libdb-5.3.28-22.fc26.x86_64
   1/4
  Uppgraderar  : libdb-utils-5.3.28-22.fc26.x86_64
   2/4
  Rensar upp   : libdb-utils-5.3.28-21.fc26.x86_64
   3/4
  Rensar upp   : libdb-5.3.28-21.fc26.x86_64
   4/4
  Kör skript   : libdb-5.3.28-21.fc26.x86_64
   4/4
  Verifierar   : libdb-5.3.28-22.fc26.x86_64
   1/4
  Verifierar   : libdb-utils-5.3.28-22.fc26.x86_64
   2/4
  Verifierar   : libdb-5.3.28-21.fc26.x86_64
   3/4
  Verifierar   : libdb-utils-5.3.28-21.fc26.x86_64
   4/4

Uppgraderade:
  libdb.x86_64 5.3.28-22.fc26         libdb-utils.x86_64 5.3.28-22.fc26


Klart!
$ sudo dnf install gnome-tweak-tool
fel: db5-fel(5) från dbenv->open: In/ut-fel
fel: kan inte öppna Packages-indexet med db5 - In/ut-fel (5)
fel: kan inte öppna paketdatabas i /var/lib/rpm
Fel: Error: rpmdb open failed
$

I guess that there is something wrong with libdb-5.3.28-21.fc26.x86_64
or libdb-utils.x86_64 5.3.28-22.fc26

Some suggestion what to do?
-- 
Regards

Jon Ingason

[Adam Williamson]

On Wed, 2017-06-14 at 19:46 +0200, Jon Ingason wrote:
>  I just installed Fedora 26 Beta 1.4 Gnome Workstation from
>  Fedora-Server-netinst-x86_64-26_Beta-1.4.iso. Then I did "sudo dnf
>  update" in terminal window:
>  
>  $ sudo dnf update --refresh
>  Fedora 26 - x86_64 - Test Updates               5.4 MB/s |  23 MB
>  00:04
>  Senaste kontroll av utgång av metadata: för 0:00:00 sedan den ons 14 jun
>  2017 19
>  :16:47.
>  Beroenden upplösta.
>  ================================================================================
>   Paket            Arkitektur  Version                Förråd
>   Storlk
>  ================================================================================
>  Uppgraderar:
>   libdb            x86_64      5.3.28-22.fc26         updates-testing
>   749 k
>   libdb-utils      x86_64      5.3.28-22.fc26         updates-testing
>   137 k
>  
>  Transaktionssammanfattning
>  ================================================================================
>  Uppgradera  2 Paket
>  
>  Total storlek att hämta: 887 k
>  Är detta ok [j/N]: j
>  Hämtar paket:
>  (1/2): libdb-utils-5.3.28-22.fc26.x86_64.rpm    1.7 MB/s | 137 kB
>  00:00
>  (2/2): libdb-5.3.28-22.fc26.x86_64.rpm          4.0 MB/s | 749 kB
>  00:00
>  --------------------------------------------------------------------------------
>  Totalt                                          691 kB/s | 887 kB     00:01
>  varning:
>  /var/cache/dnf/updates-testing-b081e891bd0bf8fd/packages/libdb-5.3.28-2
>  2.fc26.x86_64.rpm: Huvud V3 RSA/SHA256 Signature, nyckel-ID 64dab85d: NOKEY
>  Importing GPG key 0x64DAB85D:
>   Userid     : "Fedora 26 Primary (26)
> <fedora-26-primary(a)fedoraproject.org&gt;&quot;
>   Fingerprint: E641 850B 77DF 4353 78D1 D7E2 812A 6B4B 64DA B85D
>   From       : /etc/pki/rpm-gpg/RPM-GPG-KEY-fedora-26-x86_64
>  Är detta ok [j/N]: j
>  Nyckelimport lyckades
>  Kör transaktionskontroll
>  Transaktionskontrollen lyckades.
>  Kör transaktionstest
>  Transaktionstesten lyckades.
>  Kör transaktionen
>    Förbereder   :
>     1/1
>    Uppgraderar  : libdb-5.3.28-22.fc26.x86_64
>     1/4
>    Kör skript   : libdb-5.3.28-22.fc26.x86_64
>     1/4
>    Uppgraderar  : libdb-utils-5.3.28-22.fc26.x86_64
>     2/4
>    Rensar upp   : libdb-utils-5.3.28-21.fc26.x86_64
>     3/4
>    Rensar upp   : libdb-5.3.28-21.fc26.x86_64
>     4/4
>    Kör skript   : libdb-5.3.28-21.fc26.x86_64
>     4/4
>    Verifierar   : libdb-5.3.28-22.fc26.x86_64
>     1/4
>    Verifierar   : libdb-utils-5.3.28-22.fc26.x86_64
>     2/4
>    Verifierar   : libdb-5.3.28-21.fc26.x86_64
>     3/4
>    Verifierar   : libdb-utils-5.3.28-21.fc26.x86_64
>     4/4
>  
>  Uppgraderade:
>    libdb.x86_64 5.3.28-22.fc26         libdb-utils.x86_64 5.3.28-22.fc26
>  
>  
>  Klart!
>  $ sudo dnf install gnome-tweak-tool
>  fel: db5-fel(5) från dbenv->open: In/ut-fel
>  fel: kan inte öppna Packages-indexet med db5 - In/ut-fel (5)
>  fel: kan inte öppna paketdatabas i /var/lib/rpm
>  Fel: Error: rpmdb open failed
>  $
>  
>  I guess that there is something wrong with libdb-5.3.28-21.fc26.x86_64
>  or libdb-utils.x86_64 5.3.28-22.fc26
>  
>  Some suggestion what to do? 
This is known. Don't worry about the error message, it's harmless. If
you get errors when trying to run dnf, yum, etc. in future, run 'rpm --
rebuilddb' and it should fix it.

See:

https://fedoraproject.org/wiki/Common_F26_bugs#libdb-rebuilddb

Sorry for the trouble.
-- 
Adam Williamson
Fedora QA Community Monkey
IRC: adamw | Twitter: AdamW_Fedora | XMPP: adamw AT happyassassin . net
http://www.happyassassin.net

[Jon Ingason]

Den 2017-06-14 kl. 19:55, skrev Adam Williamson:
>  On Wed, 2017-06-14 at 19:46 +0200, Jon Ingason wrote:
> > I just installed Fedora 26 Beta 1.4 Gnome Workstation from
> > Fedora-Server-netinst-x86_64-26_Beta-1.4.iso. Then I did "sudo dnf
> > update" in terminal window:
> >
> > $ sudo dnf update --refresh
> > Fedora 26 - x86_64 - Test Updates               5.4 MB/s |  23 MB
> > 00:04
> > Senaste kontroll av utgång av metadata: för 0:00:00 sedan den ons 14 jun
> > 2017 19
> > :16:47.
> > Beroenden upplösta.
> > ================================================================================
> >  Paket            Arkitektur  Version                Förråd
> >  Storlk
> > ================================================================================
> > Uppgraderar:
> >  libdb            x86_64      5.3.28-22.fc26         updates-testing
> >  749 k
> >  libdb-utils      x86_64      5.3.28-22.fc26         updates-testing
> >  137 k
> >
> > Transaktionssammanfattning
> > ================================================================================
> > Uppgradera  2 Paket
> >
> > Total storlek att hämta: 887 k
> > Är detta ok [j/N]: j
> > Hämtar paket:
> > (1/2): libdb-utils-5.3.28-22.fc26.x86_64.rpm    1.7 MB/s | 137 kB
> > 00:00
> > (2/2): libdb-5.3.28-22.fc26.x86_64.rpm          4.0 MB/s | 749 kB
> > 00:00
> > --------------------------------------------------------------------------------
> > Totalt                                          691 kB/s | 887 kB     00:01
> > varning:
> > /var/cache/dnf/updates-testing-b081e891bd0bf8fd/packages/libdb-5.3.28-2
> > 2.fc26.x86_64.rpm: Huvud V3 RSA/SHA256 Signature, nyckel-ID 64dab85d: NOKEY
> > Importing GPG key 0x64DAB85D:
> >  Userid     : "Fedora 26 Primary (26)
> <fedora-26-primary(a)fedoraproject.org&gt;&quot;
> >  Fingerprint: E641 850B 77DF 4353 78D1 D7E2 812A 6B4B 64DA B85D
> >  From       : /etc/pki/rpm-gpg/RPM-GPG-KEY-fedora-26-x86_64
> > Är detta ok [j/N]: j
> > Nyckelimport lyckades
> > Kör transaktionskontroll
> > Transaktionskontrollen lyckades.
> > Kör transaktionstest
> > Transaktionstesten lyckades.
> > Kör transaktionen
> >   Förbereder   :
> >    1/1
> >   Uppgraderar  : libdb-5.3.28-22.fc26.x86_64
> >    1/4
> >   Kör skript   : libdb-5.3.28-22.fc26.x86_64
> >    1/4
> >   Uppgraderar  : libdb-utils-5.3.28-22.fc26.x86_64
> >    2/4
> >   Rensar upp   : libdb-utils-5.3.28-21.fc26.x86_64
> >    3/4
> >   Rensar upp   : libdb-5.3.28-21.fc26.x86_64
> >    4/4
> >   Kör skript   : libdb-5.3.28-21.fc26.x86_64
> >    4/4
> >   Verifierar   : libdb-5.3.28-22.fc26.x86_64
> >    1/4
> >   Verifierar   : libdb-utils-5.3.28-22.fc26.x86_64
> >    2/4
> >   Verifierar   : libdb-5.3.28-21.fc26.x86_64
> >    3/4
> >   Verifierar   : libdb-utils-5.3.28-21.fc26.x86_64
> >    4/4
> >
> > Uppgraderade:
> >   libdb.x86_64 5.3.28-22.fc26         libdb-utils.x86_64 5.3.28-22.fc26
> >
> >
> > Klart!
> > $ sudo dnf install gnome-tweak-tool
> > fel: db5-fel(5) från dbenv->open: In/ut-fel
> > fel: kan inte öppna Packages-indexet med db5 - In/ut-fel (5)
> > fel: kan inte öppna paketdatabas i /var/lib/rpm
> > Fel: Error: rpmdb open failed
> > $
> >
> > I guess that there is something wrong with libdb-5.3.28-21.fc26.x86_64
> > or libdb-utils.x86_64 5.3.28-22.fc26
> >
> > Some suggestion what to do?
>  
>  This is known. Don't worry about the error message, it's harmless. If
>  you get errors when trying to run dnf, yum, etc. in future, run 'rpm --
>  rebuilddb' and it should fix it.
>  
>  See:
>  
>  https://fedoraproject.org/wiki/Common_F26_bugs#libdb-rebuilddb
>  
>  Sorry for the trouble.
>   
:-) Reboot fixed the problem. I guess this is same problem which people
had with the FC25 version and discussed on the userlist.

-- 
Regards

Jon Ingason

[R P Herrold]

On Wed, 14 Jun 2017, Jon Ingason wrote:

>  I just installed Fedora 26 Beta 1.4 Gnome Workstation from
>  Fedora-Server-netinst-x86_64-26_Beta-1.4.iso. Then I did "sudo dnf
>  update" in terminal window:
>  
>  $ sudo dnf update --refresh
>  Fedora 26 - x86_64 - Test Updates               5.4 MB/s |  23 MB
>  00:04
>  Senaste kontroll av utgång av metadata: för 0:00:00 sedan den ons 14 jun
>  2017 19
>  :16:47.
>  Beroenden upplösta. 
Tt has long been known that using potentially 'stale' cursor 
handles, under a scripting language such as Python, which, as 
we look at the transaction, is modifying the BDB backing store 
'underneath itself'.  This will result in corruption such as 
this.  An ancient version of 'yum' back in the Seth K Vidal 
days ran into this as well.  This is nothing new, or 
unknowable as to its source

It is not RPM, it is not BDB -- it is incautious coders trying 
to change the tires on a moving vehicle without adequate 
precautions, and being surprised when 'bad stuff' TM happens

-- Russ herrold