RPM DB_VERSION_MISMATCH #47

Thorfin · 2019-09-16T12:29:27Z

Describe the bug

Run Yum update, or try to install a package using yum:

RPM: error: db5 error(-30969) from dbenv->open: BDB0091 DB_VERSION_MISMATCH: Database environment version mismatch
RPM: error: cannot open Packages index using db5 - (-30969)
RPM: error: cannot open Packages database in /var/lib/rpm
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Could not run transaction.

To Reproduce
Steps to reproduce the behavior:

Reboot
yum update
See error

Expected behavior
Updates completed succesfully

Additional context
I have deleted and started from scratch the whole WSL environment and yum works for one update cycle, then after an update and reboot I get the same error above.

Basic Troubleshooting Checklist

[x] I have searched Google for the error message.
[x] I have checked official WSL troubleshooting documentation: https://docs.microsoft.com/en-us/windows/wsl/troubleshooting#confirm-wsl-is-enabled.
[x] I have searched the official Microsoft WSL issues page: https://github.com/Microsoft/WSL/issues.
[x] I have searched the WLinux issues page: https://github.com/WhitewaterFoundry/WLinux/issues.
[x] I have reset WLinux: Settings->Apps->Apps & features->WLinux->Advanced Options->Reset.
[x] I have disabled and re-enabled WSL in Windows Features.
[x] I have run Windows 10 updates and restarted.

Windows Build

OS Version: 10.0.18362 N/A Build 18362

copy paste:

[root@SAMPC ~]# yum update
whitewaterfoundry_wslu 256 B/s | 833 B 00:03
Dependencies resolved.

Package Architecture Version Repository Size

Upgrading:
dnf noarch 4.2.8-2.fc30 updates 405 k
dnf-data noarch 4.2.8-2.fc30 updates 45 k
dnf-yum noarch 4.2.8-2.fc30 updates 42 k
fontconfig x86_64 2.13.1-9.fc30 updates 253 k
jbig2dec-libs x86_64 0.16-1.fc30 updates 69 k
libdnf x86_64 0.35.2-3.fc30 updates 589 k
libxcrypt x86_64 4.4.9-1.fc30 updates 123 k
libxcrypt-compat x86_64 4.4.9-1.fc30 updates 96 k
polkit-libs x86_64 0.116-2.fc30 updates 64 k
python3-dnf noarch 4.2.8-2.fc30 updates 413 k
python3-hawkey x86_64 0.35.2-3.fc30 updates 93 k
python3-libdnf x86_64 0.35.2-3.fc30 updates 708 k
vim-common x86_64 2:8.1.1991-2.fc30 updates 6.7 M
vim-enhanced x86_64 2:8.1.1991-2.fc30 updates 1.4 M
vim-filesystem noarch 2:8.1.1991-2.fc30 updates 28 k
vim-minimal x86_64 2:8.1.1991-2.fc30 updates 619 k

Transaction Summary

Upgrade 16 Packages

Total download size: 12 M
Is this ok [y/N]: y
Downloading Packages:
(1/16): dnf-yum-4.2.8-2.fc30.noarch.rpm 86 kB/s | 42 kB 00:00
(2/16): dnf-data-4.2.8-2.fc30.noarch.rpm 79 kB/s | 45 kB 00:00
(3/16): fontconfig-2.13.1-9.fc30.x86_64.rpm 288 kB/s | 253 kB 00:00
(4/16): jbig2dec-libs-0.16-1.fc30.x86_64.rpm 77 kB/s | 69 kB 00:00
(5/16): dnf-4.2.8-2.fc30.noarch.rpm 259 kB/s | 405 kB 00:01
(6/16): libxcrypt-compat-4.4.9-1.fc30.x86_64.rpm 265 kB/s | 96 kB 00:00
(7/16): polkit-libs-0.116-2.fc30.x86_64.rpm 269 kB/s | 64 kB 00:00
(8/16): libdnf-0.35.2-3.fc30.x86_64.rpm 609 kB/s | 589 kB 00:00
(9/16): libxcrypt-4.4.9-1.fc30.x86_64.rpm 130 kB/s | 123 kB 00:00
(10/16): python3-hawkey-0.35.2-3.fc30.x86_64.rpm 530 kB/s | 93 kB 00:00
(11/16): python3-dnf-4.2.8-2.fc30.noarch.rpm 232 kB/s | 413 kB 00:01
(12/16): python3-libdnf-0.35.2-3.fc30.x86_64.rpm 195 kB/s | 708 kB 00:03
(13/16): vim-filesystem-8.1.1991-2.fc30.noarch.rpm 272 kB/s | 28 kB 00:00
(14/16): vim-minimal-8.1.1991-2.fc30.x86_64.rpm 393 kB/s | 619 kB 00:01
(15/16): vim-enhanced-8.1.1991-2.fc30.x86_64.rpm 334 kB/s | 1.4 MB 00:04
(16/16): vim-common-8.1.1991-2.fc30.x86_64.rpm 612 kB/s | 6.7 MB 00:11

Total 809 kB/s | 12 MB 00:14
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
RPM: error: db5 error(-30969) from dbenv->open: BDB0091 DB_VERSION_MISMATCH: Database environment version mismatch
RPM: error: cannot open Packages index using db5 - (-30969)
RPM: error: cannot open Packages database in /var/lib/rpm
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Could not run transaction.
[root@SAMPC ~]#

Thorfin · 2019-09-16T12:49:23Z

I've tried "normal fixes" for this issue but they don't fix it in this case, I think it might be to do with the WSL element?

crramirez · 2019-09-16T12:50:43Z

Run this

sudo dnf upgrade --refresh rpm glibc
sudo rm /var/lib/rpm/.rpm.lock
sudo dnf upgrade dnf

And try again.

From: #46 (comment)

Thorfin · 2019-09-16T13:20:45Z

The above just hung for me and didn't do anything.

I found https://github.com/WhitewaterFoundry/Pengwin-Enterprise/issues/20 and followed:

sudo -s
cd /var/lib/rpm
rpm --rebuilddb
dd if=/dev/zero of=__db.001 bs=1M count=1
dd if=/dev/zero of=__db.002 bs=1M count=1
dd if=/dev/zero of=__db.003 bs=1M count=1
rpm -qa rpm
yum install vim

Which seems to have fixed the issue now.

Thankyou for your help.

crramirez · 2019-10-13T19:14:29Z

A fix was uploaded to the store with the version 1.30.5.0 if someone can check if the error is gone away.

PhilBarila · 2019-10-23T16:07:34Z

I can't comment on the store version, but @Thorfin's resolution worked for me in 1.30.1.0 that I downloaded from here.

cbowlesatx · 2019-10-29T04:35:06Z

sudo dnf upgrade --refresh rpm glibc
sudo rm /var/lib/rpm/.rpm.lock
sudo dnf upgrade dnf

Same issue, this worked for me.

ElvenSpellmaker · 2019-10-30T11:01:03Z

@crramirez's solution worked for me too, even if the two dnf commands said "nothing to do" haha.

ACTom · 2020-01-06T08:56:29Z

The above just hung for me and didn't do anything.

I found https://github.com/WhitewaterFoundry/Pengwin-Enterprise/issues/20 and followed:

sudo -s
cd /var/lib/rpm
rpm --rebuilddb
dd if=/dev/zero of=__db.001 bs=1M count=1
dd if=/dev/zero of=__db.002 bs=1M count=1
dd if=/dev/zero of=__db.003 bs=1M count=1
rpm -qa rpm
yum install vim

Which seems to have fixed the issue now.

Thankyou for your help.

cd /var/lib/rpm
dd if=/dev/zero of=__db.001 bs=1M count=1
dd if=/dev/zero of=__db.002 bs=1M count=1
dd if=/dev/zero of=__db.003 bs=1M count=1

this worked for me.

christianfosli · 2020-02-07T08:05:11Z

In my case it was enough to simply delete the lock file

sudo rm /var/lib/rpm/.rpm.lock

whiteear · 2020-03-04T07:29:50Z

simply, this worked in my case [windows WSL fedora 31]

In my case it was enough to simply delete the lock file
sudo rm /var/lib/rpm/.rpm.lock

WSLUser · 2020-03-13T16:46:11Z

yep, removing the lock file is enough.

fritzr · 2020-04-17T20:55:29Z

After installing many packages just fine this error randomly occurred when trying to dnf install cmake ninja-build. After removing the lock file and cleaning packages with sudo dnf clean packages I was able to successfully install the packages.

tqmillerusa · 2020-06-21T16:58:23Z

Just removing the lock file worked for me, as well.

crramirez · 2020-06-21T20:27:29Z

Try the new script upgrade.sh and see if it fixes it as well

BlackthornYugen · 2021-03-28T20:14:51Z

The above just hung for me and didn't do anything.
I found https://github.com/WhitewaterFoundry/Pengwin-Enterprise/issues/20 and followed:
sudo -s
cd /var/lib/rpm
rpm --rebuilddb
dd if=/dev/zero of=__db.001 bs=1M count=1
dd if=/dev/zero of=__db.002 bs=1M count=1
dd if=/dev/zero of=__db.003 bs=1M count=1
rpm -qa rpm
yum install vim
Which seems to have fixed the issue now.
Thankyou for your help.
cd /var/lib/rpm
dd if=/dev/zero of=__db.001 bs=1M count=1
dd if=/dev/zero of=__db.002 bs=1M count=1
dd if=/dev/zero of=__db.003 bs=1M count=1
this worked for me.

I tried this and it didn't fix my issue:

sudo dnf upgrade --refresh rpm glibc
sudo rm /var/lib/rpm/.rpm.lock
sudo dnf upgrade dnf

I'm not a fan of sudo -s so I tried this and it worked:

cd /var/lib/rpm/
sudo rpm --rebuilddb
sudo rpm -qa rpm

I didn't need to use dd to zero out __db.xxx files. I would have tried that next if I still had issues.

Miriam-CID · 2021-03-30T22:35:09Z

In my case, it was useful for installing libcanberrra in RHEL8

cd /var/lib/rpm
rpm --rebuilddb
rpm -qa rpm

yum install -y libcanberra-gtk*

Result:
Installed:
libcanberra-gtk2-0.30-16.el8.x86_64
Complete!

PROBLEM BEFORE
yum install -y libcanberra-gtk

Result:
Running transaction
RPM: error: db5 error(-30969) from dbenv->open: BDB0091 DB_VERSION_MISMATCH: Database environment version mismatch
RPM: error: cannot open Packages index using db5 - (-30969)
RPM: error: cannot open Packages database in /var/lib/rpm

crramirez · 2021-04-01T21:44:46Z

The above just hung for me and didn't do anything.
I found https://github.com/WhitewaterFoundry/Pengwin-Enterprise/issues/20 and followed:
sudo -s
cd /var/lib/rpm
rpm --rebuilddb
dd if=/dev/zero of=__db.001 bs=1M count=1
dd if=/dev/zero of=__db.002 bs=1M count=1
dd if=/dev/zero of=__db.003 bs=1M count=1
rpm -qa rpm
yum install vim
Which seems to have fixed the issue now.
Thankyou for your help.
cd /var/lib/rpm
dd if=/dev/zero of=__db.001 bs=1M count=1
dd if=/dev/zero of=__db.002 bs=1M count=1
dd if=/dev/zero of=__db.003 bs=1M count=1
this worked for me.
I tried this and it didn't fix my issue:
sudo dnf upgrade --refresh rpm glibc
sudo rm /var/lib/rpm/.rpm.lock
sudo dnf upgrade dnf
I'm not a fan of sudo -s so I tried this and it worked:
cd /var/lib/rpm/
sudo rpm --rebuilddb
sudo rpm -qa rpm
I didn't need to use dd to zero out __db.xxx files. I would have tried that next if I still had issues.

Hello @BlackthornYugen

Are you using Fedora Remix 33? or 32?

Regards

BlackthornYugen · 2021-04-03T16:24:21Z

Hello @BlackthornYugen

Are you using Fedora Remix 33? or 32?

Regards

@crramirez oops... I'm running Centos 8 Stream. This page turned up in a google search for my issue. I didn't even notice it was a Fedora for WSL issue.

==> /etc/os-release <==
NAME="CentOS Stream"
VERSION="8"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="8"
PLATFORM_ID="platform:el8"
PRETTY_NAME="CentOS Stream 8"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:8"
HOME_URL="https://centos.org/"

ggress · 2021-04-04T19:37:25Z

rpm -qa rpm

In my case, it was useful for installing libcanberrra in RHEL8

cd /var/lib/rpm
rpm --rebuilddb
rpm -qa rpm

yum install -y libcanberra-gtk*

Result:
Installed:
libcanberra-gtk2-0.30-16.el8.x86_64
Complete!

PROBLEM BEFORE
yum install -y libcanberra-gtk

Result:
Running transaction
RPM: error: db5 error(-30969) from dbenv->open: BDB0091 DB_VERSION_MISMATCH: Database environment version mismatch
RPM: error: cannot open Packages index using db5 - (-30969)
RPM: error: cannot open Packages database in /var/lib/rpm

works for me !!! RHEL8

crramirez · 2021-04-11T22:50:32Z

Hello @BlackthornYugen
Are you using Fedora Remix 33? or 32?
Regards

@crramirez oops... I'm running Centos 8 Stream. This page turned up in a google search for my issue. I didn't even notice it was a Fedora for WSL issue.
==> /etc/os-release <==
NAME="CentOS Stream"
VERSION="8"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="8"
PLATFORM_ID="platform:el8"
PRETTY_NAME="CentOS Stream 8"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:8"
HOME_URL="https://centos.org/"

Good to know that there is a solution for this for CentOS Stream and RHEL 8

MohitR1999 · 2021-06-07T08:09:18Z

The above just hung for me and didn't do anything.
I found https://github.com/WhitewaterFoundry/Pengwin-Enterprise/issues/20 and followed:
sudo -s
cd /var/lib/rpm
rpm --rebuilddb
dd if=/dev/zero of=__db.001 bs=1M count=1
dd if=/dev/zero of=__db.002 bs=1M count=1
dd if=/dev/zero of=__db.003 bs=1M count=1
rpm -qa rpm
yum install vim
Which seems to have fixed the issue now.
Thankyou for your help.
cd /var/lib/rpm
dd if=/dev/zero of=__db.001 bs=1M count=1
dd if=/dev/zero of=__db.002 bs=1M count=1
dd if=/dev/zero of=__db.003 bs=1M count=1
this worked for me.

This worked for me as well, thanks

charterchap · 2021-09-15T13:43:52Z

Does anyone know why the dd commands fix this?

crramirez · 2021-09-15T15:50:51Z

Yes, because it fails when trying to grow the files. The dd command creates files with 1MB with enough space to fill.

DrLove73 · 2022-04-07T13:09:08Z

I just had this problem and rm -f /var/lib/rpm/__db* fixed it at once.

crramirez · 2022-04-07T14:02:45Z

@DrLove73 excellent. Also, sudo rm /var/lib/rpm/.rpm.lock helps.

sumojee · 2022-05-19T15:32:11Z

Below command worked for me

rm -f /var/lib/rpm/__db*

https://barchive.wordpress.com/2016/10/28/error-db5-error-30969-from-dbenv-open-bdb0091-db_version_mismatch-database-environment-version-mismatch/

macardosa · 2022-06-21T13:29:39Z

I just had this problem and rm -f /var/lib/rpm/__db* fixed it at once.

Thanks for posting. This worked for me

cxy-uestc · 2022-07-05T18:28:37Z

What the real reason for the problem 'dbenv version mismatch'? And How to fix it in the source code? such as rpm or librpm

cgome2 · 2022-08-01T04:53:08Z

I just needed to rebuild de database and it worked:
cd /var/lib/rpm
rpm --rebuilddb

nirosha-r · 2022-11-02T06:16:58Z

Run this
sudo dnf upgrade --refresh rpm glibc
sudo rm /var/lib/rpm/.rpm.lock
sudo dnf upgrade dnf
And try again.

From: #46 (comment)

This worked for me

ganesh-at-wiw · 2023-06-08T11:34:29Z

Run this
sudo dnf upgrade --refresh rpm glibc
sudo rm /var/lib/rpm/.rpm.lock
sudo dnf upgrade dnf
And try again.

From: #46 (comment)

You made my day. :)

Thorfin closed this as completed Sep 16, 2019

mishamosher mentioned this issue Aug 1, 2022

CentOS Stream 9 on WSL1: error on importing (any) GPG key mishamosher/CentOS-WSL#14

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RPM DB_VERSION_MISMATCH #47

RPM DB_VERSION_MISMATCH #47

Thorfin commented Sep 16, 2019

Thorfin commented Sep 16, 2019

crramirez commented Sep 16, 2019

Thorfin commented Sep 16, 2019 •

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crramirez commented Oct 13, 2019 •

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PhilBarila commented Oct 23, 2019

cbowlesatx commented Oct 29, 2019

ElvenSpellmaker commented Oct 30, 2019

ACTom commented Jan 6, 2020

christianfosli commented Feb 7, 2020

whiteear commented Mar 4, 2020

WSLUser commented Mar 13, 2020

fritzr commented Apr 17, 2020

tqmillerusa commented Jun 21, 2020

crramirez commented Jun 21, 2020

BlackthornYugen commented Mar 28, 2021

Miriam-CID commented Mar 30, 2021 •

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crramirez commented Apr 1, 2021

BlackthornYugen commented Apr 3, 2021

ggress commented Apr 4, 2021

crramirez commented Apr 11, 2021

MohitR1999 commented Jun 7, 2021

charterchap commented Sep 15, 2021

crramirez commented Sep 15, 2021

DrLove73 commented Apr 7, 2022

crramirez commented Apr 7, 2022

sumojee commented May 19, 2022

macardosa commented Jun 21, 2022

cxy-uestc commented Jul 5, 2022

cgome2 commented Aug 1, 2022

nirosha-r commented Nov 2, 2022

ganesh-at-wiw commented Jun 8, 2023

RPM DB_VERSION_MISMATCH #47

RPM DB_VERSION_MISMATCH #47

Comments

Thorfin commented Sep 16, 2019

[root@SAMPC ~]# yum update whitewaterfoundry_wslu 256 B/s | 833 B 00:03 Dependencies resolved.

Package Architecture Version Repository Size

Transaction Summary

Thorfin commented Sep 16, 2019

crramirez commented Sep 16, 2019

Thorfin commented Sep 16, 2019 • edited Loading

crramirez commented Oct 13, 2019 • edited Loading

PhilBarila commented Oct 23, 2019

cbowlesatx commented Oct 29, 2019

ElvenSpellmaker commented Oct 30, 2019

ACTom commented Jan 6, 2020

christianfosli commented Feb 7, 2020

whiteear commented Mar 4, 2020

WSLUser commented Mar 13, 2020

fritzr commented Apr 17, 2020

tqmillerusa commented Jun 21, 2020

crramirez commented Jun 21, 2020

BlackthornYugen commented Mar 28, 2021

Miriam-CID commented Mar 30, 2021 • edited Loading

crramirez commented Apr 1, 2021

BlackthornYugen commented Apr 3, 2021

ggress commented Apr 4, 2021

crramirez commented Apr 11, 2021

MohitR1999 commented Jun 7, 2021

charterchap commented Sep 15, 2021

crramirez commented Sep 15, 2021

DrLove73 commented Apr 7, 2022

crramirez commented Apr 7, 2022

sumojee commented May 19, 2022

macardosa commented Jun 21, 2022

cxy-uestc commented Jul 5, 2022

cgome2 commented Aug 1, 2022

nirosha-r commented Nov 2, 2022

ganesh-at-wiw commented Jun 8, 2023

[root@SAMPC ~]# yum update
whitewaterfoundry_wslu 256 B/s | 833 B 00:03
Dependencies resolved.

Thorfin commented Sep 16, 2019 •

edited

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crramirez commented Oct 13, 2019 •

edited

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Miriam-CID commented Mar 30, 2021 •

edited

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