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  #1  
Old 21st June 2017, 02:35 PM
srakitnican Offline
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Fedora 25 Broken by upgrade

So fired up laptop today that I am rarely using, decided to do a quick upgrade.

Code:
  Upgrading   : dhcp-client-12:4.3.5-2.fc25.x86_64                                                                                            229/710 
  Upgrading   : libsane-hpaio-3.17.4-2.fc25.x86_64                                                                                            230/710 
  Upgrading   : glibc-devel-2.24-6.fc25.x86_64                                                                                                231/710 
  Installing  : qt5-qtwayland-5.7.1-2.fc25.x86_64                                                                                             232/710 
  Upgrading   : megasync-3.1.2-3.1.x86_64                                                                                                     233/710 
fs.inotify.max_user_watches = 524288
Floating point exception
So left the system with corrupted rpm database. After rebuilding the rpm database by AdamW instructions, there was many multiple versions ghost packages left that was messing with the dnf operation.

Code:
# dnf --disableplugin protected_packages remove $(dnf repoquery --duplicated --latest-limit -1 -q)
Number of included packages seemed a bit high, but I was in a hurry

Code:
# rpm -qa
bash: rpm: command not found
Bummer.
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  #2  
Old 22nd June 2017, 05:44 AM
nobody Offline
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Wink Re: Fedora 25 Broken by upgrade

Quote:
Originally Posted by srakitnican View Post
So left the system with corrupted rpm database. After rebuilding the rpm database by AdamW instructions, there was many multiple versions ghost packages left that was messing with the dnf operation.
Dear Watson, throw 'em to the hungry lions.

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  #3  
Old 3rd July 2017, 10:06 AM
srakitnican Offline
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Re: Fedora 25 Broken by upgrade

Alrighty, tried to upgrade my Fedora 26 testing instance on my desktop PC

Code:
  Upgrading        : java-1.8.0-openjdk-headless-1:1.8.0.131-7.b12.fc26.x86_64    102/1151 
  Running scriptlet: java-1.8.0-openjdk-headless-1:1.8.0.131-7.b12.fc26.x86_64    102/1151 
warning: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.131-7.b12.fc26.x86_64/jre/lib/security/java.security created as /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.131-7.b12.fc26.x86_64/jre/lib/security/java.security.rpmnew
error: db5 error(-30969) from dbenv->open: BDB0091 DB_VERSION_MISMATCH: Database environment version mismatch
error: cannot open Packages index using db5 -  (-30969)
error: cannot open Packages database in /var/lib/rpm
error: db5 error(-30969) from dbenv->open: BDB0091 DB_VERSION_MISMATCH: Database environment version mismatch
error: cannot open Packages index using db5 -  (-30969)
error: cannot open Packages database in /var/lib/rpm
error: db5 error(-30969) from dbenv->open: BDB0091 DB_VERSION_MISMATCH: Database environment version mismatch
error: cannot open Packages index using db5 -  (-30969)
error: cannot open Packages database in /var/lib/rpm
error: db5 error(-30969) from dbenv->open: BDB0091 DB_VERSION_MISMATCH: Database environment version mismatch
error: cannot open Packages index using db5 -  (-30969)
error: cannot open Packages database in /var/lib/rpm
restored /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.131-7.b12.fc26.x86_64/jre/lib/security/java.security.rpmnew to /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.131-7.b12.fc26.x86_64/jre/lib/security/java.security

...

  Upgrading        : gstreamer1-plugins-good-1.12.1-1.fc26.x86_64                 456/1151 
  Upgrading        : megasync-3.1.4-1.1.x86_64                                    457/1151 
  Running scriptlet: megasync-3.1.4-1.1.x86_64                                    457/1151 
fs.inotify.max_user_watches = 524288
Floating point exception
Code:
$ sudo dnf
error: rpmdb: BDB0113 Thread/process 6962/140191354500864 failed: BDB1507 Thread died in Berkeley DB library
error: db5 error(-30973) from dbenv->failchk: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery
error: cannot open Packages index using db5 -  (-30973)
error: cannot open Packages database in /var/lib/rpm
Error: Error: rpmdb open failed
I am guessing I should have done distrosync first for the rpm database bug? Anyway, I will try not break the system entirely this time Although it doesn't look very good with this amount of packages failed.

Last edited by srakitnican; 3rd July 2017 at 10:15 AM.
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  #4  
Old 3rd July 2017, 10:40 AM
srakitnican Offline
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Re: Fedora 25 Broken by upgrade

Went ahead and rebuilt rpm database since there seems to be no other option, now to fix "dupes". "dnf repoquery --duplicated --latest-limit -1" doesn't seems to work for some reason.

Code:
Command line error: argument --latest-limit: expected one argument
Tried out brand new dnf 2 option:

Code:
$ sudo dnf remove --duplicates
Error: 
 Problem 1: package openldap-2.4.44-10.fc26.x86_64 requires nss-tools, but none of the providers can be installed
  - package nss-tools-3.30.2-1.0.fc26.x86_64 requires nss(x86-64) = 3.30.2-1.0.fc26, but none of the providers can be installed
  - package sudo-1.8.20p2-1.fc26.x86_64 requires liblber-2.4.so.2()(64bit), but none of the providers can be installed
  - conflicting requests
  - problem with installed package sudo-1.8.20p2-1.fc26.x86_64
 Problem 2: package rpm-libs-4.13.0.1-4.fc26.x86_64 requires rpm = 4.13.0.1-4.fc26, but none of the providers can be installed
  - package deltarpm-3.6-19.fc26.x86_64 requires librpm.so.7()(64bit), but none of the providers can be installed
  - package rpm-4.13.0.1-4.fc26.x86_64 requires /usr/bin/db_stat, but none of the providers can be installed
  - package python3-dnf-2.5.1-1.fc26.noarch requires deltarpm, but none of the providers can be installed
  - package libdb-utils-5.3.28-17.fc26.x86_64 requires libdb(x86-64) = 5.3.28-17.fc26, but none of the providers can be installed
  - package dnf-2.5.1-1.fc26.noarch requires python3-dnf = 2.5.1-1.fc26, but none of the providers can be installed
  - conflicting requests
  - problem with installed package dnf-2.5.1-1.fc26.noarch
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  #5  
Old 3rd July 2017, 01:04 PM
srakitnican Offline
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Re: Fedora 25 Broken by upgrade

For the --latest-limit, this seems to be a bug in dnf 2 with argument parser. There are some workarounds in the bug report.

But this action would remove most of the system, a little bit more then 1000 including package manager because of dependencies regardless of --latest-limit=-1 being only 447 packages. So I've decided to take a different approach with this one. Instead of removing packages duplicate of an older version (that is most of the system because of dependencies), will remove only newer version (483 packages, that includes some "unused dependencies"). That would hopefully leave system if not perfect, then in much better shape. So the command for this action is:

Code:
$ sudo dnf --setopt=protected_packages= remove $(sudo dnf repoquery --duplicated --latest-limit 1 -q | grep -v i686)
Here I am grepping out i686 packages because they are not really dupes and yet they come up with this command. I've verified that I have only one version of the same i686 package installed with command sudo dnf repoquery --duplicated --latest-limit 1 -q | grep i686 | less

Also, method of disabling protected packages changed with dnf 2, now it is disabled with --setopt=protected_packages= exactly as it is written with nothing after = .
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  #6  
Old 3rd July 2017, 01:34 PM
srakitnican Offline
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Re: Fedora 25 Broken by upgrade

Not sure if it is necessary, but I went ahead and upgraded libdb from 5.3.28-17 to newest version that of the time of writing is 5.3.28-21 before I upgrade the whole system again.

Code:
$ sudo dnf upgrade libdb
$ sudo dnf upgrade
Commands finished successfully this time, and most importantly rpm is still installed

Code:
$ rpm -q rpm
rpm-4.13.0.1-4.fc26.x86_64
$ rpm -qa | wc -l
1937
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  #7  
Old 3rd July 2017, 05:08 PM
nobody Offline
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Thumbs down Re: Fedora 25 Broken by upgrade

Quote:
[user@localhost ~]$ rpm -q rpm
rpm-4.13.0.1-5.fc26.x86_64
[user@localhost ~]$ rpm -qa | wc -l
2466
[user@localhost ~]$ uname -r
4.11.8-300.fc26.x86_64
[user@localhost ~]$
I have yet other problem on Wayland... My VMWare Tools on Wayland are completely dead!

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  #8  
Old 16th July 2017, 10:15 AM
srakitnican Offline
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Re: Fedora 25 Broken by upgrade

Hmm happened again on my daily Fedora 25 install, this time with libdb-5.3.28-21. However rpm db seems fine, upgrade completed successfully this time and dnf or rpm seems to work fine still.

Code:
  Upgrading   : camotics-1.1.1-7.fc25.x86_64                                           153/382 
  Upgrading   : opera-stable-46.0.2597.46-0.x86_64                                     154/382 
Redirecting to /bin/systemctl start  atd.service
  Upgrading   : megasync-3.1.4-1.1.x86_64                                              155/382 
error: db5 error(-30969) from dbenv->open: BDB0091 DB_VERSION_MISMATCH: Database environment version mismatch
error: cannot open Packages index using db5 -  (-30969)
error: cannot open Packages database in /var/lib/rpm
error: db5 error(-30969) from dbenv->open: BDB0091 DB_VERSION_MISMATCH: Database environment version mismatch
error: cannot open Packages index using db5 -  (-30969)
error: cannot open Packages database in /var/lib/rpm
fs.inotify.max_user_watches = 524288
  Upgrading   : sqlite-3.14.2-2.fc25.x86_64                                            156/382 
  Upgrading   : tracker-1.10.5-2.fc25.x86_64                                           157/382
Code:
    Upgraded   libdb-5.3.28-21.fc25.i686                              @updates
    Upgraded   libdb-5.3.28-21.fc25.x86_64                            @updates
    Upgrade          5.3.28-24.fc25.i686                              @updates
    Upgrade          5.3.28-24.fc25.x86_64                            @updates
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  #9  
Old 16th July 2017, 07:54 PM
nobody Offline
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Talking Re: Fedora 25 Broken by upgrade

Hello Dear Watson/Mr. Rakitnican,

I just updated my FC25 VM on my HDD. And here is what I have (kernel 4.11.9-200.fc25.x86_64):

Code:
[root@localhost ~]# uname -r
4.11.9-200.fc25.x86_64
[root@localhost ~]# dnf clean all
20 files removed
[root@localhost ~]# dnf clean all
0 files removed
[root@localhost ~]# dnf upgrade --refresh
RPM Fusion for Fedora 25 - Free - Updates                                                        546 kB/s | 287 kB     00:00    
Fedora 25 - x86_64                                                                               5.6 MB/s |  50 MB     00:08    
RPM Fusion for Fedora 25 - Nonfree - Updates                                                      58 kB/s |  40 kB     00:00    
Fedora 25 - x86_64 - Updates                                                                     3.9 MB/s |  24 MB     00:06    
RPM Fusion for Fedora 25 - Free                                                                  769 kB/s | 515 kB     00:00    
RPM Fusion for Fedora 25 - Nonfree                                                               104 kB/s | 144 kB     00:01    
Dependencies resolved.
====================================================================================
 Package                                     Arch                  Version                          Repository              Size
====================================================================================

[snap]

Install   1 Package
Upgrade  50 Packages

Total download size: 117 M
Is this ok [y/N]: y
Downloading Packages:
(1/51): autocorr-en-5.2.7.2-4.fc25_5.2.7.2-5.fc25.noarch.drpm                                    320 kB/s |  78 kB     00:00    

[snap]

(51/51): xscreensaver-base-5.37-1.fc25.x86_64.rpm                                                1.8 MB/s | 426 kB     00:00    
[DRPM] httpd-2.4.25-1.fc25_2.4.27-2.fc25.x86_64.drpm: done                                                                      
[DRPM] libreoffice-pyuno-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                        
[DRPM] libreoffice-ure-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                          
[DRPM] libreoffice-opensymbol-fonts-5.2.7.2-4.fc25_5.2.7.2-5.fc25.noarch.drpm: done                                             
[DRPM] libreoffice-gtk3-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                         
[DRPM] libreoffice-data-5.2.7.2-4.fc25_5.2.7.2-5.fc25.noarch.drpm: done                                                         
[DRPM] libreoffice-ure-common-5.2.7.2-4.fc25_5.2.7.2-5.fc25.noarch.drpm: done                                                   
[DRPM] libreoffice-draw-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                         
[DRPM] libreoffice-calc-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                         
[DRPM] evince-3.22.1-4.fc25_3.22.1-5.fc25.x86_64.drpm: done                                                                     
[DRPM] libreoffice-graphicfilter-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                
[DRPM] libreoffice-math-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                         
[DRPM] libreoffice-impress-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                      
[DRPM] libreoffice-x11-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                          
[DRPM] libreoffice-pdfimport-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                    
[DRPM] libreoffice-gtk2-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                         
[DRPM] libreoffice-xsltfilter-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                   
[DRPM] pciutils-libs-3.5.4-1.fc25_3.5.5-1.fc25.x86_64.drpm: done                                                                
[DRPM] spice-glib-0.33-2.fc25_0.33-5.fc25.x86_64.drpm: done                                                                     
[DRPM] spice-gtk3-0.33-2.fc25_0.33-5.fc25.x86_64.drpm: done                                                                     
[DRPM] microcode_ctl-2.1-15.fc25_2.1-16.fc25.x86_64.drpm: done                                                                  
[DRPM] sqlite-libs-3.14.2-1.fc25_3.14.2-2.fc25.x86_64.drpm: done                                                                
[DRPM] libreoffice-writer-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                       
[DRPM] samba-client-libs-4.5.10-0.fc25_4.5.11-0.fc25.x86_64.drpm: done                                                          
[DRPM] valgrind-3.12.0-1.fc25_3.12.0-9.fc25.x86_64.drpm: done                                                                   
[DRPM] libreoffice-core-5.2.7.2-4.fc25_5.2.7.2-5.fc25.x86_64.drpm: done                                                         
---------------------------------------------------------------------------------------------------------------------------------
Total                                                                                            139 kB/s |  11 MB     01:20     
Delta RPMs reduced 117.3 MB of updates to 10.9 MB (90.1% saved)
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Upgrading   : libreoffice-data-1:5.2.7.2-5.fc25.noarch                                                                   1/101 

[snap]

  Upgrading   : microcode_ctl-2:2.1-16.fc25.x86_64                                                                        51/101 
  Cleanup     : samba-client-2:4.5.10-0.fc25.x86_64                                                                       52/101 

[snap]

  Cleanup     : valgrind-1:3.12.0-1.fc25.x86_64                                                                          101/101 
Error in file "/usr/share/applications/evince.desktop": "" is an invalid MIME type ("" does not contain a subtype)
Error in file "/usr/share/applications/evince.desktop": "" is an invalid MIME type ("" does not contain a subtype)

[snap]

  Verifying   : autocorr-en-1:5.2.7.2-4.fc25.noarch                                                                      101/101 

Installed:
  nghttp2.x86_64 1.13.0-2.fc25                                                                                                   

Upgraded:

[snap]      

Complete!
[root@localhost ~]#
Noticed this one?

Quote:
Error in file "/usr/share/applications/evince.desktop": "" is an invalid MIME type ("" does not contain a subtype)
Error in file "/usr/share/applications/evince.desktop": "" is an invalid MIME type ("" does not contain a subtype)
Considering libdb-5.3.28-21, I have the following situation:

Quote:
[root@localhost ~]# dnf list installed | grep libdb
libdb.x86_64 5.3.28-24.fc25 @updates
libdb-utils.x86_64 5.3.28-24.fc25 @updates
[root@localhost ~]#
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  #10  
Old 16th July 2017, 10:40 PM
antikythera Offline
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Re: Fedora 25 Broken by upgrade

Quote:
[antikythera@akira ~]$ yum-deprecated list installed | grep libdb
libdb.x86_64 5.3.28-24.fc25 @updates
libdb-utils.x86_64 5.3.28-24.fc25 @updates
libdbusmenu.x86_64 16.04.0-2.fc25 @updates
libdbusmenu-gtk3.x86_64 16.04.0-2.fc25 @updates
I still use yumex with yum-deprecated backend. It hasn't been affected by these libdb issues at all. I still can't get my head round why the developers felt the need to re-invent the wheel in this instance with dnf.

Yumex and yum-deprecated are still available from raveit65's copr
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  #11  
Old 17th July 2017, 09:08 AM
srakitnican Offline
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Re: Fedora 25 Broken by upgrade

Quote:
Originally Posted by nobody View Post
Noticed this one?



_nobody_
Yes, I don't think this is not caused by package manager, though. More of the output of command desktop-file-validate.
https://bugzilla.redhat.com/show_bug.cgi?id=1471474
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  #12  
Old 17th July 2017, 09:26 AM
srakitnican Offline
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Re: Fedora 25 Broken by upgrade

Quote:
Originally Posted by antikythera View Post
I still use yumex with yum-deprecated backend. It hasn't been affected by these libdb issues at all. I still can't get my head round why the developers felt the need to re-invent the wheel in this instance with dnf.

Yumex and yum-deprecated are still available from raveit65's copr
I don't think this is a dnf bug, more of an rpm/libdb which both of them are interfacing. Why you haven't encountered it, I don't know, luck I guess, or you just haven't noticed it. Not everyone enjoys watching commands output Or maybe yum just hides this stuff.

To be fair Fedora 25 with libdb-5.3.28-21 at least did finish the upgrade, so maybe they've changed it so that this error is not fatal. This issue might have been from before where older libdb corrupted the rpmdb and now it self-healed? Not sure what happened.
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