4:50 a.m.
Hi,
I had an enforced "not able to upgrade Fedora Rawhide for too long" period.
On doing the updates, one of my four computers updated fine, the other three
however got into problems. They are now in a state where "dnf check-updates"
reports a number of obsoletes, but "dnf upgrade" says nothing to do, and
"dnf check" reports 2000+ duplicates. I am certain someone in the past told
me how to get out of this as I am fairly sure I had a not dissimilar
situation early last year. However, I cannot find the email that I am sure I
kept somewhere.
In desperation I tried "dnf remove --duplicates" and after downloading 2.3GB
it reports large numbers of dependency fails and does nothing.
I am confident there must be a way of solving this short of re-installation,
hopefully someone knows the magic I need to fix these three computers.
--
Russel.
=========================================
Dr Russel Winder t:+44 20 7585 2200
41 Buckmaster Road m:+44 7770 465 077
London SW11 1EN, UK w: www.russel.org.uk
8:23 a.m.
On Sun, 05 Aug 2018 10:50:09 +0100
Russel Winder <russel(a)winder.org.uk> wrote:
Hi,
I had an enforced "not able to upgrade Fedora Rawhide for too long"
period. On doing the updates, one of my four computers updated fine,
the other three however got into problems. They are now in a state
where "dnf check-updates" reports a number of obsoletes, but "dnf
upgrade" says nothing to do, and "dnf check" reports 2000+
duplicates. I am certain someone in the past told me how to get out
of this as I am fairly sure I had a not dissimilar situation early
last year. However, I cannot find the email that I am sure I kept
somewhere.
In desperation I tried "dnf remove --duplicates" and after
downloading 2.3GB it reports large numbers of dependency fails and
does nothing.
I am confident there must be a way of solving this short of
re-installation, hopefully someone knows the magic I need to fix
these three computers.
I think you want to see what the issues are. Do
dnf --best update 2> dnf_errors.txt
and look at the output file. It is kind of like a log jam. There are
probably a few key packages that are orphaned, and they depend on older
libraries that are common to many other packages. Once they are
removed, the logjam will resolve itself. Using this technique allows
you to manually determine whether the updates are more important than a
package you have installed that is blocking the update.
If you use
dnf --best --allowerasing update
it will remove anything that blocks updates, but that can be a lot of
packages, some of which you might want to keep. You can use the dnf
logs in /var/log to re-install packages that have been removed that you
want to still have installed. Sometimes this fails because a version
that works with the updated libraries is not available, though.
10:15 a.m.
On Sun, 2018-08-05 at 06:23 -0700, stan wrote:
[…]
I think you want to see what the issues are. Do
dnf --best update 2> dnf_errors.txt
and look at the output file. It is kind of like a log jam. There
are
probably a few key packages that are orphaned, and they depend on
older
libraries that are common to many other packages. Once they are
removed, the logjam will resolve itself. Using this technique allows
you to manually determine whether the updates are more important than
a
package you have installed that is blocking the update.
There are no errors!
[root@anglides ~]# dnf check-update --refresh
bintray--pony-language-pony-stable-rpm 8.0 kB/s | 1.3
kB 00:00
bintray--pony-language-ponyc-rpm 7.7 kB/s | 1.3
kB 00:00
Crystal 1.9 kB/s | 2.9
kB 00:01
Fedora - Modular Rawhide - Developmental packag 37 kB/s | 20
kB 00:00
Fedora - Rawhide - Developmental packages for t 24 kB/s | 2.3
kB 00:00
local 110 kB/s | 3.0
kB 00:00
RPM Fusion for Fedora Rawhide - Free 83 kB/s | 11
kB 00:00
RPM Fusion for Fedora Rawhide - Nonfree 27 kB/s | 11
kB 00:00
Vivaldi Browser 82 kB/s | 2.9
kB 00:00
Last metadata expiration check: 0:00:00 ago on Sun 05 Aug 2018 16:10:08
BST.
Obsoleting Packages
grub2-tools.x86_64 1:2.02-
46.fc29 @rawhide
grub2-tools.x86_64 1:2.02-
37.fc29 @System
grub2-tools.x86_64 1:2.02-
46.fc29 rawhide
grub2-tools.x86_64 1:2.02-
37.fc29 @System
grub2-tools-efi.x86_64 1:2.02-
46.fc29 @rawhide
grub2-tools.x86_64 1:2.02-
37.fc29 @System
grub2-tools-efi.x86_64 1:2.02-
46.fc29 rawhide
grub2-tools.x86_64 1:2.02-
37.fc29 @System
grub2-tools-extra.x86_64 1:2.02-
46.fc29 @rawhide
grub2-tools.x86_64 1:2.02-
37.fc29 @System
grub2-tools-extra.x86_64 1:2.02-
46.fc29 rawhide
grub2-tools.x86_64 1:2.02-
37.fc29 @System
grub2-tools-minimal.x86_64 1:2.02-
46.fc29 @rawhide
grub2-tools.x86_64 1:2.02-
37.fc29 @System
grub2-tools-minimal.x86_64 1:2.02-
46.fc29 rawhide
grub2-tools.x86_64 1:2.02-
37.fc29 @System
libmodulemd.i686 1.6.1-
2.fc29 rawhide
python2-modulemd.noarch 1.3.3-
2.fc29 @System
libmodulemd.x86_64 1.6.1-
2.fc29 @rawhide
python2-modulemd.noarch 1.3.3-
2.fc29 @System
libmodulemd.x86_64 1.6.1-
2.fc29 rawhide
python2-modulemd.noarch 1.3.3-
2.fc29 @System
nss-pem.x86_64 1.0.3-
10.fc29 @rawhide
nss-pem.x86_64 1.0.3-
9.fc29 @System
nss-pem.x86_64 1.0.3-
10.fc29 rawhide
nss-pem.x86_64 1.0.3-
9.fc29 @System
redhat-lsb-printing.i686 4.1-
45.fc29 rawhide
redhat-lsb-printing.x86_64 4.1-
44.fc28 @System
redhat-lsb-printing.x86_64 4.1-
45.fc29 @rawhide
redhat-lsb-printing.x86_64 4.1-
44.fc28 @System
redhat-lsb-printing.x86_64 4.1-
45.fc29 rawhide
redhat-lsb-printing.x86_64 4.1-
44.fc28 @System
wireless-regdb.noarch 2018.05.31-
3.fc29 rawhide
crda.x86_64 3.18_2018.05.31-
1.fc29 @System
[root@anglides ~]# dnf upgrade --best
Last metadata expiration check: 0:00:41 ago on Sun 05 Aug 2018 16:10:08
BST.
Dependencies resolved.
Nothing to do.
Complete!
[root@anglides ~]# dnf check
…
zsh-5.5.1-1.fc29.x86_64 is a duplicate with zsh-5.5.1-2.fc29.x86_64
zvbi-0.2.35-5.fc28.x86_64 is a duplicate with zvbi-0.2.35-6.fc29.x86_64
zziplib-0.13.68-2.fc29.x86_64 is a duplicate with zziplib-0.13.69-
1.fc29.x86_64
Error: Check discovered 2242 problem(s)
[…]
--
Russel.
===========================================
Dr Russel Winder t: +44 20 7585 2200
41 Buckmaster Road m: +44 7770 465 077
London SW11 1EN, UK w: www.russel.org.uk
12:22 p.m.
On Sun, 05 Aug 2018 16:15:19 +0100
Russel Winder <russel(a)winder.org.uk> wrote:
[snip]
[root@anglides ~]# dnf upgrade --best
Last metadata expiration check: 0:00:41 ago on Sun 05 Aug 2018
16:10:08 BST.
Dependencies resolved.
Nothing to do.
Complete!
[root@anglides ~]# dnf check
…
zsh-5.5.1-1.fc29.x86_64 is a duplicate with zsh-5.5.1-2.fc29.x86_64
zvbi-0.2.35-5.fc28.x86_64 is a duplicate with
zvbi-0.2.35-6.fc29.x86_64 zziplib-0.13.68-2.fc29.x86_64 is a
duplicate with zziplib-0.13.69- 1.fc29.x86_64
Error: Check discovered 2242 problem(s)
I recently saw this with a package in F28. This shouldn't happen, as
far as I know, because the later package is replacing the earlier
package and dnf should know that. My take is that some change to the
package gives the later version a different signature, so that dnf
actually thinks they are different packages, but that is just a guess.
I resolved the issue by running, for your case,
dnf -x zsh -x zvbi -x zziplib upgrade
After that completed, I did
dnf remove zsh zvbi zziplib
dnf install zsh zvbi zziplib
In my case, the package was a leaf package, so this was trivial. If
your packages have a lot of dependencies, all those will be taken out
by the remove, and will have to be installed along with zsh, zvbi, and
zziplib. Some of them might not be available for the new version.
12:48 p.m.
On Sun, 2018-08-05 at 10:22 -0700, stan wrote:
[…]
I recently saw this with a package in F28. This shouldn't happen, as
far as I know, because the later package is replacing the earlier
package and dnf should know that. My take is that some change to the
package gives the later version a different signature, so that dnf
actually thinks they are different packages, but that is just a
guess.
I resolved the issue by running, for your case,
dnf -x zsh -x zvbi -x zziplib upgrade
After that completed, I did
dnf remove zsh zvbi zziplib
dnf install zsh zvbi zziplib
In my case, the package was a leaf package, so this was trivial. If
your packages have a lot of dependencies, all those will be taken out
by the remove, and will have to be installed along with zsh, zvbi,
and
zziplib. Some of them might not be available for the new version.
I tried "dnf remove --duplicates" but that downloaded 2.3GB and then
failed to do anything due to dependency failures.
Pragmatically I am not sure can try your suggestion as actually there
are 2242 problem packages not just three. :-(
--
Russel.
===========================================
Dr Russel Winder t: +44 20 7585 2200
41 Buckmaster Road m: +44 7770 465 077
London SW11 1EN, UK w: www.russel.org.uk
1:23 p.m.
On Sun, 2018-08-05 at 18:48 +0100, Russel Winder wrote:
[…]
> I tried "dnf remove --duplicates" but that downloaded 2.3GB and then
> failed to do anything due to dependency failures.
> Pragmatically I am not sure can try your suggestion as
actually there
> are 2242 problem packages not just three. :-(
On the other hand it seems that the output of "dnf check" can be piped
through "grep 'is a duplicate with'" and awk to select the first column
which is the name of the package that is being replaced so it can go
into a "xargs dnf remove" assuming dnf can take 2000+ arguments.
I had assumed this is what "dnf remove --duplicates" would do, but it
doesn't.
--
Russel.
===========================================
Dr Russel Winder t: +44 20 7585 2200
41 Buckmaster Road m: +44 7770 465 077
London SW11 1EN, UK w: www.russel.org.uk
1:27 p.m.
Except of course that the packages sudo, systemd, and systemd-udev are
protected and you cannot do "dnf remove" on them even if you are
removing a duplicate :-(
On Sun, 2018-08-05 at 19:23 +0100, Russel Winder wrote:
On Sun, 2018-08-05 at 18:48 +0100, Russel Winder wrote:
>
[…]
> I tried "dnf remove --duplicates" but that downloaded 2.3GB and
> then
> failed to do anything due to dependency failures.
>
> Pragmatically I am not sure can try your suggestion as actually
> there
> are 2242 problem packages not just three. :-(
On the other hand it seems that the output of "dnf check" can be
piped
through "grep 'is a duplicate with'" and awk to select the first
column
which is the name of the package that is being replaced so it can go
into a "xargs dnf remove" assuming dnf can take 2000+ arguments.
I had assumed this is what "dnf remove --duplicates" would do, but it
doesn't.
--
Russel.
===========================================
Dr Russel Winder t: +44 20 7585 2200
41 Buckmaster Road m: +44 7770 465 077
London SW11 1EN, UK w: www.russel.org.uk
1:59 p.m.
By judicious used of dnf, grep, and awk, I am now down to:
[root@anglides ~]# dnf check-update
Last metadata expiration check: 0:00:28 ago on Sun 05 Aug 2018 19:57:06
BST.
[root@anglides ~]# dnf check
sudo-1.8.23-1.fc29.x86_64 is a duplicate with sudo-1.8.23-3.fc29.x86_64
systemd-239-1.fc29.x86_64 is a duplicate with systemd-239-3.fc29.x86_64
systemd-container-239-1.fc29.x86_64 is a duplicate with systemd-
container-239-3.fc29.x86_64
systemd-devel-239-1.fc29.x86_64 is a duplicate with systemd-devel-239-
3.fc29.x86_64
systemd-libs-239-1.fc29.x86_64 is a duplicate with systemd-libs-239-
3.fc29.x86_64
systemd-pam-239-1.fc29.x86_64 is a duplicate with systemd-pam-239-
3.fc29.x86_64
systemd-udev-239-1.fc29.x86_64 is a duplicate with systemd-udev-239-
3.fc29.x86_64
Error: Check discovered 7 problem(s)
but I have no idea if stuff is actually internally self consistent.
--
Russel.
===========================================
Dr Russel Winder t: +44 20 7585 2200
41 Buckmaster Road m: +44 7770 465 077
London SW11 1EN, UK w: www.russel.org.uk
4:17 p.m.
On Sun, 05 Aug 2018 19:59:55 +0100
Russel Winder <russel(a)winder.org.uk> wrote:
By judicious used of dnf, grep, and awk, I am now down to:
[root@anglides ~]# dnf check-update
Last metadata expiration check: 0:00:28 ago on Sun 05 Aug 2018
19:57:06 BST.
[root@anglides ~]# dnf check
sudo-1.8.23-1.fc29.x86_64 is a duplicate with
sudo-1.8.23-3.fc29.x86_64 systemd-239-1.fc29.x86_64 is a duplicate
with systemd-239-3.fc29.x86_64 systemd-container-239-1.fc29.x86_64 is
a duplicate with systemd- container-239-3.fc29.x86_64
systemd-devel-239-1.fc29.x86_64 is a duplicate with systemd-devel-239-
3.fc29.x86_64
systemd-libs-239-1.fc29.x86_64 is a duplicate with systemd-libs-239-
3.fc29.x86_64
systemd-pam-239-1.fc29.x86_64 is a duplicate with systemd-pam-239-
3.fc29.x86_64
systemd-udev-239-1.fc29.x86_64 is a duplicate with systemd-udev-239-
3.fc29.x86_64
Error: Check discovered 7 problem(s)
but I have no idea if stuff is actually internally self consistent.
You can, of course, use rpm directly to force install of these rpms.
But the fact that this is such a large problem leads me to think there
is a bug in some fundamental part of the update chain. As you say,
there is no way to know if things are consistent at this point. Would
the replacements function as well as the originals if you did force
install them? If you are experimenting on only one system, and you do
go the force install route, you might want to hold off on updating the
other systems for a while to see if this is fixed in newer updates.
There must be other people experiencing this problem.
Really strange.
6:10 p.m.
On 08/05/2018 02:50 AM, Russel Winder wrote:
I had an enforced "not able to upgrade Fedora Rawhide for too
long" period.
On doing the updates, one of my four computers updated fine, the other three
however got into problems. They are now in a state where "dnf check-updates"
reports a number of obsoletes, but "dnf upgrade" says nothing to do, and
"dnf check" reports 2000+ duplicates. I am certain someone in the past told
me how to get out of this as I am fairly sure I had a not dissimilar
situation early last year. However, I cannot find the email that I am sure I
kept somewhere.
I have no idea why you have so many duplicates. That usually happens
when the update process gets interrupted part way through. Try running
"dnf distro-sync".
2:42 p.m.
On Sun, 2018-08-05 at 16:10 -0700, Samuel Sieb wrote:
[…]
I have no idea why you have so many duplicates. That usually happens
when the update process gets interrupted part way through. Try running
"dnf distro-sync".
[…]
[root@lionors ~]# dnf distro-sync
Last metadata expiration check: 0:01:08 ago on Mon 06 Aug 2018 20:38:26 BST.
Error:
Problem: The operation would result in removing the following protected packages: sudo,
systemd, systemd-udev
:-(
--
Russel.
=========================================
Dr Russel Winder t:+44 20 7585 2200
41 Buckmaster Road m:+44 7770 465 077
London SW11 1EN, UK w: www.russel.org.uk
2:48 p.m.
On Mon, 2018-08-06 at 20:42 +0100, Russel Winder wrote:
On Sun, 2018-08-05 at 16:10 -0700, Samuel Sieb wrote:
[…]
>
> I have no idea why you have so many duplicates. That usually happens
> when the update process gets interrupted part way through. Try running
> "dnf distro-sync".
[…]
[root@lionors ~]# dnf distro-sync
Last metadata expiration check: 0:01:08 ago on Mon 06 Aug 2018 20:38:26
BST.
Error:
Problem: The operation would result in removing the following protected
packages: sudo, systemd, systemd-udev
:-(
So I tried:
[root@lionors ~]# dnf distro-sync -x sudo -x systemd -x systemd-udev
Last metadata expiration check: 0:04:24 ago on Mon 06 Aug 2018 20:38:26 BST.
Dependencies resolved.
======================================================================================
Package Arch Version Repository
Size
======================================================================================
Removing dependent packages:
systemd x86_64 239-1.fc29 @System 11 M
systemd-container x86_64 239-1.fc29 @System 1.1 M
systemd-devel x86_64 239-1.fc29 @System 295 k
systemd-libs x86_64 239-1.fc29 @System 1.7 M
systemd-pam x86_64 239-1.fc29 @System 372 k
systemd-udev x86_64 239-1.fc29 @System 7.5 M
Downgrading:
dtv-scan-tables noarch 1-2.20171226git07b18ecef174.fc29 rawhide 565 k
dtv-scan-tables-legacy noarch 1-2.20171226git07b18ecef174.fc29 rawhide 230 k
librados2 x86_64 1:12.2.6-1.fc29 rawhide 3.0 M
Transaction Summary
======================================================================================
Remove 6 Packages
Downgrade 3 Packages
Total download size: 3.8 M
Is this ok [y/N]: y
Downloading Packages:
(1/3): dtv-scan-tables-legacy-1-2.20171226git07b18ece 166 kB/s | 230 kB 00:01
(2/3): dtv-scan-tables-1-2.20171226git07b18ecef174.fc 385 kB/s | 565 kB 00:01
(3/3): librados2-12.2.6-1.fc29.x86_64.rpm 1.3 MB/s | 3.0 MB 00:02
--------------------------------------------------------------------------------------
Total 1.7 MB/s | 3.8 MB 00:02
/usr/lib/python3.7/site-packages/dnf/cli/cli.py:231: DeprecationWarning: Using or
importing the ABCs from 'collections' instead of from 'collections.abc' is
deprecated, and in 3.8 it will stop working
if not isinstance(display, collections.Sequence):
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Preparing : 1/1
Running scriptlet: librados2-1:12.2.6-1.fc29.x86_64 1/1
Downgrading : librados2-1:12.2.6-1.fc29.x86_64 1/12
Downgrading : dtv-scan-tables-legacy-1-2.20171226git07b18ecef174.fc29. 2/12
Downgrading : dtv-scan-tables-1-2.20171226git07b18ecef174.fc29.noarch 3/12
Erasing : systemd-devel-239-1.fc29.x86_64 4/12
Cleanup : dtv-scan-tables-legacy-1-8.20161007git0b42d8e8b44e.fc28. 5/12
Cleanup : dtv-scan-tables-1-8.20161007git0b42d8e8b44e.fc28.noarch 6/12
Running scriptlet: systemd-udev-239-1.fc29.x86_64 7/12
Erasing : systemd-udev-239-1.fc29.x86_64 7/12
Running scriptlet: systemd-udev-239-1.fc29.x86_64 7/12
Erasing : systemd-container-239-1.fc29.x86_64 8/12
Erasing : systemd-pam-239-1.fc29.x86_64 9/12
Running scriptlet: systemd-239-1.fc29.x86_64 10/12
Erasing : systemd-239-1.fc29.x86_64 10/12
Erasing : systemd-libs-239-1.fc29.x86_64 11/12
Cleanup : librados2-1:12.2.7-1.fc29.x86_64 12/12
Running scriptlet: librados2-1:12.2.7-1.fc29.x86_64 12/12
Verifying : dtv-scan-tables-1-2.20171226git07b18ecef174.fc29.noarch 1/12
Verifying : dtv-scan-tables-1-8.20161007git0b42d8e8b44e.fc28.noarch 2/12
Verifying : dtv-scan-tables-legacy-1-2.20171226git07b18ecef174.fc29. 3/12
Verifying : dtv-scan-tables-legacy-1-8.20161007git0b42d8e8b44e.fc28. 4/12
Verifying : librados2-1:12.2.6-1.fc29.x86_64 5/12
Verifying : librados2-1:12.2.7-1.fc29.x86_64 6/12
Verifying : systemd-239-1.fc29.x86_64 7/12
Verifying : systemd-container-239-1.fc29.x86_64 8/12
Verifying : systemd-devel-239-1.fc29.x86_64 9/12
Verifying : systemd-libs-239-1.fc29.x86_64 10/12
Verifying : systemd-pam-239-1.fc29.x86_64 11/12
Verifying : systemd-udev-239-1.fc29.x86_64 12/12
Downgraded:
dtv-scan-tables-1-2.20171226git07b18ecef174.fc29.noarch
dtv-scan-tables-legacy-1-2.20171226git07b18ecef174.fc29.noarch
librados2-1:12.2.6-1.fc29.x86_64
Removed:
systemd-239-1.fc29.x86_64 systemd-container-239-1.fc29.x86_64
systemd-devel-239-1.fc29.x86_64 systemd-libs-239-1.fc29.x86_64
systemd-pam-239-1.fc29.x86_64 systemd-udev-239-1.fc29.x86_64
Complete!
[root@lionors ~]# dnf check-update
Last metadata expiration check: 0:05:53 ago on Mon 06 Aug 2018 20:38:26 BST.
[root@lionors ~]# dnf upgrade
Last metadata expiration check: 0:06:00 ago on Mon 06 Aug 2018 20:38:26 BST.
Dependencies resolved.
Nothing to do.
Complete!
[root@lionors ~]# dnf check
sudo-1.8.23-1.fc29.x86_64 is a duplicate with sudo-1.8.23-3.fc29.x86_64
Error: Check discovered 1 problem(s)
Which I think has to come under the heading weird.
--
Russel.
=========================================
Dr Russel Winder t:+44 20 7585 2200
41 Buckmaster Road m:+44 7770 465 077
London SW11 1EN, UK w: www.russel.org.uk
2:53 p.m.
On 08/06/2018 12:48 PM, Russel Winder wrote:
[root@lionors ~]# dnf check
sudo-1.8.23-1.fc29.x86_64 is a duplicate with sudo-1.8.23-3.fc29.x86_64
Error: Check discovered 1 problem(s)
Which I think has to come under the heading weird.
I agree. Why did it erase the systemd packages? But at least it is
mostly fixed now. I expect it will be resolved on the next sudo update.
Shouldn't be a problem for now.
2088
days inactive
2089
days old
12 comments
3 participants
participants (3)
-
Russel Winder -
Samuel Sieb -
stan