My latest attempts to update my Fedora 37 system fail because one of my installed packages now has python3-mysqlclient-2.1.0-3.fc37.x86_64 as a dependency and several files in that package conflict with files in python3-mysql-1.4.6-11.fc37.x86_64 which is already installed on my system. In turn, a number of other packages fail to update because they need python3-mysql-1.4.6-11.fc37.x86_64. Any suggestions? Any help greatly appreciated!
Darron
$ dnf repoquery -l python3-mysql{,client} should give you an idea of what’s going on here. Alternatively, you might consider using pip with venv to manage python dependencies per-project and avoid global conflicts that way.
In this case, it looks like these are basically different versions of the same Python “site-package” (MySQLdb), which is why they conflict. If dnf allowed you to install both, one package would overwrite at least part of the other’s files.
Scott,
Thanks for the guidance! I’ll follow up on your suggestions and see what I can learn.
Darron
When there are conflicting packages like that from the same repo it often is a case of the mirrors not being in sync and thus 2 different versions are seen. The fix in that case is to wait a few hours or a day and try again. Once the mirrors are in sync the issue usually goes away.
If the packages are from fedora and some other 3rd party repo then the conflicts will need to be solved by only using one of the two conflicting repos.
I just checked and python3-mysql 1.4.6-11and python3-mysqlclient 2.1.0-3 both come from fedora and do not conflict if both are installed.
You said this is a result of some other package you already have installed and trying to do an update so we would need to know exactly what other *mysql* packages are installed that are causing the issue.
A list of all the packages that are showing the conflicts would be helpful in narrowing down the one that is at issue, assuming that this is not caused by a temporary issue such as mirrors out of sync and that it does not disappear once the mirrors finish syncing.
I do get conflicts, however.
[root@newbox ~]# dnf install python3-mysql python3-mysqlclient
Last metadata expiration check: 0:50:12 ago on Thu 15 Dec 2022 06:12:32 CET.
Dependencies resolved.
====================================================================================================================
Package Architecture Version Repository Size
====================================================================================================================
Installing:
python3-mysql x86_64 1.4.6-11.fc37 fedora 117 k
python3-mysqlclient x86_64 2.1.0-3.fc37 fedora 106 k
Transaction Summary
====================================================================================================================
Install 2 Packages
Total download size: 223 k
Installed size: 660 k
Is this ok [y/N]: y
Downloading Packages:
(1/2): python3-mysqlclient-2.1.0-3.fc37.x86_64.rpm 503 kB/s | 106 kB 00:00
(2/2): python3-mysql-1.4.6-11.fc37.x86_64.rpm 545 kB/s | 117 kB 00:00
--------------------------------------------------------------------------------------------------------------------
Total 341 kB/s | 223 kB 00:00
Running transaction check
Transaction check succeeded.
Running transaction test
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Transaction test error:
file /usr/lib64/python3.11/site-packages/MySQLdb/__init__.py conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/__init__.cpython-311.opt-1.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/__init__.cpython-311.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/_exceptions.cpython-311.opt-1.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/_exceptions.cpython-311.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/connections.cpython-311.opt-1.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/connections.cpython-311.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/converters.cpython-311.opt-1.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/converters.cpython-311.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/cursors.cpython-311.opt-1.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/cursors.cpython-311.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/release.cpython-311.opt-1.pyc conflicts between attempted installs of
and quite a bit more.
I’m not sure how you confirmed this, but they definitely conflict.
@knutsondc Please file a bug report on one or both of python-mysql/python-mysqlclient. If they conflict in files, they should have explicit Conflicts. Or if no-one uses the old version, it should be retired.
I had just done the preliminary test and saw no conflict. When I went further and got the actual installation conflicts so there should definitely be a bug filed and the older one retired.
If there are other packages triggering the conflict by requiring the conflicting packages as dependencies then that should be included in the bug report.
i have the same problem on Rel36 Fedora, glad to see someone is posting it too, here’s my info if it helps, this sample is from trying to update mythtv. Conflict between python3-mysqlclient-2.0.3-4 conflicts with file from package python3-mysql-1.4.6-9. Is it best to wait for a fix or try the python pip upgrade, and is the pip upgrade a commitment to do that going forward versus using dnf? Thanks.
Output
dnf update mythtv
Last metadata expiration check: 3:33:01 ago on Thu 15 Dec 2022 08:45:54 AM EST.
Dependencies resolved.
===============================================================================
Package Arch Version Repository Size
===============================================================================
Upgrading:
mytharchive x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 12 M
mythbrowser x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 106 k
mythffmpeg x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 8.3 M
mythgame x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 179 k
mythmusic x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 644 k
mythnews x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 111 k
mythplugins x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 11 k
mythtv x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 26 k
mythtv-backend x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 7.7 M
mythtv-base-themes x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 13 M
mythtv-common x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 4.4 M
mythtv-docs noarch 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 114 k
mythtv-frontend x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 12 M
mythtv-libs x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 8.3 M
mythtv-setup x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 143 k
mythweather x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 412 k
mythzoneminder x86_64 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 175 k
perl-MythTV noarch 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 32 k
php-MythTV noarch 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 22 k
python3-MythTV noarch 32.0-6.76.20221129git44f88ed468.fc36
rpmfusion-free-updates 335 k
Installing dependencies:
python3-mysqlclient x86_64 2.0.3-4.fc36 fedora 89 k
Transaction Summary
===============================================================================
Install 1 Package
Upgrade 20 Packages
Total size: 68 M
Is this ok [y/N]: y
.....................................
Error: Transaction test error:
file /usr/lib64/python3.10/site-packages/MySQLdb/__init__.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/__init__.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/__init__.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/_exceptions.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/_exceptions.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/connections.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/connections.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/converters.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/converters.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/cursors.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/cursors.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/release.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/release.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/times.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/__pycache__/times.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/_exceptions.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/_mysql.cpython-310-x86_64-linux-gnu.so from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/connections.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/CLIENT.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/CR.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/ER.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__init__.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/CLIENT.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/CLIENT.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/CR.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/CR.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/ER.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/ER.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/FIELD_TYPE.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/FIELD_TYPE.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/FLAG.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/FLAG.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/__init__.cpython-310.opt-1.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/constants/__pycache__/__init__.cpython-310.pyc from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/converters.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/cursors.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/release.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
file /usr/lib64/python3.10/site-packages/MySQLdb/times.py from install of python3-mysqlclient-2.0.3-4.fc36.x86_64 conflicts with file from package python3-mysql-1.4.6-9.fc36.x86_64
See https://bugzilla.redhat.com/show_bug.cgi?id=2153769
The pip command can be risky if you are not careful. If if happens to override a module that is used by dnf, you may not be able to run dnf.
Thanks much I was wondering about that. I cannot break dnf, I will wait for a fix. Is there a place to look for the fix? Fedora, python, mythtv? where is ground zero? Thanks again
Sorry i see the link you sent looks like the root bug report I will monitor there
I think that here you can find the explanation of the issue. Hopefully it will be resolved soon.
Thanks. Wow this had been around a long time, Feb 2021. Doesn’t sound like it will get fixed soon. I will try and report it to mythtv too, maybe its in their wheelhouse.
Just to re-iterate from my previous response - Package conflicts can happen. As long as I’ve been using Fedora, I can’t think of a time where you could actually install every single package and not have a conflict.
If you could install both of these, one would overwrite the other and it would break your python library since they both provide the same python site-package (MySqlDb). dnf blocking this isn’t a bug but a feature! That said, the packages could be named to reflect different versions of the same driver rather than using different package names altogether.
If for some reason you need both versions of the driver, I suggest using pip with venv or container toolbox. Do not use pip outside of a venv/container context, especially as root, because you might overwrite rpm provided libraries and cause very bad things to happen. That said, running pip in a venv or container is perfectly sane.
For what it’s worth, I maintain Python server environments (JupyterHub) for a very large organization as part of my dayjob.
Here’s a fix from the good people at myth tv. HTH, thanks all I will open a bug at RPM Fusion also which is apparently root cause.
from Gary:
This is not a MythTV issue. It is an issue upstream (and should be closed accordingly). This was a result of the RPMFusion maintainer apparently changing requirements (and then apparently not testing the upgrade path) combined with the open upstream bug 1929101 – Retire "python-mysql" package in favor of "python-mysqlclient" PyPI package
You should, however, consider opening a RPMFusion bug to remind the maintainer of QA.
Instructions as to how to deal with the issue have been posted on the mythtv-users list.
I performed the ugprade using these commands in “dnf shell”:
remove python3-mysql
install python3-mysqlclient
upgrade
run
Bill - thanks for posting the feedback you got from the mythtv people! I have mythtv on the system where I experienced this problem that in turn led me to ask for help here.
Thanks also to everyone else who jumped into the discussion! I know that package conflicts are inevitable, but I’m glad that there are so many interested folks in the community that fixes and workarounds can nearly always be found.
Darron
Hi -
I’m hitting this while trying to upgrade from FC35 to FC37.
Does anyone know how to avoid the problem as part of the upgrade?
This:
dnf system-upgrade -y download --refresh --releasever=37
[ ... ]
The downloaded packages were saved in cache until the next successful transaction.
You can remove cached packages by executing 'dnf clean packages'.
Error: Transaction test error:
file /usr/lib64/python3.11/site-packages/MySQLdb/__init__.py conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/__init__.cpython-311.opt-1.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
file /usr/lib64/python3.11/site-packages/MySQLdb/__pycache__/__init__.cpython-311.pyc conflicts between attempted installs of python3-mysql-1.4.6-11.fc37.x86_64 and python3-mysqlclient-2.1.0-3.fc37.x86_64
[ ... ]
I do not think that both those packages are required and they do definitely have conflicts.
I think you could remove python3-mysql and it would eliminate the error while allowing python3-mysqlclient to be installed.
According to @candelabra and the error reports python3-mysqlclient is a replacement for python3-mysql.
I have submitted updates that should fix this conflict. They are now pending, and should be in testing at the next compose.
Rawhide/F38: https://bodhi.fedoraproject.org/updates/FEDORA-2022-13aa6fbdb1
F37: https://bodhi.fedoraproject.org/updates/FEDORA-2022-713080ea38
F36: https://bodhi.fedoraproject.org/updates/FEDORA-2022-dbbe1b44c0
There may be some delay for it to get to stable as it will need to go through testing first.