Arch Linux

tmb

Member

Registered: 2018-03-14

Posts: 16

[SOLVED] python-h5py and hdf5-openmpi are in conflict

Hello,

I want to do an update but I ran into trouble with a package conflict and I am not sure how to solve it
as both packages seem to be from official repositories (no aur, no manual installation).
I would be thankful for help.

Regards,
Tobias

[tmb@desktop ~]$ sudo pacman -Syu
[sudo] password for tmb: 
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...
:: python-h5py and hdf5-openmpi are in conflict. Remove hdf5-openmpi? [y/N] y
error: failed to prepare transaction (could not satisfy dependencies)
:: unable to satisfy dependency 'hdf5' required by netcdf
:: unable to satisfy dependency 'hdf5' required by python-h5py
:: removing hdf5-openmpi breaks dependency 'hdf5' required by alembic
:: removing hdf5-openmpi breaks dependency 'hdf5' required by cgns
:: removing hdf5-openmpi breaks dependency 'hdf5' required by paraview

Last edited by tmb (2018-10-13 20:26:05)

WorMzy

Forum Moderator

From: Scotland

Registered: 2010-06-16

Posts: 11,869

Website

Re: [SOLVED] python-h5py and hdf5-openmpi are in conflict

Please use code tags for terminal output: https://wiki.archlinux.org/index.php/Co … s_and_code

I guess you have tensorboard installed. It has a new dependency: python-tensorflow-serving-api, which depends on python-tensorflow, which depends on python-h5py, which is kicking off this conflict. Unfortunately, python-h5py depends on hdf5, but on your system hdf5 is provided by hdf5-openmpi, so pacman thinks the dependency is resolved, then tries to remove the package that provides it, resulting in the error you're getting.

I believe that a workaround would be to run

pacman -Syu hdf5

but I'm not sure if this should be reported on the bug tracker. It seems to be a bug in hdf5 packaging, but I'm not sure.

EDIT: Not an installation issue, moving to Pacman issues.

Last edited by WorMzy (2018-10-13 14:24:21)

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tmb

Member

Registered: 2018-03-14

Posts: 16

Re: [SOLVED] python-h5py and hdf5-openmpi are in conflict

Thank you very much. Your suggestion solved the problem.