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Bug 1782129 - After installing avogadro, there are unresolvable dependency issues when updating
Summary: After installing avogadro, there are unresolvable dependency issues when upda...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: avogadro
Version: 31
Hardware: x86_64
OS: Linux
unspecified
low
Target Milestone: ---
Assignee: Antonio T. (sagitter)
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
: 1792872 (view as bug list)
Depends On:
Blocks: 1792872
TreeView+ depends on / blocked
 
Reported: 2019-12-11 09:03 UTC by David Jansen
Modified: 2020-01-31 02:00 UTC (History)
6 users (show)

Fixed In Version: avogadro-1.2.0-28.fc30 avogadro-1.2.0-29.fc31
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
: 1792872 (view as bug list)
Environment:
Last Closed: 2020-01-26 01:00:25 UTC
Type: Bug
Embargoed:

Attachments (Terms of Use)

Description David Jansen 2019-12-11 09:03:46 UTC 
Description of problem:

On a newly installed and fully upgraded Fedora 31 workstation, I installed the avogadro package. That went ok, without errors. But now, dnf finds unresolvable dependency issues when updating. 
The problem might be in the sip packages that were installed as a dependency.

Version-Release number of selected component (if applicable):
avogadro-1.2.0-26.fc31.x86_64
avogadro-libs-1.2.0-26.fc31.x86_64
sip-4.19.18-6.fc31.x86_64
python2-sip-4.19.18-6.fc31.x86_64

How reproducible:


Steps to Reproduce:
1. dnf install avogadro
2. dnf upgrade


Actual results:
# dnf upgrade
Last metadata expiration check: 2:13:20 ago on Wed 11 Dec 2019 07:36:55 CET.
Dependencies resolved.

 Problem: package avogadro-libs-1.2.0-26.fc31.x86_64 requires sip-api(12) >= 12.6, but none of the providers can be installed
  - package sip-4.19.19-1.fc31.x86_64 obsoletes python2-sip < 4.19.19-1.fc31 provided by python2-sip-4.19.18-6.fc31.x86_64
  - cannot install the best update candidate for package python2-sip-4.19.18-6.fc31.x86_64
  - cannot install the best update candidate for package avogadro-libs-1.2.0-26.fc31.x86_64
Nothing to do.
Complete!


Expected results:
no errors, and the ability to upgrade the packages to their latest versions

Additional info:
Might this be because python2-sip is the dependency that was installed, and not python3-sip?
Comment 1 Fedora Update System 2020-01-17 13:05:26 UTC 
FEDORA-2020-398a99a935 has been submitted as an update to Fedora 30. https://bodhi.fedoraproject.org/updates/FEDORA-2020-398a99a935
Comment 2 Fedora Update System 2020-01-17 13:05:27 UTC 
FEDORA-2020-4637c0d5bb has been submitted as an update to Fedora 31. https://bodhi.fedoraproject.org/updates/FEDORA-2020-4637c0d5bb
Comment 3 Susi Lehtola 2020-01-17 20:32:53 UTC 
*** Bug 1792202 has been marked as a duplicate of this bug. ***
Comment 4 Fedora Update System 2020-01-18 01:25:25 UTC 
avogadro-1.2.0-28.fc30 has been pushed to the Fedora 30 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-398a99a935
Comment 5 Fedora Update System 2020-01-18 01:44:15 UTC 
avogadro-1.2.0-28.fc31 has been pushed to the Fedora 31 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-4637c0d5bb
Comment 6 Eduardo 2020-01-19 16:40:26 UTC 
I tried installing avogadro after uninstalling the old version:
$ sudo dnf install --enablerepo=updates-testing avogadro --refresh

I got this error, so still it only offers to install the old version and downgrade other packages:
 Problem: package avogadro-1.2.0-28.fc31.x86_64 requires avogadro-libs(x86-64) = 1.2.0-28.fc31, but none of the providers can be installed
  - cannot install the best candidate for the job
  - nothing provides sip-api(12) >= 12.7 needed by avogadro-libs-1.2.0-28.fc31.x86_64
Comment 7 Fedora Update System 2020-01-19 18:56:11 UTC 
FEDORA-2020-4637c0d5bb has been submitted as an update to Fedora 31. https://bodhi.fedoraproject.org/updates/FEDORA-2020-4637c0d5bb
Comment 8 Susi Lehtola 2020-01-20 09:50:31 UTC 
I don't think removing the sip-api requirement makes sense; it's there for a reason, and the macro exists:

$ rpm -q python2-sip
python2-sip-4.19.18-6.fc31.x86_64
$ rpm -q --provides python2-sip
python2-sip = 4.19.18-6.fc31
python2-sip(x86-64) = 4.19.18-6.fc31
python2-sip-api(12) = 12.6
python2-sip-api(12)(x86-64) = 12.6
python2.7dist(sip) = 4.19.18
python2dist(sip) = 4.19.18
sip-api(12) = 12.6
sip-api(12)(x86-64) = 12.6

The real problem appears to be that the version of sip in the buildroot is newer than in F31 proper, as can be seen from the avogadro build log:

python2-sip-devel                x86_64 4.19.19-1.fc31             build  64 k

If there are changes in the SIP api, it's likely that avogadro won't work with the current version.
Comment 9 Rex Dieter 2020-01-20 14:52:43 UTC 
*** Bug 1792872 has been marked as a duplicate of this bug. ***
Comment 10 Rex Dieter 2020-01-20 14:57:44 UTC 
The assertion in comment #8 is invalid

The *real* issue is documented in bug #1753069 , where sip no longer provides non-namespaced modules.

I suspect that simply removing the dependency is probably not correct either, but you can test to see if loading python-related stuff in avogadro works without it.
Comment 11 Rex Dieter 2020-01-20 19:02:39 UTC 
Fwiw, python(2) support was essentially removed with commit:
https://src.fedoraproject.org/rpms/avogadro/c/c5c17c00523ed359e54ff99992d02f3c84e2735f

So there's no point in keeping
BuildRequires:  python2-sip-devel
in avogadro.spec at this point either
Comment 12 Fedora Update System 2020-01-20 23:33:04 UTC 
avogadro-1.2.0-29.fc31 has been pushed to the Fedora 31 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-4637c0d5bb
Comment 13 Fedora Update System 2020-01-26 01:00:25 UTC 
avogadro-1.2.0-28.fc30 has been pushed to the Fedora 30 stable repository. If problems still persist, please make note of it in this bug report.
Comment 14 Fedora Update System 2020-01-31 02:00:18 UTC 
avogadro-1.2.0-29.fc31 has been pushed to the Fedora 31 stable repository. If problems still persist, please make note of it in this bug report.
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