Bug 1767792
| Summary: | Please package bcftools, which has split off from samtools | ||||||||||||||
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| Product: | [Fedora] Fedora | Reporter: | John Marshall <jmarshall> | ||||||||||||
| Component: | samtools | Assignee: | Adam Huffman <bloch> | ||||||||||||
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> | ||||||||||||
| Severity: | unspecified | Docs Contact: | |||||||||||||
| Priority: | unspecified | ||||||||||||||
| Version: | rawhide | CC: | bloch, jaruga, ron | ||||||||||||
| Target Milestone: | --- | ||||||||||||||
| Target Release: | --- | ||||||||||||||
| Hardware: | Unspecified | ||||||||||||||
| OS: | Unspecified | ||||||||||||||
| Whiteboard: | |||||||||||||||
| Fixed In Version: | Doc Type: | If docs needed, set a value | |||||||||||||
| Doc Text: | Story Points: | --- | |||||||||||||
| Clone Of: | Environment: | ||||||||||||||
| Last Closed: | 2019-12-12 01:06:49 UTC | Type: | Bug | ||||||||||||
| Regression: | --- | Mount Type: | --- | ||||||||||||
| Documentation: | --- | CRM: | |||||||||||||
| Verified Versions: | Category: | --- | |||||||||||||
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |||||||||||||
| Cloudforms Team: | --- | Target Upstream Version: | |||||||||||||
| Embargoed: | |||||||||||||||
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Description
John Marshall
2019-11-01 12:36:29 UTC
Created attachment 1633495 [details]
Draft spec file
Created attachment 1633496 [details]
Backported upstream basic Python 3 fixes
Created attachment 1633497 [details]
Backported upstream configure fixes
Created attachment 1633604 [details]
Draft spec file
Created attachment 1633624 [details]
Draft spec file
Hi John, thank you for your spec file. Could you upload bcftools-1.9-python3.patch and bcftools-1.9-configure.patch file somewhere for me to to try to build your spec file? Do you have a plan to send a review request for bcftools? https://fedoraproject.org/wiki/Package_Review_Process#Contributor Sorry I found that you already uploaded the patch files to this Bugzilla tickets. I just ran the scratch build. https://koji.fedoraproject.org/koji/taskinfo?taskID=38888199 Only s390x case is failed. It might be a big endian specific issue, as s390x is only big endian in the list of the architectures. I do not wish to learn Fedora's tools or become a Fedora contributor, so I don't plan to send a review request for bcftools. I think it's less than ideal for someone involved with upstream to be the Fedora packager on a project. Instead it seems better for someone aligned with Fedora and separate from upstream to have an interest in keeping Fedora's package up to date independently. So I was hoping that you or someone interested in Fedora's samtools/htslib packages would like to take this one on, as you did with Sam's htslib spec file. (I would, of course, be happy to continue to review future changes to it from an upstream perspective.) That person would be free to start from this draft spec file if they thought that was advantageous (it is) or from a clean slate. Re s390x, there are indeed endianness issues with this project. See for example <https://github.com/samtools/htslib/issues/355> (parts of the report pertain to BCFtools). While the maintainers would prefer the code to work portably, there is little demand from users on such platforms and little motivation to fix it especially when the maintainers do not have access to such hardware to test on. So the usual advice (and the approach taken by e.g. Debian) has been to suppress the build on architectures where bcftools is known not to work. > Instead it seems better for someone aligned with Fedora and separate from upstream to have an interest in keeping Fedora's package up to date independently. Okay, thanks for sharing your intent. Maybe I am the person for that. > That person would be free to start from this draft spec file if they thought that was advantageous (it is) or from a clean slate. I will send the package request using a spec file based on your spec file later when I have a time. > Re s390x, there are indeed endianness issues with this project. See for example <https://github.com/samtools/htslib/issues/355> (parts of the report pertain to BCFtools). While the maintainers would prefer the code to work portably, there is little demand from users on such platforms and little motivation to fix it especially when the maintainers do not have access to such hardware to test on. So the usual advice (and the approach taken by e.g. Debian) has been to suppress the build on architectures where bcftools is known not to work. I introduced Travis s390x (big endian) feature in the page now. I think this makes maintainers access and debug to the hardware. https://blog.travis-ci.com/2019-11-12-multi-cpu-architecture-ibm-power-ibm-z FEDORA-2019-309d17cf8d has been submitted as an update to Fedora 30. https://bodhi.fedoraproject.org/updates/FEDORA-2019-309d17cf8d FEDORA-2019-389d258c80 has been submitted as an update to Fedora 31. https://bodhi.fedoraproject.org/updates/FEDORA-2019-389d258c80 bcftools-1.9-1.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-2019-309d17cf8d bcftools-1.9-1.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-2019-389d258c80 bcftools-1.9-1.fc30 has been pushed to the Fedora 30 stable repository. If problems still persist, please make note of it in this bug report. bcftools-1.9-1.fc31 has been pushed to the Fedora 31 stable repository. If problems still persist, please make note of it in this bug report. |