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Bug 1328025 - pypy-devel 5.0.1 contains files which conflict with numpy header files from CentOS 7 base package
Summary: pypy-devel 5.0.1 contains files which conflict with numpy header files from C...
Keywords:
Status: CLOSED CURRENTRELEASE
Alias: None
Product: Fedora EPEL
Classification: Fedora
Component: pypy
Version: epel7
Hardware: x86_64
OS: Linux
unspecified
unspecified
Target Milestone: ---
Assignee: Miro Hrončok
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2016-04-18 09:03 UTC by David Gardner
Modified: 2017-11-23 13:40 UTC (History)
4 users (show)

Fixed In Version:
Doc Type: Bug Fix
Doc Text:
Clone Of:
Environment:
Last Closed: 2017-11-23 13:40:21 UTC
Type: Bug
Embargoed:

Attachments (Terms of Use)

Description David Gardner 2016-04-18 09:03:36 UTC 
Description of problem:

Update to upgrade to pypy-devel-5.0.1 (from pypy-devel-2.2.1) as files conflict with those in numpy-1.7.1 :

  # yum install pypy-devel
  Loaded plugins: fastestmirror, langpacks
  Loading mirror speeds from cached hostfile
  Resolving Dependencies
  --> Running transaction check
  ---> Package pypy-devel.x86_64 0:5.0.1-1.el7 will be installed
  --> Finished Dependency Resolution

  Dependencies Resolved

  ========================================================================================================================================
   Package                           Arch                          Version                            Repository                     Size
  ========================================================================================================================================
  Installing:
   pypy-devel                        x86_64                        5.0.1-1.el7                        EPEL-7                         62 k

  Transaction Summary
  ========================================================================================================================================
  Install  1 Package

  Total size: 62 k
  Installed size: 215 k
  Is this ok [y/d/N]: y
  Downloading packages:
  Running transaction check
  Running transaction test


  Transaction check error:
    file /usr/include/numpy/__multiarray_api.h from install of pypy-devel-5.0.1-1.el7.x86_64 conflicts with file from package numpy-1:1.7.1-11.el7.x86_64
    file /usr/include/numpy/arrayobject.h from install of pypy-devel-5.0.1-1.el7.x86_64 conflicts with file from package numpy-1:1.7.1-11.el7.x86_64
    file /usr/include/numpy/ndarraytypes.h from install of pypy-devel-5.0.1-1.el7.x86_64 conflicts with file from package numpy-1:1.7.1-11.el7.x86_64
    file /usr/include/numpy/npy_3kcompat.h from install of pypy-devel-5.0.1-1.el7.x86_64 conflicts with file from package numpy-1:1.7.1-11.el7.x86_64
    file /usr/include/numpy/npy_common.h from install of pypy-devel-5.0.1-1.el7.x86_64 conflicts with file from package numpy-1:1.7.1-11.el7.x86_64
    file /usr/include/numpy/old_defines.h from install of pypy-devel-5.0.1-1.el7.x86_64 conflicts with file from package numpy-1:1.7.1-11.el7.x86_64

  Error Summary
  -------------


Version-Release number of selected component (if applicable):

pypy-devel-5.0.1-1.el7.x86_64
  

How reproducible:

"yum install pypy-devel" shows this with any current CentOS 7 install which includes the "numpy" package.


Steps to Reproduce:
1. Basic CentOS 7 install and add EPEL-7 repo.
2. yum install numpy
3. yum install pypy-devel

Actual results:

Conflict and pypy-devel refuses to install.

Expected results:

pypy-devel installs alongside numpy.

Additional info:
Comment 1 David Gardner 2016-04-25 08:45:28 UTC 
This blocks any updates from happening if pypy-devel is not either pinned to the older version or uninstalled.
Comment 2 Miro Hrončok 2016-05-13 10:19:33 UTC 
This happens on F23 with pypy-4.0.1-1 as well, so I suspect it happens on F24 and rawhide as well, will check.
Comment 3 Miro Hrončok 2016-05-13 10:31:40 UTC 
I'v also checked that the header files form numpy and from pypy are different.

pypy-devel -> /usr/include
pypy3-devel -> /usr/lib64/pypy3-2.4.0/include
python-devel -> /usr/include/python2.7/
python3-devel -> /usr/include/python3.4m/

I don't like /usr/lib64/pypy3-2.4.0/include much, but we can keep it that way until somebody complains.

Now what about pypy include files, where should we put them not to conflict and how to make it work with setuptools/distutils?
Comment 4 Miro Hrončok 2016-05-13 10:44:46 UTC 
I believe this is the responsible section:

http://pkgs.fedoraproject.org/cgit/rpms/pypy.git/tree/pypy.spec#n528

I will try to undo the part about headers, and than I'll try building a native extension package against it. If it works, I'll push updates to all affected branches.
Comment 5 Miro Hrončok 2016-05-13 18:09:56 UTC 
OK, that works, I've pushed this to rawhide and epel7.
Will push backport the fix top f24, f23 if the rawhide build goes fine (I had some trouble with ARM in the scratch builds).

Building now:

rawhide: http://koji.fedoraproject.org/koji/taskinfo?taskID=14047542
epel7: http://koji.fedoraproject.org/koji/taskinfo?taskID=14047563
Comment 6 Fedora Update System 2016-05-13 22:23:27 UTC 
pypy-5.0.1-2.el7 has been submitted as an update to Fedora EPEL 7. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2016-40e243f1f2
Comment 7 Miro Hrončok 2016-05-14 09:18:52 UTC 
The rawhide build has frozen for ARM for a 12+ hours, so I've cancelled it and am trying again.
Comment 8 Miro Hrončok 2016-05-14 21:12:18 UTC 
Fixed in Rawhide
Comment 9 Fedora Update System 2016-05-15 06:25:06 UTC 
pypy-5.0.1-2.el7 has been pushed to the Fedora EPEL 7 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-EPEL-2016-40e243f1f2
Comment 10 Fedora Update System 2016-05-15 10:14:49 UTC 
pypy-5.0.1-2.fc24 has been submitted as an update to Fedora 24. https://bodhi.fedoraproject.org/updates/FEDORA-2016-79a4933393
Comment 11 Fedora Update System 2016-05-16 05:36:45 UTC 
pypy-4.0.1-2.fc23 has been submitted as an update to Fedora 23. https://bodhi.fedoraproject.org/updates/FEDORA-2016-c03ccae4d2
Comment 12 David Gardner 2016-05-16 08:37:53 UTC 
Looks to install and work OK now with the EPEL 7 testing version, thanks!  :)
Comment 13 Miro Hrončok 2016-05-16 09:00:43 UTC 
Please add karma in bodhi.

I'm struggling to build pypy in arm in Fedora 22 due to a completely different issue. Otherwise the fix is ready for all Fedoras and EPEL7.

I thought that older EPELs are fine, but it appears that EPEL6 was also affected, so building there as well.

http://koji.fedoraproject.org/koji/taskinfo?taskID=14103179
Comment 14 Miro Hrončok 2016-05-16 10:59:14 UTC 
Ha, in EPEL6 the problematic change was commited, but never built, so no porblem there (fixed in dist git).
Comment 15 Fedora Update System 2016-05-16 23:57:00 UTC 
pypy-5.0.1-2.fc24 has been pushed to the Fedora 24 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-2016-79a4933393
Comment 16 Fedora Update System 2016-05-17 04:24:37 UTC 
pypy-4.0.1-2.fc23 has been pushed to the Fedora 23 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-2016-c03ccae4d2
Comment 17 Fedora Update System 2016-05-20 17:38:06 UTC 
pypy-5.0.1-2.fc24 has been pushed to the Fedora 24 stable repository. If problems still persist, please make note of it in this bug report.
Comment 18 Fedora Update System 2016-05-23 22:47:57 UTC 
pypy-5.0.1-2.el7 has been pushed to the Fedora EPEL 7 stable repository. If problems still persist, please make note of it in this bug report.
Comment 19 Fedora Update System 2016-05-24 01:24:43 UTC 
pypy-4.0.1-2.fc23 has been pushed to the Fedora 23 stable repository. If problems still persist, please make note of it in this bug report.
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