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Bug 1606315 - scipy: FTBFS in Fedora rawhide
Summary: scipy: FTBFS in Fedora rawhide
Keywords:
Status: CLOSED RAWHIDE
Alias: None
Product: Fedora
Classification: Fedora
Component: scipy
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
urgent
Target Milestone: ---
Assignee: Marcel Plch
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: F31FTBFS PYTHON38 1705227 1732841
TreeView+ depends on / blocked
 
Reported: 2018-07-20 19:28 UTC by Mohan Boddu
Modified: 2019-07-31 22:40 UTC (History)
4 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2019-07-08 09:58:17 UTC
Type: ---
Embargoed:

Attachments (Terms of Use)
build.log (32.00 KB, text/plain)
2018-07-20 19:28 UTC, Mohan Boddu 		no flags Details
root.log (32.00 KB, text/plain)
2018-07-20 19:29 UTC, Mohan Boddu 		no flags Details
state.log (611 bytes, text/plain)
2018-07-20 19:29 UTC, Mohan Boddu 		no flags Details
View All

Description Mohan Boddu 2018-07-20 19:28:40 UTC 
scipy failed to build from source in Fedora rawhide

https://koji.fedoraproject.org/koji/taskinfo?taskID=28233152


For details on the mass rebuild see:

https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
Please fix scipy at your earliest convenience and set the bug's status to
ASSIGNED when you start fixing it. If the bug remains in NEW state for 8 weeks,
scipy will be orphaned. Before branching of Fedora 30,
scipy will be retired, if it still fails to build.

For more details on the FTBFS policy, please visit:
https://fedoraproject.org/wiki/Fails_to_build_from_source
Comment 1 Mohan Boddu 2018-07-20 19:28:54 UTC 
Created attachment 1467964 [details]
build.log

file build.log too big, will only attach last 32768 bytes
Comment 2 Mohan Boddu 2018-07-20 19:29:02 UTC 
Created attachment 1467965 [details]
root.log

file root.log too big, will only attach last 32768 bytes
Comment 3 Mohan Boddu 2018-07-20 19:29:05 UTC 
Created attachment 1467966 [details]
state.log
Comment 4 Jan Kurik 2018-08-14 08:57:17 UTC 
This bug appears to have been reported against 'rawhide' during the Fedora 29 development cycle.
Changing version to '29'.
Comment 5 Charalampos Stratakis 2019-02-06 14:26:25 UTC 
Working on making this build on F30, a rebase to 1.2.0 seems to be sufficient.
Comment 6 Miro Hrončok 2019-05-20 14:27:13 UTC 
It appears that scipy once again fails to build in rawhide.

In regards of python 3.8 rebuild, it is needed to recythonize the sources as proposed in https://src.fedoraproject.org/rpms/scipy/pull-request/7

Yet that makes the failure even worse.

BUILDSTDERR: Traceback (most recent call last):
BUILDSTDERR:   File "/usr/lib64/python3.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 499, in run_code
BUILDSTDERR:     exec(code, ns)
BUILDSTDERR:   File "<string>", line 15, in <module>
BUILDSTDERR:   File "/builddir/build/BUILD/scipy-1.2.1/build/lib.linux-x86_64-3.7/scipy/interpolate/_bsplines.py", line 1017, in make_lsq_spline
BUILDSTDERR:     check_finite=check_finite)
BUILDSTDERR:   File "/builddir/build/BUILD/scipy-1.2.1/build/lib.linux-x86_64-3.7/scipy/linalg/decomp_cholesky.py", line 280, in cholesky_banded
BUILDSTDERR:     c, info = pbtrf(ab, lower=lower, overwrite_ab=overwrite_ab)
BUILDSTDERR: SystemError: <fortran object> returned NULL without setting an error
BUILDSTDERR: /usr/lib64/python3.7/site-packages/numpy/lib/utils.py:docstring of scipy.interpolate.spleval:15: WARNING: Block quote ends without a blank line; unexpected unindent.
BUILDSTDERR: /usr/lib64/python3.7/site-packages/numpy/lib/utils.py:docstring of scipy.interpolate.spline:11: WARNING: Block quote ends without a blank line; unexpected unindent.
BUILDSTDERR: /usr/lib64/python3.7/site-packages/numpy/lib/utils.py:docstring of scipy.interpolate.splmake:11: WARNING: Block quote ends without a blank line; unexpected unindent.
BUILDSTDERR: /builddir/build/BUILD/scipy-1.2.1/build/lib.linux-x86_64-3.7/scipy/misc/common.py:docstring of scipy.misc.ascent:28: WARNING: Exception occurred in plotting scipy-misc-ascent-1
BUILDSTDERR:  from /builddir/build/BUILD/scipy-1.2.1/doc/source/generated/scipy.misc.ascent.rst:
BUILDSTDERR: Traceback (most recent call last):
BUILDSTDERR:   File "/usr/lib64/python3.7/site-packages/matplotlib/sphinxext/plot_directive.py", line 499, in run_code
BUILDSTDERR:     exec(code, ns)
BUILDSTDERR:   File "<string>", line 2, in <module>
BUILDSTDERR:   File "/builddir/build/BUILD/scipy-1.2.1/build/lib.linux-x86_64-3.7/scipy/misc/common.py", line 157, in ascent
BUILDSTDERR:     with open(fname, 'rb') as f:
BUILDSTDERR: FileNotFoundError: [Errno 2] No such file or directory: '/builddir/build/BUILD/scipy-1.2.1/build/lib.linux-x86_64-3.7/scipy/misc/ascent.dat'

scipy blocks a large pile of packages, so this is a serious blocker for the 3.8 rebuilds.
Comment 7 Marcel Plch 2019-06-10 12:38:20 UTC 
Pull request created at: https://src.fedoraproject.org/rpms/scipy/pull-request/9
Comment 8 Marcel Plch 2019-06-18 11:22:14 UTC 
I have created a Dockerfile for OpenBLAS upstream to provide them with an environment where they can debug the issue with broken Fortran calls:
https://github.com/xianyi/OpenBLAS/issues/2137
Comment 9 Marcel Plch 2019-07-01 11:05:59 UTC 
Upstream claims that our build seems to cause the problem.

Setting needinfo on OpenBLAS Fedora maintainer.

Hello, Susi,
may I ask you to take a look at the upstream issue? Do you have any idea what can we do to resolve the issue?
Comment 10 Susi Lehtola 2019-07-01 12:29:35 UTC 
Is this related to #1709161?
The broken linkage issue should be solved ASAP.

The Fedora package is standard OpenBLAS, so the problem can't originate from the packaging. (You may be using the wrong flavor though.)
Comment 11 Susi Lehtola 2019-07-05 10:07:43 UTC 
It might be that this is the GCC bug discussed in
https://lwn.net/Articles/791393/
Comment 12 Miro Hrončok 2019-07-08 09:58:17 UTC 
I've merged https://src.fedoraproject.org/rpms/scipy/pull-request/9
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