question-mark
Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

threads.h not available on OpenBSD, scipy assumes it is present

See original GitHub issue

My issue is about building scipy on OpenBSD.

Error message:

  creating build/temp.openbsd-6.9-amd64-3.8/build/src.openbsd-6.9-amd64-3.8/build/src.openbsd-6.9-amd64-3.8/scipy/integrate
  compile options: '-DNO_ATLAS_INFO=1 -DHAVE_CBLAS -I/home/dima/sagetrac-mirror/local/include -Ibuild/src.openbsd-6.9-amd64-3.8/build/src.openbsd-6.9-amd64-3.8/scipy/integrate -I/home/dima/sagetrac-mirror/local/
lib/python3.8/site-packages/numpy/core/include -Ibuild/src.openbsd-6.9-amd64-3.8/numpy/distutils/include -I/home/dima/sagetrac-mirror/local/include -I/usr/local/include/python3.8 -c'
  extra options: '-msse -msse2 -msse3'
  clang: build/src.openbsd-6.9-amd64-3.8/scipy/integrate/vodemodule.c
  In file included from build/src.openbsd-6.9-amd64-3.8/scipy/integrate/vodemodule.c:16:
  In file included from build/src.openbsd-6.9-amd64-3.8/build/src.openbsd-6.9-amd64-3.8/scipy/integrate/fortranobject.h:13:
  In file included from /home/dima/sagetrac-mirror/local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
  In file included from /home/dima/sagetrac-mirror/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
  In file included from /home/dima/sagetrac-mirror/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
  /home/dima/sagetrac-mirror/local/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_
API NPY_1_7_API_VERSION" [-W#warnings]
  #warning "Using deprecated NumPy API, disable it with " \
   ^
  build/src.openbsd-6.9-amd64-3.8/scipy/integrate/vodemodule.c:88:10: fatal error: 'threads.h' file not found
  #include <threads.h>
           ^~~~~~~~~~~
  1 warning and 1 error generated.

Scipy/Numpy/Python version information:

building scipy 1.6.3

Python 3.8.8 (default, Apr 19 2021, 10:23:47) 
[Clang 10.0.1 ] on openbsd6
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys, numpy; print(numpy.__version__, sys.version_info)
1.20.3 sys.version_info(major=3, minor=8, micro=8, releaselevel='final', serial=0)

Issue Analytics

  • State:closed
  • Created 2 years ago
  • Comments:13 (11 by maintainers)

github_iconTop GitHub Comments

1reaction
dimpasecommented, Jul 8, 2021

I’ve opened numpy/numpy#19437

0reactions
dimpasecommented, Jan 24, 2022
Read more comments on GitHub >

github_iconTop Results From Across the Web

C11 GCC threads.h not found? - Stack Overflow
The gcc document C11 status indicates that it does not support threading, it says: Threading [Optional] | Library issue (not implemented).
Read more >
Multithreading issue - python, zope, opensbd, et al - misc@openbsd ...
So with openBSD, there seems a requirement for both pthread.h (found) and thread.h (not found). I assume with these that if they wre...
Read more >
OpenBSD 5.2 Changelog
OpenBSD 5.2 Changelog. This selection is intended to include all important and all user-visible changes. For a complete record of all changes, ...
Read more >
Bad assumption on thread stack size makes python crash with ...
Python assumes that the system default thread stack size is big enough for python, except for OSX and FreeBSD where stack size is...
Read more >
Build mongo current on OpenBSD : find egcc, ssl.h - MongoDB
various pathing tricks, but python buildscripts/scons.py ... so it isn't surprising to me that there are some incorrect assumptions.
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Dev.to Post

No results found

github_iconTop Related Hashnode Post

No results found