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GitHub actions mysql libstdc++.so.6: cannot allocate memory in static TLS block #3834

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peterjc opened this issue Jan 4, 2022 · 0 comments

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peterjc commented Jan 4, 2022

GitHub actions recently broke under Linux, e.g.

======================================================================
ERROR: Bio.motifs.jaspar.db
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/MySQLdb/__init__.py", line 18, in <module>
    from . import _mysql
ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: cannot allocate memory in static TLS block

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "run_tests.py", line 298, in runTest
    module = __import__(name, fromlist=name.split("."))
  File "/home/runner/work/biopython/biopython/build/lib.linux-x86_64-3.7/Bio/motifs/jaspar/db.py", line 62, in <module>
    import MySQLdb as mdb
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/MySQLdb/__init__.py", line 24, in <module>
    version_info, _mysql.version_info, _mysql.__file__
NameError: name '_mysql' is not defined
----------------------------------------------------------------------

Appears to be due to actions/runner-images#4799

peterjc added a commit to peterjc/biopython that referenced this issue Jan 6, 2022
peterjc added a commit that referenced this issue Jan 7, 2022
JoaoRodrigues pushed a commit to cbalbin-bio/biopython that referenced this issue Aug 7, 2022
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