1712818 – python-tables fails to build with Python 3.8

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Bug 1712818 - python-tables fails to build with Python 3.8

Summary: python-tables fails to build with Python 3.8

Keywords:
Status:	CLOSED RAWHIDE
Alias:	None
Product:	Fedora
Classification:	Fedora
Component:	python-tables
Sub Component:
Version:	rawhide
Hardware:	Unspecified
OS:	Unspecified
Priority:	unspecified
Severity:	high
Target Milestone:	---
Assignee:	Thibault North
QA Contact:	Fedora Extras Quality Assurance
Docs Contact:
URL:
Whiteboard:
Depends On:
Blocks:	PYTHON38
TreeView+	depends on / blocked

Reported:	2019-05-22 10:04 UTC by Miro Hrončok
Modified:	2019-06-02 13:08 UTC (History)
CC List:	2 users (show)
Fixed In Version:	python-tables-3.5.2-1.fc31
Doc Type:	If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed:	2019-06-02 13:08:57 UTC
Type:	Bug
Embargoed:
Dependent Products:

Attachments	(Terms of Use)
Full log from Copr (1.83 MB, text/plain) 2019-05-22 10:04 UTC, Miro Hrončok	no flags	Details
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Links
System	ID	Private	Priority	Status	Summary	Last Updated
Github	PyTables PyTables issues 733	0	None	None	None	2019-05-22 11:08:37 UTC
Github	PyTables PyTables pull 737	0	None	None	None	2019-05-27 13:26:15 UTC

Description Miro Hrončok 2019-05-22 10:04:14 UTC

Created attachment 1571952 [details]
Full log from Copr

python-tables 3.4.4-7.fc31 and 3.5.1-1.fc31 fail to build with Python 3.8.0a4:


======================================================================
ERROR: None (tables.tests.test_basics.NoNodeCacheOpenFile)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_basics.py", line 565, in test09e_renameGroup
    self.h5file.rename_node('/', name='agroup', newname='agroup_')
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 1701, in rename_node
    obj._f_rename(newname, overwrite)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 605, in _f_rename
    self._f_move(newname=newname, overwrite=overwrite)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.BasicReadTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.ZlibReadTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.BloscReadTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.LZOReadTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.Bzip2ReadTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.ShuffleReadTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.Fletcher32ReadTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.ShuffleFletcher32ReadTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.OneHalfTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.UpperBoundTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

======================================================================
ERROR: None (tables.tests.test_indexes.LowerBoundTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/tests/test_indexes.py", line 566, in test10d_moveIndex
    table.move(agroup, "table2")
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/leaf.py", line 625, in move
    self._f_move(newparent, newname, overwrite, createparents)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/node.py", line 689, in _f_move
    self._g_move(newparent, newname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/table.py", line 2678, in _g_move
    itgroup._g_move(newigroup, newiname)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/group.py", line 603, in _g_move
    self._v_file._update_node_locations(oldpath, newpath)
  File "/builddir/build/BUILDROOT/python-tables-3.4.4-7.fc31.x86_64/usr/lib64/python3.8/site-packages/tables/file.py", line 2852, in _update_node_locations
    for nodepath in cache:
  File "/usr/lib64/python3.8/weakref.py", line 223, in keys
    for k, wr in self.data.items():
RuntimeError: dictionary keys changed during iteration

----------------------------------------------------------------------
Ran 6191 tests in 276.473s

FAILED (errors=12, skipped=44)

This blocks pandas.

Full log attached.

Comment 1 Miro Hrončok 2019-05-22 11:08:37 UTC

https://github.com/PyTables/PyTables/issues/733

Comment 2 Miro Hrončok 2019-05-27 13:26:16 UTC

Fix: https://github.com/PyTables/PyTables/pull/737

Comment 3 Miro Hrončok 2019-05-27 14:09:38 UTC

https://src.fedoraproject.org/rpms/python-tables/pull-request/3

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