[Debichem-devel] Bug#1150834: mdtraj: FTBFS: E pyparsing.exceptions.ParseException: Expected '(', found '=' (at char 6), (line:1, col:7)
Santiago Vila
sanvila at debian.org
Tue Oct 13 18:44:49 BST 2026
Package: src:mdtraj
Version: 1.11.1.post1-3
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202610/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:mdtraj, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
def parseImpl(self, instring, loc, do_actions=True) -> ParseImplReturnType:
if instring[loc] == self.firstMatchChar:
return loc + 1, self.match
> raise ParseException(instring, loc, self.errmsg, self)
E pyparsing.exceptions.ParseException: Expected '(', found '=' (at char 6), (line:1, col:7)
/usr/lib/python3/dist-packages/pyparsing/core.py:2783: ParseException
During handling of the above exception, another exception occurred:
self = <mdtraj.core.selection.parse_selection object at 0x7f5eb091de80>
selection = 'name >= 1'
def __call__(self, selection):
if not self.is_initialized:
self._initialize()
try:
> parse_result = self.expression.parse_string(selection, parse_all=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
mdtraj/core/selection.py:397:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = {Group:({'all' | 'backbone' | 'chainid' | 'code' | 'element' | 'everything' | 'index' | 'is_backbone' | 'is_nucleic' |...|' | '!' | 'not '}} {W:(.0-9) | quoted string using single or double quotes | W:(A-Za-z, 0-9A-Za-z)}}} infix expression
instring = 'name >= 1', parse_all = True, kwargs = {'parseAll': False}
def parse_string(
self, instring: str, parse_all: bool = False, **kwargs
) -> ParseResults:
"""
Parse a string with respect to the parser definition. This function is intended as the primary interface to the
client code.
:param instring: The input string to be parsed.
:param parse_all: If set, the entire input string must match the grammar.
:param parseAll: retained for pre-PEP8 compatibility, will be removed in a future release.
:raises ParseException: Raised if ``parse_all`` is set and the input string does not match the whole grammar.
:returns: the parsed data as a :class:`ParseResults` object, which may be accessed as a `list`, a `dict`, or
an object with attributes if the given parser includes results names.
If the input string is required to match the entire grammar, ``parse_all`` flag must be set to ``True``. This
is also equivalent to ending the grammar with :class:`StringEnd`\\ ().
To report proper column numbers, ``parse_string`` operates on a copy of the input string where all tabs are
converted to spaces (8 spaces per tab, as per the default in ``string.expandtabs``). If the input string
contains tabs and the grammar uses parse actions that use the ``loc`` argument to index into the string
being parsed, one can ensure a consistent view of the input string by doing one of the following:
- calling ``parse_with_tabs`` on your grammar before calling ``parse_string`` (see :class:`parse_with_tabs`),
- define your parse action using the full ``(s,loc,toks)`` signature, and reference the input string using the
parse action's ``s`` argument, or
- explicitly expand the tabs in your input string before calling ``parse_string``.
Examples:
By default, partial matches are OK.
.. doctest::
>>> res = Word('a').parse_string('aaaaabaaa')
>>> print(res)
['aaaaa']
The parsing behavior varies by the inheriting class of this abstract class. Please refer to the children
directly to see more examples.
It raises an exception if parse_all flag is set and instring does not match the whole grammar.
.. doctest::
>>> res = Word('a').parse_string('aaaaabaaa', parse_all=True)
Traceback (most recent call last):
ParseException: Expected end of text, found 'b' ...
"""
parseAll: bool = deprecate_argument(kwargs, "parseAll", False)
parse_all = parse_all or parseAll
ParserElement.reset_cache()
if not self.streamlined:
self.streamline()
for e in self.ignoreExprs:
e.streamline()
if not self.keepTabs:
instring = instring.expandtabs()
try:
loc, tokens = self._parse(instring, 0)
if parse_all:
loc = self.preParse(instring, loc)
se = Empty() + StringEnd().set_debug(False)
se._parse(instring, loc)
except _ParseActionIndexError as pa_exc:
raise pa_exc.exc
except ParseBaseException as exc:
if ParserElement.verbose_stacktrace:
raise
# catch and re-raise exception from here, clearing out pyparsing internal stack trace
> raise exc.with_traceback(None)
E pyparsing.exceptions.ParseException: Expected {G [too-long-redacted] ' (at char 6), (line:1, col:7)
/usr/lib/python3/dist-packages/pyparsing/core.py:1346: ParseException
During handling of the above exception, another exception occurred:
def test_binary_selection_operator():
eq(parse_selection("name < 1").astnode, pnode("atom.name < 1"))
eq(parse_selection("name lt 1").astnode, pnode("atom.name < 1"))
eq(parse_selection("name > 1").astnode, pnode("atom.name > 1"))
eq(parse_selection("name gt 1").astnode, pnode("atom.name > 1"))
eq(parse_selection("name == 1").astnode, pnode("atom.name == 1"))
eq(parse_selection("name eq 1").astnode, pnode("atom.name == 1"))
eq(parse_selection("name != 1").astnode, pnode("atom.name != 1"))
eq(parse_selection("name ne 1").astnode, pnode("atom.name != 1"))
> eq(parse_selection("name >= 1").astnode, pnode("atom.name >= 1"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
tests/test_selection.py:174:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <mdtraj.core.selection.parse_selection object at 0x7f5eb091de80>
selection = 'name >= 1'
def __call__(self, selection):
if not self.is_initialized:
self._initialize()
try:
parse_result = self.expression.parse_string(selection, parse_all=True)
except ParseException as e:
msg = str(e)
lines = [
f"{msg}: {selection}",
" " * (12 + len("%s: " % msg) + e.loc) + "^^^",
]
> raise ValueError("\n".join(lines))
E ValueError: Expected {Group:({'all' | 'backbone' [too-long-redacted] 6), (line:1, col:7): name >= 1
E [too-long-redacted] ^^^
mdtraj/core/selection.py:404: ValueError
=============================== warnings summary ===============================
tests/test_distance.py::Test_Distance::test_6
<frozen importlib._bootstrap>:491: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found
SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found
SKIPPED [15] tests/test_docstrings.py:38: Skip checking certain modules' docstrings
SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing
SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing
SKIPPED [1] tests/test_hdf5.py:105: requires openmm.units
SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units
SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units
SKIPPED [1] tests/test_mol2.py:65: Requires obabel
SKIPPED [1] tests/test_netcdf.py:274: This test requires cpptraj from AmberTools to be installed (http://ambermd.org)
SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found
SKIPPED [1] tests/test_nmr.py:26: PPM binary not found
SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis.
SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/
SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently.
SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently.
SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM.
SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM.
SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM.
SKIPPED [1] tests/test_selection.py:267: failed to parse selection
SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work.
SKIPPED [1] tests/test_topology.py:66: needs OpenMM
SKIPPED [1] tests/test_topology.py:83: needs OpenMM
SKIPPED [1] tests/test_topology.py:93: needs OpenMM
SKIPPED [1] tests/test_topology.py:102: needs OpenMM
SKIPPED [1] tests/test_topology.py:112: needs OpenMM
SKIPPED [1] tests/test_topology.py:119: requires openmm >= 8.2
SKIPPED [1] tests/test_topology.py:295: needs OpenMM
SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information
SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information
SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information
SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information
SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information
SKIPPED [1] tests/test_trajectory.py:225: mdcrd can only store rectilinear boxes
SKIPPED [1] tests/test_trajectory.py:223: ncrst can only store 1 frame per file
SKIPPED [1] tests/test_trajectory.py:223: rst7 can only store 1 frame per file
SKIPPED [14] tests/test_trajectory.py:247: mdcrd can only store rectilinear boxes
SKIPPED [14] tests/test_trajectory.py:245: ncrst can only store 1 frame per file
SKIPPED [14] tests/test_trajectory.py:245: rst7 can only store 1 frame per file
SKIPPED [4] tests/test_trajectory.py:255: dtr needs to write unitcells
SKIPPED [4] tests/test_trajectory.py:255: lammpstrj needs to write unitcells
SKIPPED [2] tests/test_trajectory.py:641: Only 1 frame per file format
XFAIL tests/test_trajectory.py::test_read_path[ncrst] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_path[rst7] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_load[ncrst] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_load[rst7] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_load_combination[rst7] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - This is broken
XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - PDB Files don't support seeking
XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - PDB Files don't support seeking
XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - This is broken
XFAIL tests/test_trajectory.py::test_load_frame[dtr] - DTR doesn't load a single frame properly
XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_load_frame[rst7] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_load_frame[gro] - Gro doesn't implement seek
XFAIL tests/test_trajectory.py::test_iterload[dtr] - This is broken with dtr
XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - PDB Iterloads an extra frame!!
XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - PDB Iterloads an extra frame!!
XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - These reference files don't exist yet
XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - Not implemented for some reason
XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - This is broken with dtr
XFAIL tests/test_trajectory.py::test_unitcell[dtr] - dtr seems to need unit vectors
XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - lammpstrj seems to need unit vectors
XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - ncrst seems to need unit vectors
XFAIL tests/test_trajectory.py::test_unitcell[rst7] - rst7 seems to need unit vectors
FAILED tests/test_selection.py::test_binary_selection_operator - ValueError: ...
= 1 failed, 986 passed, 103 skipped, 24 deselected, 61 xfailed, 1 warning in 105.57s (0:01:45) =
lugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_mdtraj/build; python3.14 -m pytest -k 'not ( mdconvert or pi_stacking.ipynb or nmr.ipynb or test_image_molecules or test_3 or from_url or test_1vii_url_and_gz or test_1vii_load_from_mixture )'
rm -fr -- /tmp/dh-xdg-rundir-mVnoy5_r
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.14 --parallel=2 returned exit code 13
make: *** [debian/rules:32: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
--------------------------------------------------------------------------------
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