Your message dated Fri, 12 Jun 2026 08:21:48 +0000
with message-id <[email protected]>
and subject line Bug#1136864: fixed in dcmstack 0.9+git20260610.ed4d27c-1
has caused the Debian Bug report #1136864,
regarding dcmstack: FTBFS: E AttributeError: module 'pydicom' has no
attribute 'read_file'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1136864: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1136864
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:dcmstack
Version: 0.9-3
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/202605/
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:dcmstack, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
pybuild --clean -i python{version} -p "3.14 3.13" --parallel=2
I: pybuild base:385: python3.14 setup.py clean
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning:
Unknown distribution option: 'test_suite'
warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/dist.py:759:
SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX
license expression:
License :: OSI Approved :: MIT License
[... snipped ...]
test/test_cli.py:56: AssertionError
----------------------------- Captured stdout call -----------------------------
No DICOM files found in /tmp/dcmstack_cli_test_innmxkt4dw
__________________________ TestDcmstackCli.test_embed __________________________
self = <test.test_cli.TestDcmstackCli object at 0x7fe50b1b34d0>
def test_embed(self):
nii_paths = make_niftis(self.out_dir, ['--embed'])
> assert len(nii_paths) == 1
E assert 0 == 1
E + where 0 = len([])
test/test_cli.py:60: AssertionError
----------------------------- Captured stdout call -----------------------------
No DICOM files found in /tmp/dcmstack_cli_test_innmxkt4dw
___________________________ TestNitoolCli.test_basic ___________________________
self = <test.test_cli.TestNitoolCli object at 0x7fe50b1b3610>
def test_basic(self):
> nii_path = make_niftis(self.out_dir, ['--embed'])[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
E IndexError: list index out of range
test/test_cli.py:65: IndexError
----------------------------- Captured stdout call -----------------------------
No DICOM files found in /tmp/dcmstack_cli_test_innmxkt4dw
_______________________________ test_from_dicom ________________________________
def test_from_dicom():
data_dir = path.join(test_dir,
'data',
'dcmstack',
'2D_16Echo_qT2')
src_fn = path.join(data_dir, 'TE_40_SlcPos_-33.707626341697.dcm')
> src_dcm = pydicom.read_file(src_fn)
^^^^^^^^^^^^^^^^^
E AttributeError: module 'pydicom' has no attribute 'read_file'
test/test_dcmmeta.py:1042: AttributeError
_____________________________ test_image_collision _____________________________
def test_image_collision():
dcm_path = path.join(test_dir,
'data',
'dcmstack',
'2D_16Echo_qT2',
'TE_20_SlcPos_-33.707626341697.dcm')
> dcm = pydicom.read_file(dcm_path)
^^^^^^^^^^^^^^^^^
E AttributeError: module 'pydicom' has no attribute 'read_file'
test/test_dcmstack.py:212: AttributeError
________________________ TestParseAndGroup.test_default ________________________
self = <test.test_dcmstack.TestParseAndGroup object at 0x7fe50b07a5d0>
def test_default(self):
> res = dcmstack.parse_and_group(self.in_paths)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
test/test_dcmstack.py:640:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src_paths =
['/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/test/data/dcmstack/2D_16Echo_qT2/TE_20_Slc...dcmstack-0.9/.pybuild/cpython3_3.13_dcmstack/build/test/data/dcmstack/2D_16Echo_qT2/TE_40_SlcPos_-23.207628249046.dcm']
group_by = ('SeriesInstanceUID', 'SeriesNumber', 'ProtocolName',
'ImageOrientationPatient')
extractor = <dcmstack.extract.MetaExtractor object at 0x7fe50b176ba0>
force = False, warn_on_except = False
close_tests = ('ImageOrientationPatient',)
def parse_and_group(src_paths, group_by=default_group_keys, extractor=None,
force=False, warn_on_except=False,
close_tests=default_close_keys):
'''Parse the given dicom files and group them together. Each group is
stored as a (list) value in a dict where the key is a tuple of values
corresponding to the keys in 'group_by'
Parameters
----------
src_paths : sequence
A list of paths to the source DICOM files.
group_by : tuple
Meta data keys to group data sets with. Any data set with the same
values for these keys will be grouped together. This tuple of values
will also be the key in the result dictionary.
extractor : callable
Should take a pydicom.dataset.Dataset and return a dictionary of the
extracted meta data.
force : bool
Force reading source files even if they do not appear to be DICOM.
warn_on_except : bool
Convert exceptions into warnings, possibly allowing some results to
be
returned.
close_tests : sequence
Any `group_by` key listed here is tested with `numpy.allclose`
instead
of straight equality when determining group membership.
Returns
-------
groups : dict
A dict mapping tuples of values (corresponding to 'group_by') to
groups
of data sets. Each element in the list is a tuple containing the
dicom
object, the parsed meta data, and the filename.
'''
if extractor is None:
from .extract import default_extractor
extractor = default_extractor
results = {}
close_elems = {}
for dcm_path in src_paths:
#Read the DICOM file
try:
> dcm = pydicom.read_file(dcm_path, force=force)
^^^^^^^^^^^^^^^^^
E AttributeError: module 'pydicom' has no attribute 'read_file'
dcmstack/dcmstack.py:1046: AttributeError
________________________ TestParseAndStack.test_default ________________________
self = <test.test_dcmstack.TestParseAndStack object at 0x7fe50b07a710>
def test_default(self):
> res = dcmstack.parse_and_stack(self.in_paths)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
test/test_dcmstack.py:666:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
dcmstack/dcmstack.py:1156: in parse_and_stack
results = parse_and_group(src_paths,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src_paths =
['/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/test/data/dcmstack/2D_16Echo_qT2/TE_20_Slc...dcmstack-0.9/.pybuild/cpython3_3.13_dcmstack/build/test/data/dcmstack/2D_16Echo_qT2/TE_40_SlcPos_-23.207628249046.dcm']
group_by = ('SeriesInstanceUID', 'SeriesNumber', 'ProtocolName',
'ImageOrientationPatient')
extractor = <dcmstack.extract.MetaExtractor object at 0x7fe50b176ba0>
force = False, warn_on_except = False
close_tests = ('ImageOrientationPatient',)
def parse_and_group(src_paths, group_by=default_group_keys, extractor=None,
force=False, warn_on_except=False,
close_tests=default_close_keys):
'''Parse the given dicom files and group them together. Each group is
stored as a (list) value in a dict where the key is a tuple of values
corresponding to the keys in 'group_by'
Parameters
----------
src_paths : sequence
A list of paths to the source DICOM files.
group_by : tuple
Meta data keys to group data sets with. Any data set with the same
values for these keys will be grouped together. This tuple of values
will also be the key in the result dictionary.
extractor : callable
Should take a pydicom.dataset.Dataset and return a dictionary of the
extracted meta data.
force : bool
Force reading source files even if they do not appear to be DICOM.
warn_on_except : bool
Convert exceptions into warnings, possibly allowing some results to
be
returned.
close_tests : sequence
Any `group_by` key listed here is tested with `numpy.allclose`
instead
of straight equality when determining group membership.
Returns
-------
groups : dict
A dict mapping tuples of values (corresponding to 'group_by') to
groups
of data sets. Each element in the list is a tuple containing the
dicom
object, the parsed meta data, and the filename.
'''
if extractor is None:
from .extract import default_extractor
extractor = default_extractor
results = {}
close_elems = {}
for dcm_path in src_paths:
#Read the DICOM file
try:
> dcm = pydicom.read_file(dcm_path, force=force)
^^^^^^^^^^^^^^^^^
E AttributeError: module 'pydicom' has no attribute 'read_file'
dcmstack/dcmstack.py:1046: AttributeError
=============================== warnings summary ===============================
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_basic
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_embed
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestNitoolCli::test_basic
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/dcmstack/dcmstack.py:1049:
UserWarning: Error reading file
/tmp/dcmstack_cli_test_innmxkt4dw/TE_20_SlcPos_-23.207628249046.dcm: module
'pydicom' has no attribute 'read_file'
warnings.warn('Error reading file %s: %s' % (dcm_path, str(e)))
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_basic
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_embed
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestNitoolCli::test_basic
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/dcmstack/dcmstack.py:1049:
UserWarning: Error reading file
/tmp/dcmstack_cli_test_innmxkt4dw/TE_20_SlcPos_-33.707626341697.dcm: module
'pydicom' has no attribute 'read_file'
warnings.warn('Error reading file %s: %s' % (dcm_path, str(e)))
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_basic
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_embed
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestNitoolCli::test_basic
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/dcmstack/dcmstack.py:1049:
UserWarning: Error reading file
/tmp/dcmstack_cli_test_innmxkt4dw/TE_40_SlcPos_-33.707626341697.dcm: module
'pydicom' has no attribute 'read_file'
warnings.warn('Error reading file %s: %s' % (dcm_path, str(e)))
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_basic
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_embed
.pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestNitoolCli::test_basic
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/dcmstack/dcmstack.py:1049:
UserWarning: Error reading file
/tmp/dcmstack_cli_test_innmxkt4dw/TE_40_SlcPos_-23.207628249046.dcm: module
'pydicom' has no attribute 'read_file'
warnings.warn('Error reading file %s: %s' % (dcm_path, str(e)))
.pybuild/cpython3_3.13_dcmstack/build/test/test_dcmstack.py::test_fsl_hack
.pybuild/cpython3_3.13_dcmstack/build/test/test_dcmstack.py::test_pix_overflow
/usr/lib/python3/dist-packages/pydicom/dataset.py:1378: DeprecationWarning:
'Dataset.is_little_endian' will be removed in v4.0, set the Transfer Syntax UID
or use the 'little_endian' argument with Dataset.save_as() or dcmwrite() instead
warn_and_log(
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED test/test_cli.py::TestDcmstackCli::test_basic - assert 0 == 1
FAILED test/test_cli.py::TestDcmstackCli::test_embed - assert 0 == 1
FAILED test/test_cli.py::TestNitoolCli::test_basic - IndexError: list index o...
FAILED test/test_dcmmeta.py::test_from_dicom - AttributeError: module 'pydico...
FAILED test/test_dcmstack.py::test_image_collision - AttributeError: module '...
FAILED test/test_dcmstack.py::TestParseAndGroup::test_default - AttributeErro...
FAILED test/test_dcmstack.py::TestParseAndStack::test_default - AttributeErro...
ERROR test/test_dcmstack.py::TestIncongruentImage::test_rows - AttributeError...
ERROR test/test_dcmstack.py::TestIncongruentImage::test_columns - AttributeEr...
ERROR test/test_dcmstack.py::TestIncongruentImage::test_pix_space - Attribute...
ERROR test/test_dcmstack.py::TestIncongruentImage::test_close_pix_space - Att...
ERROR test/test_dcmstack.py::TestIncongruentImage::test_orientation - Attribu...
ERROR test/test_dcmstack.py::TestIncongruentImage::test_close_orientation - A...
ERROR test/test_dcmstack.py::TestInvalidStack::test_empty - AttributeError: m...
ERROR test/test_dcmstack.py::TestInvalidStack::test_missing_slice - Attribute...
ERROR test/test_dcmstack.py::TestInvalidStack::test_wrong_number_of_files - A...
ERROR test/test_dcmstack.py::TestInvalidStack::test_vector_var_over_vol - Att...
ERROR test/test_dcmstack.py::TestGetShape::test_single_slice - AttributeError...
ERROR test/test_dcmstack.py::TestGetShape::test_three_dim - AttributeError: m...
ERROR test/test_dcmstack.py::TestGetShape::test_four_dim - AttributeError: mo...
ERROR test/test_dcmstack.py::TestGetShape::test_five_dim - AttributeError: mo...
ERROR test/test_dcmstack.py::TestGuessDim::test_single_guess - AttributeError...
ERROR test/test_dcmstack.py::TestGuessDim::test_wrong_guess_first - Attribute...
ERROR test/test_dcmstack.py::TestGetData::test_single_slice - AttributeError:...
ERROR test/test_dcmstack.py::TestGetData::test_three_dim - AttributeError: mo...
ERROR test/test_dcmstack.py::TestGetData::test_four_dim - AttributeError: mod...
ERROR test/test_dcmstack.py::TestGetData::test_five_dim - AttributeError: mod...
ERROR test/test_dcmstack.py::TestGetAffine::test_single_slice - AttributeErro...
ERROR test/test_dcmstack.py::TestGetAffine::test_three_dim - AttributeError: ...
ERROR test/test_dcmstack.py::TestToNifti::test_single_slice - AttributeError:...
ERROR test/test_dcmstack.py::TestToNifti::test_single_vol - AttributeError: m...
ERROR test/test_dcmstack.py::TestToNifti::test_slice_dim_reorient - Attribute...
ERROR test/test_dcmstack.py::TestToNifti::test_two_time_vol - AttributeError:...
ERROR test/test_dcmstack.py::TestToNifti::test_two_vector_vol - AttributeErro...
ERROR test/test_extract.py::TestCsa::test_simplify - AttributeError: module '...
ERROR test/test_extract.py::TestCsa::test_csa_image_trans - AttributeError: m...
ERROR test/test_extract.py::TestCsa::test_parse_phx_line - AttributeError: mo...
ERROR test/test_extract.py::TestCsa::test_csa_series_trans - AttributeError: ...
ERROR test/test_extract.py::TestMetaExtractor::test_get_elem_key - AttributeE...
ERROR test/test_extract.py::TestMetaExtractor::test_get_elem_value - Attribut...
ERROR test/test_extract.py::TestMetaExtractor::test_dup_trans - AttributeErro...
ERROR test/test_extract.py::TestMetaExtractor::test_reloc_private - Attribute...
ERROR test/test_extract.py::TestMetaExtractor::test_non_reloc_private - Attri...
============= 7 failed, 88 passed, 14 warnings, 36 errors in 0.70s =============
E: pybuild pybuild:485: test: plugin distutils failed with: exit code=1: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build; python3.13 -m pytest
test
rm -fr -- /tmp/dh-xdg-rundir-iH1DLbmb
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14
3.13" --parallel=2 returned exit code 13
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: dcmstack
Source-Version: 0.9+git20260610.ed4d27c-1
Done: Karsten Schöke <[email protected]>
We believe that the bug you reported is fixed in the latest version of
dcmstack, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Karsten Schöke <[email protected]> (supplier of updated dcmstack
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 11 Jun 2026 19:11:57 +0200
Source: dcmstack
Architecture: source
Version: 0.9+git20260610.ed4d27c-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Karsten Schöke <[email protected]>
Closes: 1136864
Changes:
dcmstack (0.9+git20260610.ed4d27c-1) unstable; urgency=medium
.
* Team upload.
* New upstream version 0.9+git20260610.ed4d27c
Closes: #1136864
* Removing patches merged from upstream.
* insert fix-typo-in-modulimport.patch
* d/control: Update B-D.
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Remove Priority field (cme)
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* debputy lint --auto-fix (routine-update)
* insert doc-base-registration
* remove egg-info from package.
* d/watch: Convert to version 5
* insert test depends on pint.
* d/salsa-ci.yml: deactivate uscan test
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