Package: src:promod3
Version: 3.4.1+ds-1
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3
dh_clean
debian/rules binary
dh binary --with python3
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
-DOPTIMIZE=ON -DDISABLE_DOCUMENTATION=ON -DOST_ROOT=/usr
-DCOMPOUND_LIB=/var/cache/openstructure/compounds.chemlib
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb
PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr
-DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc
-DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON
-DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON
-DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run
-DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles"
-DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu
-DOPTIMIZE=ON -DDISABLE_DOCUMENTATION=ON -DOST_ROOT=/usr
-DCOMPOUND_LIB=/var/cache/openstructure/compounds.chemlib ..
-- The CXX compiler identification is GNU 14.2.0
-- The C compiler identification is GNU 14.2.0
[... snipped ...]
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 815, in
testAddAlignmentClustal
opts = parser.Parse(['--clustal', 'data/aln_tpl/2jlp-1.aln',
'-c', 'data/aln_tpl/2jlp-1.aln'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 758, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "clustal")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAddAlignmentGzipIn (__main__.PM3ArgParseTests.testAddAlignmentGzipIn)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 219, in
testAddAlignmentGzipIn
opts = parser.Parse(['--fasta', 'data/fasta/1ake.fas.gz',
'--fasta', 'data/fasta/1ake.fas'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAddAlignmentMultipleTargets
(__main__.PM3ArgParseTests.testAddAlignmentMultipleTargets)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 197, in
testAddAlignmentMultipleTargets
parser.Parse(['--fasta', 'data/fasta/1ake_2trg.fas'])
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAddAlignmentSwitchSeqs
(__main__.PM3ArgParseTests.testAddAlignmentSwitchSeqs)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 250, in
testAddAlignmentSwitchSeqs
opts = parser.Parse(['--fasta', 'data/fasta/1ake.fas'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAddAlignmentToMany (__main__.PM3ArgParseTests.testAddAlignmentToMany)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 291, in
testAddAlignmentToMany
opts = parser.Parse(['--fasta', 'data/fasta/1ake_3.fas'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAdditionalProfile (__main__.PM3ArgParseTests.testAdditionalProfile)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1098, in
testAdditionalProfile
parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'-s', 'data/aln_tpl/1crn.hhm',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'-s', 'data/aln_tpl/5ua4_B.hhm'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAllCovered (__main__.PM3ArgParseTests.testAllCovered)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1122, in
testAllCovered
parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'-f', 'data/aln_tpl/5d52-1_cut_A.fasta',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'-s', 'data/aln_tpl/1crn.hhm'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAllGoodHeteroOligo (__main__.PM3ArgParseTests.testAllGoodHeteroOligo)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1164, in
testAllGoodHeteroOligo
opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
'-f', 'data/aln_tpl/5ua4_B.fasta',
'-s', 'data/aln_tpl/1crn.hhm',
'-s', 'data/aln_tpl/5ua4_B.hhm'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAllGoodHomoOligo (__main__.PM3ArgParseTests.testAllGoodHomoOligo)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1148, in
testAllGoodHomoOligo
opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
'-f', 'data/aln_tpl/1crn.fasta',
'-s', 'data/aln_tpl/1crn.hhm'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAllGoodOneChain (__main__.PM3ArgParseTests.testAllGoodOneChain)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1134, in
testAllGoodOneChain
opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
'-s', 'data/aln_tpl/1crn.hhm'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAttachView (__main__.PM3ArgParseTests.testAttachView)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 929, in
testAttachView
opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
'-e', 'data/aln_tpl/1crn_cut.pdb'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAttachViewHetero (__main__.PM3ArgParseTests.testAttachViewHetero)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 980, in
testAttachViewHetero
opts = parser.Parse(['-p', 'data/aln_tpl/5d52-1_cut.pdb',
'-f', 'data/aln_tpl/5d52-1_cut_A.fasta',
'-f', 'data/aln_tpl/5d52-1_cut_B.fasta'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAttachViewHomo (__main__.PM3ArgParseTests.testAttachViewHomo)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 939, in
testAttachViewHomo
opts = parser.Parse(['-f', 'data/aln_tpl/2aoh-1_cut_A.fasta',
'-p', 'data/aln_tpl/2aoh-1_cut.pdb',
'-f', 'data/aln_tpl/2aoh-1_cut_B.fasta'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAttachViewOffset (__main__.PM3ArgParseTests.testAttachViewOffset)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 950, in
testAttachViewOffset
opts = parser.Parse(['-p', 'data/aln_tpl/2jlp-1.pdb',
'-f', 'data/aln_tpl/2jlp-1.fasta'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAttachViewOffsetClustal
(__main__.PM3ArgParseTests.testAttachViewOffsetClustal)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 960, in
testAttachViewOffsetClustal
opts = parser.Parse(['-p', 'data/aln_tpl/2jlp-1.pdb',
'-c', 'data/aln_tpl/2jlp-1.aln'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 758, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "clustal")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testAttachViewUnknownChain
(__main__.PM3ArgParseTests.testAttachViewUnknownChain)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1061, in
testAttachViewUnknownChain
parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'-p', 'data/aln_tpl/1crn_cut.pdb',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'-p', 'data/aln_tpl/2jlp-1.pdb'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testFraggerAttachedWithProfile
(__main__.PM3ArgParseTests.testFraggerAttachedWithProfile)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1218, in
testFraggerAttachedWithProfile
opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
'-f', 'data/aln_tpl/5ua4_B.fasta',
'-s', 'data/aln_tpl/1crn.hhm',
'-s', 'data/aln_tpl/5ua4_B.hhm',
'--use-fragments'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testFraggerAttachedWithoutProfile
(__main__.PM3ArgParseTests.testFraggerAttachedWithoutProfile)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1191, in
testFraggerAttachedWithoutProfile
opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
'-f', 'data/aln_tpl/5ua4_B.fasta',
'--use-fragments'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testFraggerNotRequested
(__main__.PM3ArgParseTests.testFraggerNotRequested)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1181, in
testFraggerNotRequested
opts = parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
'-f', 'data/aln_tpl/5ua4_B.fasta'])
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testProfileDoesNotExist
(__main__.PM3ArgParseTests.testProfileDoesNotExist)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1076, in
testProfileDoesNotExist
parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'-s', 'data/aln_tpl/IDoNotExist.hhm'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testProfileIsFuckedUp (__main__.PM3ArgParseTests.testProfileIsFuckedUp)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1087, in
testProfileIsFuckedUp
parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'-s', 'data/aln_tpl/1crn_corrupted.hhm'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
======================================================================
ERROR: testUniqueProfiles (__main__.PM3ArgParseTests.testUniqueProfiles)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/core/tests/test_pm3argparse.py", line 1110, in
testUniqueProfiles
parser.Parse(['-f', 'data/aln_tpl/1crn.fasta',
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'-s', 'data/aln_tpl/1crn.hhm',
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
'-s', 'data/aln_tpl/1crn.hhm'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 424, in Parse
opts.PostProcess(self.activate)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 735, in PostProcess
self._PostProcessAlignment()
~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 753, in _PostProcessAlignment
new_aln = _FetchAlnFromFile(src, self.allow_multitemplate, "fasta")
File
"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/core/pm3argparse.py",
line 204, in _FetchAlnFromFile
sequences = [(s.name.strip(),s.string) for s in aln.sequences]
^^^^^^^^^^^^^
TypeError: 'ConstSeqListIter' object is not iterable
----------------------------------------------------------------------
Ran 66 tests in 0.191s
FAILED (errors=23)
make[5]: *** [core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make:74:
core/tests/CMakeFiles/test_pm3argparse.py_run] Error 1
make[5]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[4]: *** [CMakeFiles/Makefile2:1770:
core/tests/CMakeFiles/test_pm3argparse.py_run.dir/all] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:1034: CMakeFiles/check.dir/rule] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:172: check] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j1 check ARGS\+=--verbose
ARGS\+=-j1 returned exit code 2
make[1]: *** [debian/rules:11: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:4: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202503/
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 could not 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:promod3, so that this is still
visible in the BTS web page for this package.
Thanks.
