[Debian-med-packaging] Bug#1071780: sepp: FTBFS: ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel'
Santiago Vila
sanvila at debian.org
Fri May 24 20:36:25 BST 2024
Package: src:sepp
Version: 4.5.1+really4.5.1+dfsg-5
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --with python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p tools/bundled/Linux
mkdir -p tools/merge/lib
# Building the jar for sepp.
cd tools/merge && \
CLASSPATH=/usr/share/java/jenkins-json-lib.jar:/usr/share/java/gson.jar ant
Buildfile: /<<PKGBUILDDIR>>/tools/merge/build.xml
clean:
compile:
[mkdir] Created dir: /<<PKGBUILDDIR>>/tools/merge/classes
[javac] /<<PKGBUILDDIR>>/tools/merge/build.xml:32: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
[javac] Compiling 23 source files to /<<PKGBUILDDIR>>/tools/merge/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[javac] /<<PKGBUILDDIR>>/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/util/Trees.java:32: warning: SunGraphicsEnvironment is internal proprietary API and may be removed in a future release
[javac] import sun.java2d.SunGraphicsEnvironment;
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/algos/lca/SchieberVishkinLCA.java:188: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
[javac] _tnode_idx_lookup.put(n, new Integer(i++));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/io/NewickReader.java:341: warning: [removal] Double(double) in Double has been deprecated and marked for removal
[javac] node.setData(new Double(0));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/sti/STITree.java:221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
[javac] return _nodes.get(new Integer(id));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/JSONMerger.java:264: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal
[javac] newRecord.set(locEdgeNum, new Integer(newLab));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/JSONMerger.java:275: warning: [removal] Double(double) in Double has been deprecated and marked for removal
[javac] Double newLWR = new Double(prior * precord.getDouble(2));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/JSONMerger.java:519: warning: [removal] Double(String) in Double has been deprecated and marked for removal
[javac] mainEdgeLen.put(edgeLenMatcher.group(2), new Double(edgeLenMatcher.group(1)));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/JSONMerger.java:616: warning: [removal] Double(String) in Double has been deprecated and marked for removal
[javac] cutoff = new Double(args[i]);
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/JSONMerger.java:656: warning: [removal] Double(String) in Double has been deprecated and marked for removal
[javac] threshold = new Double(args[i]);
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java:177: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal
[javac] pr.set(locEdgeNum, new Integer(newLab));
[javac] ^
[javac] /<<PKGBUILDDIR>>/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java:269: warning: [removal] Double(String) in Double has been deprecated and marked for removal
[javac] Double len = new Double(matcher.group(1));
[javac] ^
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 12 warnings
jar:
[jar] Building jar: /<<PKGBUILDDIR>>/tools/merge/seppJsonMerger.jar
BUILD SUCCESSFUL
Total time: 2 seconds
dh_auto_configure
I: pybuild base:311: python3.11 setup.py config
Creating main sepp config file at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/.sepp/main.config and tools at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/.sepp
# dh_auto_configure only calls the config for sepp, we need it for upp as well.
pybuild --configure --configure-args "upp"
I: pybuild base:311: python3.11 setup.py config upp
Creating main sepp config file at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/.sepp/main.config and tools at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/.sepp
Creating main UPP config file at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/.sepp/upp.config and tools at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/.sepp
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
I: pybuild base:311: /usr/bin/python3 setup.py build
# Preparing a conffile with Debian paths for sepp.
sed 's,path=.*\(pplacer\)$,path=/usr/bin/\1,' `find . -name main.config` | \
sed 's,path=.*\(hmm[a-z]*\)$,path=/usr/bin/\1,' | \
sed 's,path=.*\(seppJsonMerger.jar\)$,path=/usr/share/sepp/\1,' > sepp.config
# Preparing a conffile with Debian paths for upp.
sed 's,path=.*\(pplacer\)$,path=/usr/bin/\1,' `find . -name upp.config` | \
sed 's,path=.*\(hmm[a-z]*\)$,path=/usr/bin/\1,' | \
sed 's,path=.*\(seppJsonMerger.jar\)$,path=/usr/share/sepp/\1,' > upp.config
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
ORIGIN_FOLDER=`pwd` && \
TEST_FOLDER=`mktemp -d` && \
cp -r test/ $TEST_FOLDER && \
cd $TEST_FOLDER && \
mkdir sepp/ && \
for F in $(ls $ORIGIN_FOLDER/sepp/*.py); do \
sed "s,/etc/sepp,$TEST_FOLDER," $F > sepp/${F##*/}; \
done && \
for F in $(ls $ORIGIN_FOLDER/*.config); do \
sed "s,/usr/share/sepp,$ORIGIN_FOLDER/tools/merge," $F > ${F##*/}; \
done && \
cd test/unittest/ && \
sed "s,\".*\.jar\",\"$ORIGIN_FOLDER/tools/merge/seppJsonMerger.jar\"," testMerge.py > testMergeCp.py && \
mv testMergeCp.py testMerge.py && \
PYTHONPATH=$PYTHONPATH:../../ python3 -m unittest discover -v
testAlignmentReadFasta (testAlignment.Test.testAlignmentReadFasta) ... /tmp/tmp.QLlJH3vkmZ/test/unittest/testAlignment.py:38: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/mock/pyrg/sate.fasta' mode='r' encoding='UTF-8'>
alg.read_filepath(get_data_path("mock/pyrg/sate.fasta"))
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
testExtendedAlignment (testAlignment.Test.testExtendedAlignment) ... /tmp/tmp.QLlJH3vkmZ/test/unittest/testAlignment.py:107: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/simulated/test.fasta' mode='r' encoding='UTF-8'>
alg.read_filepath(get_data_path("simulated/test.fasta"))
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/tmp/tmp.QLlJH3vkmZ/test/unittest/testAlignment.py:112: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/simulated/test.fas' mode='r' encoding='UTF-8'>
frg.read_filepath(get_data_path("simulated/test.fas"))
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/tmp/tmp.QLlJH3vkmZ/test/unittest/testAlignment.py:130: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpi2zg_u1i' mode='r' encoding='UTF-8'>
tmp = MutableAlignment().read_filepath(self.fp_dummy1)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/tmp/tmp.QLlJH3vkmZ/test/unittest/testAlignment.py:133: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp0g51ej8d' mode='r' encoding='UTF-8'>
tmp = MutableAlignment().read_filepath(self.fp_dummy2)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/tmp/tmp.QLlJH3vkmZ/sepp/alignment.py:555: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpi2zg_u1i' mode='r' encoding='UTF-8'>
self.read_filepath(base_alignment, "FASTA")
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/tmp/tmp.QLlJH3vkmZ/sepp/alignment.py:566: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/tmp/cp1.extended.sto' mode='r' encoding='UTF-8'>
ext.read_extended_alignment(path)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
[19:11:53] alignment.py (line 567): INFO: Merging extension sto file (/tmp/tmp.QLlJH3vkmZ/test/unittest/data/tmp/cp1.extended.sto) into base alignment (/tmp/tmpi2zg_u1i).
/tmp/tmp.QLlJH3vkmZ/sepp/alignment.py:555: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp0g51ej8d' mode='r' encoding='UTF-8'>
self.read_filepath(base_alignment, "FASTA")
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/tmp/tmp.QLlJH3vkmZ/sepp/alignment.py:566: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/tmp/cp2.extended.sto' mode='r' encoding='UTF-8'>
ext.read_extended_alignment(path)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
[19:11:53] alignment.py (line 567): INFO: Merging extension sto file (/tmp/tmp.QLlJH3vkmZ/test/unittest/data/tmp/cp2.extended.sto) into base alignment (/tmp/tmp0g51ej8d).
ok
testReadOnlySubAlignment (testAlignment.Test.testReadOnlySubAlignment) ... /tmp/tmp.QLlJH3vkmZ/test/unittest/testAlignment.py:46: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/mock/pyrg/sate.fasta' mode='r' encoding='UTF-8'>
alg.read_filepath(get_data_path("mock/pyrg/sate.fasta"))
ResourceWarning: Enable tracemalloc to get the object allocation traceback
ok
testCheckPoint (unittest.loader._FailedTest.testCheckPoint) ... ERROR
testConfigFile (testConfig.Test.testConfigFile) ... /usr/lib/python3.11/argparse.py:971: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/configs/test.config' mode='r' encoding='UTF-8'>
setattr(namespace, self.dest, values)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
[19:11:53] config.py (line 371): INFO: Seed number: 297834
ok
testConfigFileMissingFile (testConfig.Test.testConfigFileMissingFile) ... /tmp/tmp.QLlJH3vkmZ/test/unittest/testConfig.py:66: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/configs/test.config' mode='r' encoding='UTF-8'>
config._options_singelton = None
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/usr/lib/python3.11/argparse.py:971: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/configs/test2.config' mode='r' encoding='UTF-8'>
setattr(namespace, self.dest, values)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/usr/lib/python3.11/argparse.py:971: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/simulated/test.fas' mode='r' encoding='UTF-8'>
setattr(namespace, self.dest, values)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/usr/lib/python3.11/argparse.py:971: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/simulated/test.small.fas' mode='r' encoding='UTF-8'>
setattr(namespace, self.dest, values)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
[19:11:53] config.py (line 371): INFO: Seed number: 297834
ok
testCpuCount (testConfig.Test.testCpuCount) ... /tmp/tmp.QLlJH3vkmZ/test/unittest/testConfig.py:120: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/configs/test2.config' mode='r' encoding='UTF-8'>
config._options_singelton = None
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/tmp/tmp.QLlJH3vkmZ/test/unittest/testConfig.py:120: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/simulated/test.small.fas' mode='r' encoding='UTF-8'>
config._options_singelton = None
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/tmp/tmp.QLlJH3vkmZ/test/unittest/testConfig.py:120: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/simulated/test.fas' mode='r' encoding='UTF-8'>
config._options_singelton = None
ResourceWarning: Enable tracemalloc to get the object allocation traceback
[19:11:53] config.py (line 371): INFO: Seed number: 297834
[19:11:53] config.py (line 371): INFO: Seed number: 297834
ok
testLog (testConfig.Test.testLog) ... ERROR
testMainConfigFile (testConfig.Test.testMainConfigFile) ... [19:11:53] config.py (line 337): WARNING: Main configuration file was not found at: /tmp/tmpn7e6tvrn
Proceeding without the main configuration...
[19:11:53] config.py (line 371): INFO: Seed number: 297834
ok
testExternalJobs (unittest.loader._FailedTest.testExternalJobs) ... ERROR
testMerge (unittest.loader._FailedTest.testMerge) ... ERROR
testMidpoint (unittest.loader._FailedTest.testMidpoint) ... ERROR
testSepp (unittest.loader._FailedTest.testSepp) ... ERROR
testUPP (unittest.loader._FailedTest.testUPP) ... ERROR
======================================================================
ERROR: testCheckPoint (unittest.loader._FailedTest.testCheckPoint)
----------------------------------------------------------------------
ImportError: Failed to import test module: testCheckPoint
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/tmp/tmp.QLlJH3vkmZ/test/unittest/testCheckPoint.py", line 15, in <module>
from sepp.exhaustive import ExhaustiveAlgorithm
File "/tmp/tmp.QLlJH3vkmZ/sepp/exhaustive.py", line 6, in <module>
from sepp.algorithm import AbstractAlgorithm
File "/tmp/tmp.QLlJH3vkmZ/sepp/algorithm.py", line 12, in <module>
from sepp.tree import PhylogeneticTree
File "/tmp/tmp.QLlJH3vkmZ/sepp/tree.py", line 25, in <module>
from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py)
======================================================================
ERROR: testLog (testConfig.Test.testLog)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/tmp/tmp.QLlJH3vkmZ/test/unittest/testConfig.py", line 141, in testLog
import sepp.jobs
File "/tmp/tmp.QLlJH3vkmZ/sepp/jobs.py", line 16, in <module>
from sepp.tree import PhylogeneticTree
File "/tmp/tmp.QLlJH3vkmZ/sepp/tree.py", line 25, in <module>
from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py)
======================================================================
ERROR: testExternalJobs (unittest.loader._FailedTest.testExternalJobs)
----------------------------------------------------------------------
ImportError: Failed to import test module: testExternalJobs
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/tmp/tmp.QLlJH3vkmZ/test/unittest/testExternalJobs.py", line 7, in <module>
from sepp.jobs import ExternalSeppJob
File "/tmp/tmp.QLlJH3vkmZ/sepp/jobs.py", line 16, in <module>
from sepp.tree import PhylogeneticTree
File "/tmp/tmp.QLlJH3vkmZ/sepp/tree.py", line 25, in <module>
from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py)
======================================================================
ERROR: testMerge (unittest.loader._FailedTest.testMerge)
----------------------------------------------------------------------
ImportError: Failed to import test module: testMerge
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/tmp/tmp.QLlJH3vkmZ/test/unittest/testMerge.py", line 7, in <module>
from sepp.jobs import MergeJsonJob
File "/tmp/tmp.QLlJH3vkmZ/sepp/jobs.py", line 16, in <module>
from sepp.tree import PhylogeneticTree
File "/tmp/tmp.QLlJH3vkmZ/sepp/tree.py", line 25, in <module>
from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py)
======================================================================
ERROR: testMidpoint (unittest.loader._FailedTest.testMidpoint)
----------------------------------------------------------------------
ImportError: Failed to import test module: testMidpoint
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/tmp/tmp.QLlJH3vkmZ/test/unittest/testMidpoint.py", line 16, in <module>
from sepp.exhaustive import ExhaustiveAlgorithm
File "/tmp/tmp.QLlJH3vkmZ/sepp/exhaustive.py", line 6, in <module>
from sepp.algorithm import AbstractAlgorithm
File "/tmp/tmp.QLlJH3vkmZ/sepp/algorithm.py", line 12, in <module>
from sepp.tree import PhylogeneticTree
File "/tmp/tmp.QLlJH3vkmZ/sepp/tree.py", line 25, in <module>
from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py)
======================================================================
ERROR: testSepp (unittest.loader._FailedTest.testSepp)
----------------------------------------------------------------------
ImportError: Failed to import test module: testSepp
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/tmp/tmp.QLlJH3vkmZ/test/unittest/testSepp.py", line 15, in <module>
from sepp.exhaustive import ExhaustiveAlgorithm
File "/tmp/tmp.QLlJH3vkmZ/sepp/exhaustive.py", line 6, in <module>
from sepp.algorithm import AbstractAlgorithm
File "/tmp/tmp.QLlJH3vkmZ/sepp/algorithm.py", line 12, in <module>
from sepp.tree import PhylogeneticTree
File "/tmp/tmp.QLlJH3vkmZ/sepp/tree.py", line 25, in <module>
from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py)
======================================================================
ERROR: testUPP (unittest.loader._FailedTest.testUPP)
----------------------------------------------------------------------
ImportError: Failed to import test module: testUPP
Traceback (most recent call last):
File "/usr/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
module = self._get_module_from_name(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
__import__(name)
File "/tmp/tmp.QLlJH3vkmZ/test/unittest/testUPP.py", line 11, in <module>
from sepp.exhaustive_upp import UPPExhaustiveAlgorithm
File "/tmp/tmp.QLlJH3vkmZ/sepp/exhaustive_upp.py", line 13, in <module>
from sepp.exhaustive import JoinAlignJobs, ExhaustiveAlgorithm
File "/tmp/tmp.QLlJH3vkmZ/sepp/exhaustive.py", line 6, in <module>
from sepp.algorithm import AbstractAlgorithm
File "/tmp/tmp.QLlJH3vkmZ/sepp/algorithm.py", line 12, in <module>
from sepp.tree import PhylogeneticTree
File "/tmp/tmp.QLlJH3vkmZ/sepp/tree.py", line 25, in <module>
from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \
ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/usr/lib/python3/dist-packages/dendropy/datamodel/treemodel/__init__.py)
----------------------------------------------------------------------
Ran 14 tests in 0.609s
FAILED (errors=7)
sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmp.QLlJH3vkmZ/test/unittest/data/configs/test2.config' mode='r' encoding='UTF-8'>
/usr/lib/python3.11/multiprocessing/pool.py:268: ResourceWarning: unclosed running multiprocessing pool <multiprocessing.pool.Pool state=RUN pool_size=2>
make[1]: *** [debian/rules:61: override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:8: 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/202405/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large 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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
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