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$ planemo test
git --git-dir /home/pvh/.planemo/gx_repo fetch >/dev/null 2>&1
cd /tmp/tmp292k01; git clone --branch 'master' '/home/pvh/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/pvh/.planemo/gx_venv_None; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/pvh/.virtualenvs/planemo/bin/virtualenv -p /home/pvh/.virtualenvs/planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}
Cloning into 'galaxy-dev'...
done.
Set COMMON_STARTUP_ARGS to --dev-wheels
Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample
Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample
Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample
Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample
Initializing static/welcome.html from welcome.html.sample
Activating virtualenv at /home/pvh/.planemo/gx_venv_None
Traceback (most recent call last):
File "/home/pvh/.planemo/gx_venv_None/bin/pip", line 7, in <module>
from pip._internal import main
File "/home/pvh/.planemo/gx_venv_None/local/lib/python2.7/site-packages/pip/_internal/__init__.py", line 5, in <module>
import logging
File "/usr/lib/python2.7/logging/__init__.py", line 26, in <module>
import sys, os, time, cStringIO, traceback, warnings, weakref, collections
File "/usr/lib/python2.7/weakref.py", line 14, in <module>
from _weakref import (
ImportError: cannot import name _remove_dead_weakref
Testing using galaxy_root /tmp/tmp292k01/galaxy-dev
Testing tools with command [cd /tmp/tmp292k01/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/pvh/.planemo/gx_venv_None; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/pvh/.virtualenvs/planemo/bin/virtualenv -p /home/pvh/.virtualenvs/planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /home/pvh/Documents/code/Masters/refseq_data_manager/tool_test_output.html --xunit_report_file /tmp/tmp292k01/xunit.xml --structured_data_report_file /home/pvh/Documents/code/Masters/refseq_data_manager/tool_test_output.json functional.test_toolbox]
Activating virtualenv at /home/pvh/.planemo/gx_venv_None
Traceback (most recent call last):
File "/home/pvh/.planemo/gx_venv_None/bin/pip", line 7, in <module>
from pip._internal import main
File "/home/pvh/.planemo/gx_venv_None/local/lib/python2.7/site-packages/pip/_internal/__init__.py", line 5, in <module>
import logging
File "/usr/lib/python2.7/logging/__init__.py", line 26, in <module>
import sys, os, time, cStringIO, traceback, warnings, weakref, collections
File "/usr/lib/python2.7/weakref.py", line 14, in <module>
from _weakref import (
ImportError: cannot import name _remove_dead_weakref
Cannot locate xUnit report [/tmp/tmp292k01/xunit.xml] for tests - required to build planemo report and summarize tests.
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