Hi
So I was using our cluster-wide installation of conda, which of course I cannot update.
So I downloaded and installed Miniconda locally, and followed the installation instructions.
This appeared to work, and I got the final message:
Executing transaction: done
To activate this environment, use:
> source activate qiime2-2017.12
To deactivate an active environment, use:
> source deactivate
So I activated the environment, then tried:
%> qimme
What I got was
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: compiletime version 3.4 of module ‘pandas._libs.tslib’ does not match runtime version 3.5
return f(*args, **kwds)
/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: builtins.type size changed, may indicate binary incompatibility. Expected 864, got 824
return f(*args, **kwds)
/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: compiletime version 3.4 of module ‘pandas._libs.tslibs.timezones’ does not match runtime version 3.5
return f(*args, **kwds)
/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: compiletime version 3.4 of module ‘pandas._libs.tslibs.parsing’ does not match runtime version 3.5
return f(*args, **kwds)
/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: compiletime version 3.4 of module ‘pandas._libs.tslibs.fields’ does not match runtime version 3.5
return f(*args, **kwds)
/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: compiletime version 3.4 of module ‘pandas._libs.hashtable’ does not match runtime version 3.5
return f(*args, **kwds)
/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: compiletime version 3.4 of module ‘pandas._libs.lib’ does not match runtime version 3.5
return f(*args, **kwds)
/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: compiletime version 3.4 of module ‘pandas._libs.interval’ does not match runtime version 3.5
return f(*args, **kwds)
Traceback (most recent call last):
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/bin/qiime”, line 11, in
sys.exit(qiime())
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 722, in call
return self.main(*args, **kwargs)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 696, in main
with self.make_context(prog_name, args, **extra) as ctx:
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 621, in make_context
self.parse_args(ctx, args)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 1015, in parse_args
echo(ctx.get_help(), color=ctx.color)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 496, in get_help
return self.command.get_help(self)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 830, in get_help
self.format_help(ctx, formatter)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 845, in format_help
self.format_options(ctx, formatter)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 956, in format_options
self.format_commands(ctx, formatter)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 1000, in format_commands
for subcommand in self.list_commands(ctx):
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py”, line 69, in list_commands
plugins = sorted(self._plugin_lookup)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py”, line 53, in _plugin_lookup
import q2cli.cache
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/q2cli/cache.py”, line 302, in
CACHE = DeploymentCache()
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/q2cli/cache.py”, line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/q2cli/cache.py”, line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/q2cli/cache.py”, line 200, in _cache_current_state
state = self._get_current_state()
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/q2cli/cache.py”, line 232, in _get_current_state
import qiime2.sdk
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/qiime2/init.py”, line 10, in
from qiime2.metadata import Metadata, MetadataCategory
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/site-packages/qiime2/metadata.py”, line 15, in
import pandas as pd
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython3.4/lib/python3.4/site-packages/pandas-0.21.0rc1-py3.4-linux-x86_64.egg/pandas/init.py”, line 26, in
from pandas._libs import (hashtable as _hashtable,
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython3.4/lib/python3.4/site-packages/pandas-0.21.0rc1-py3.4-linux-x86_64.egg/pandas/_libs/hashtable.py”, line 7, in
bootstrap()
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython3.4/lib/python3.4/site-packages/pandas-0.21.0rc1-py3.4-linux-x86_64.egg/pandas/_libs/hashtable.py”, line 6, in bootstrap
imp.load_dynamic(name,file)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/imp.py”, line 343, in load_dynamic
return _load(spec)
File “pandas/_libs/hashtable.pyx”, line 1, in init pandas._libs.hashtable
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython3.4/lib/python3.4/site-packages/pandas-0.21.0rc1-py3.4-linux-x86_64.egg/pandas/_libs/lib.py”, line 7, in
bootstrap()
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython3.4/lib/python3.4/site-packages/pandas-0.21.0rc1-py3.4-linux-x86_64.egg/pandas/_libs/lib.py”, line 6, in bootstrap
imp.load_dynamic(name,file)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/imp.py”, line 343, in load_dynamic
return _load(spec)
File “pandas/_libs/lib.pyx”, line 59, in init pandas._libs.lib
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython3.4/lib/python3.4/site-packages/pandas-0.21.0rc1-py3.4-linux-x86_64.egg/pandas/_libs/interval.py”, line 7, in
bootstrap()
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/mypython3.4/lib/python3.4/site-packages/pandas-0.21.0rc1-py3.4-linux-x86_64.egg/pandas/_libs/interval.py”, line 6, in bootstrap
imp.load_dynamic(name,file)
File “/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/qiime2-2017.12/lib/python3.5/imp.py”, line 343, in load_dynamic
return _load(spec)
File “pandas/_libs/hashtable.pxd”, line 7, in init pandas._libs.interval
AttributeError: module ‘pandas._libs.hashtable’ has no attribute ‘HashTable’
Any clues?