ALDEx2 Troubleshooting Installation

Community Plugin Support
1

Hello,

I just encountered an issue while I was installing ALDEx2 package. I dowload th R package and then tried to install it under Qiime but I got this followinf issue:
conda install bioconductor-aldex2 -c defaults -c bioconda -c conda-forge
[
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 75, in _plugin_lookup
import q2cli.core.cache
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 400, in
CACHE = DeploymentCache()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 200, in _cache_current_state
state = self._get_current_state()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 238, in _get_current_state
plugin_manager = qiime2.sdk.PluginManager()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 44, in new
self._init()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 59, in _init
plugin = entry_point.load()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/pkg_resources/init.py”, line 2434, in load
return self.resolve()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/pkg_resources/init.py”, line 2440, in resolve
module = import(self.module_name, fromlist=[‘name’], level=0)
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_aldex2/plugin_setup.py”, line 5, in
from q2_types.feature_data import FeatureData, Differential
ImportError: cannot import name ‘Differential’

With that, I can not load Qiime2 anymore since I git the same exact error message. I will appreciate if I can get a quick help.
@dgiguer, do you have an idea regarding this issue?

Thanks again
Cheers,
Clothilde

2

Hello,

I just tried to install ALDEx2 package and I encontoured the following issue:

[ QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
File “/home/villot/.conda/envs/qiime2-2019.4/bin/qiime”, line 11, in
sys.exit(qiime())
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 764, in call
return self.main(*args, **kwargs)
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 717, in main
rv = self.invoke(ctx)
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 1132, in invoke
cmd_name, cmd, args = self.resolve_command(ctx, args)
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 1171, in resolve_command
cmd = self.get_command(ctx, cmd_name)
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 99, in get_command
plugin = self._plugin_lookup[name]
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 75, in _plugin_lookup
import q2cli.core.cache
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 400, in
CACHE = DeploymentCache()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 200, in _cache_current_state
state = self._get_current_state()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 238, in _get_current_state
plugin_manager = qiime2.sdk.PluginManager()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 44, in new
self._init()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 59, in _init
plugin = entry_point.load()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/pkg_resources/init.py”, line 2434, in load
return self.resolve()
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/pkg_resources/init.py”, line 2440, in resolve
module = import(self.module_name, fromlist=[‘name’], level=0)
File “/home/villot/.conda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_aldex2/plugin_setup.py”, line 5, in
from q2_types.feature_data import FeatureData, Differential
ImportError: cannot import name ‘Differential’ ]

It is a shame since I can not have access to Qiime 2 anymore neither… @dgiguer - do you have an idea what is the issue? I will appreciate your quick help,
Cheers,
Clothilde

3

@Nicheca1, I’m not sure what is causing your ALDEx2 errors, but you may be able to get (the rest of) QIIME2 up and running again quickly by re-installing with a different name. This is a bit of a hack, but if it keeps you productive, that’s what counts.

Is this a native installation within a Conda environment? If so, you can follow the normal installation process, changing the name of the environment in the conda env create -n qiime2-2020.6 ... step. (The name here is qiime2-2020.6). You can then activate the new environment and carry on with your non-aldex2 work.

I don’t have much experience with VMs/containers, but if you’re working with QIIME 2 in one of those ways, you may be able to take a similar tactic, creating a second VM image or container to let you keep plugging for now.

Best of luck!
CK

4

The FeatureData[Differential] type (which is used by the q2-ALDEx2 and q2-Songbird community plugins) wasn’t integrated into the main QIIME 2 distribution until the 2019.7 release. @Nicheca1, if you install a more recent version of QIIME 2 (at least 2019.7) then you should be able to use q2-ALDEx2 with that QIIME 2 version!

Edit: Also, I think you may be able to get your existing installation of QIIME 2 working again by uninstalling the q2-ALDEx2 software.

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