mmvec: Unable to install both in Qiime2 environments and as standalone

I’ve tried installing within qiime2-2019.7 conda environments both on a cluster (barnacle) and on my local machine, I get the errors when I try to refresh the cache. I’ve also tried install mmvec alone on barnacle and got similar errors. Throwing them here – they are all related to tensorflow.

Local Machine Error (qiime2 conda-env): "Traceback (most recent call last): File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/pywrap_tensorflow.py”, line 58, in <module> from tensorflow.python.pywrap_tensorflow_internal import * File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/pywrap_tensorflow_internal.py”, line 28, in <module> _pywrap_tensorflow_internal = swig_import_helper() File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/pywrap_tensorflow_internal.py”, line 24, in swig_import_helper _mod = imp.load_module(‘_pywrap_tensorflow_internal’, fp, pathname, description) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/imp.py”, line 243, in load_module return load_dynamic(name, filename, file) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/imp.py”, line 343, in load_dynamic return _load(spec) ImportError: dlopen(/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _SecKeyCopyExternalRepresentation Referenced from: /Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/…/libtensorflow_framework.2.dylib Expected in: /System/Library/Frameworks/Security.framework/Versions/A/Security in /Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/…/libtensorflow_framework.2.dylib

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/bin/qiime”, line 11, in <module> sys.exit(qiime()) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 764, in call return self.main(*args, **kwargs) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 717, in main rv = self.invoke(ctx) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1132, in invoke cmd_name, cmd, args = self.resolve_command(ctx, args) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1171, in resolve_command cmd = self.get_command(ctx, cmd_name) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 101, in get_command plugin = self._plugin_lookup[name] File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 77, in _plugin_lookup import q2cli.core.cache File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/core/cache.py”, line 403, in <module> CACHE = DeploymentCache() File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/core/cache.py”, line 61, in init self._state = self._get_cached_state(refresh=refresh) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/core/cache.py”, line 107, in _get_cached_state self._cache_current_state(current_requirements) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/core/cache.py”, line 200, in _cache_current_state state = self._get_current_state() File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/core/cache.py”, line 238, in _get_current_state plugin_manager = qiime2.sdk.PluginManager() File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 44, in new self._init() File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 59, in _init plugin = entry_point.load() File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/pkg_resources/init.py”, line 2434, in load return self.resolve() File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/pkg_resources/init.py”, line 2440, in resolve module = import(self.module_name, fromlist=[‘name’], level=0) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/mmvec/q2/init.py”, line 2, in <module> from ._method import paired_omics File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/mmvec/q2/_method.py”, line 4, in <module> import tensorflow as tf File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow/init.py”, line 98, in <module> from tensorflow_core import * File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/init.py”, line 40, in <module> from tensorflow.python.tools import module_util as _module_util File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow/init.py”, line 50, in getattr module = self._load() File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow/init.py”, line 44, in _load module = _importlib.import_module(self.name) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/importlib/init.py”, line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/init.py”, line 49, in <module> from tensorflow.python import pywrap_tensorflow File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/pywrap_tensorflow.py”, line 74, in <module> raise ImportError(msg) ImportError: Traceback (most recent call last): File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/pywrap_tensorflow.py”, line 58, in <module> from tensorflow.python.pywrap_tensorflow_internal import * File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/pywrap_tensorflow_internal.py”, line 28, in <module> _pywrap_tensorflow_internal = swig_import_helper() File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/pywrap_tensorflow_internal.py”, line 24, in swig_import_helper _mod = imp.load_module(‘_pywrap_tensorflow_internal’, fp, pathname, description) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/imp.py”, line 243, in load_module return load_dynamic(name, filename, file) File “/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/imp.py”, line 343, in load_dynamic return _load(spec) ImportError: dlopen(/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _SecKeyCopyExternalRepresentation Referenced from: /Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/…/libtensorflow_framework.2.dylib Expected in: /System/Library/Frameworks/Security.framework/Versions/A/Security in /Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/python/…/libtensorflow_framework.2.dylib

Failed to load the native TensorFlow runtime. "

Barnacle Error (qiime2 conda): “Traceback (most recent call last): File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/bin/qiime”, line 11, in <module> sys.exit(qiime()) File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 764, in call return self.main(*args, **kwargs) File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 717, in main rv = self.invoke(ctx) File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/click/core.py”, line 555, in invoke return callback(*args, **kwargs) File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/builtin/dev.py”, line 31, in refresh_cache import q2cli.core.cache File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/core/cache.py”, line 403, in <module> CACHE = DeploymentCache() File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/core/cache.py”, line 61, in init self._state = self._get_cached_state(refresh=refresh) File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/core/cache.py”, line 107, in _get_cached_state self._cache_current_state(current_requirements) File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/core/cache.py”, line 200, in _cache_current_state state = self._get_current_state() File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/core/cache.py”, line 238, in _get_current_state plugin_manager = qiime2.sdk.PluginManager() File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 44, in new self._init() File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 59, in _init plugin = entry_point.load() File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/pkg_resources/init.py”, line 2434, in load return self.resolve() File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/pkg_resources/init.py”, line 2440, in resolve module = import(self.module_name, fromlist=[‘name’], level=0) File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/mmvec/q2/init.py”, line 2, in <module> from ._method import paired_omics File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/mmvec/q2/_method.py”, line 7, in <module> from mmvec.multimodal import MMvec File “/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/mmvec/multimodal.py”, line 6, in <module> from tensorflow.contrib.distributions import Multinomial, Normal ModuleNotFoundError: No module named ‘tensorflow.contrib’”

Barnacle Error (standalone mmvec): "Traceback (most recent call last): File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py”, line 58, in <module> from tensorflow.python.pywrap_tensorflow_internal import * File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py”, line 28, in <module> _pywrap_tensorflow_internal = swig_import_helper() File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py”, line 24, in swig_import_helper _mod = imp.load_module(‘_pywrap_tensorflow_internal’, fp, pathname, description) File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/imp.py”, line 243, in load_module return load_dynamic(name, filename, file) File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/imp.py”, line 343, in load_dynamic return _load(spec) ImportError: /lib64/libc.so.6: version `GLIBC_2.17’ not found (required by /home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File “/home/avrbanac/miniconda2/envs/mmvec/bin/mmvec”, line 17, in <module> import tensorflow as tf File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/init.py”, line 22, in <module> from tensorflow.python import pywrap_tensorflow # pylint: disable=unused-import File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/python/init.py”, line 49, in <module> from tensorflow.python import pywrap_tensorflow File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py”, line 74, in <module> raise ImportError(msg) ImportError: Traceback (most recent call last): File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py”, line 58, in <module> from tensorflow.python.pywrap_tensorflow_internal import * File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py”, line 28, in <module> _pywrap_tensorflow_internal = swig_import_helper() File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py”, line 24, in swig_import_helper _mod = imp.load_module(‘_pywrap_tensorflow_internal’, fp, pathname, description) File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/imp.py”, line 243, in load_module return load_dynamic(name, filename, file) File “/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/imp.py”, line 343, in load_dynamic return _load(spec) ImportError: /lib64/libc.so.6: version `GLIBC_2.17’ not found (required by /home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)

Failed to load the native TensorFlow runtime."