Comments (16)
afvrbanac
commented on August 15, 2024
1
So I couldn't get virtualenv working on barnacle, but I did a fresh miniconda install on barnacle and got your frozen conda env to successfully install. It just gives me tons of deprecated warnings related to the tensorflow dtypes and numpy every time I run a command, buuut it works! :)
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mortonjt
commented on August 15, 2024
Yea, I need to fix that. Tensorflow2.0 was just released a few days ago.
Argh.
The fix in the meantime is to install tensorflow==1.14.0
…On Thu, Oct 10, 2019, 5:00 PM Alison Vrbanac ***@***.***> wrote:
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
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
_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
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
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
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
import tensorflow as tf
File
"/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow/
*init*.py", line 98, in
from tensorflow_core import *
File
"/Users/avrbanac/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow_core/
*init*.py", line 40, in
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
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
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
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
_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
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
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
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
from mmvec.multimodal import MMvec
File
"/home/avrbanac/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/mmvec/multimodal.py",
line 6, in
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
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
_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
import tensorflow as tf
File
"/home/avrbanac/miniconda2/envs/mmvec/lib/python3.6/site-packages/tensorflow/
*init*.py", line 22, in
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
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
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
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
_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."
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afvrbanac
commented on August 15, 2024
So just "pip install tensorflow==1.14.0"?
Unfortunately, that doesn't seem to fix either the standalone install or the one within qiime2
Edit: I do still have rhapsody and minstrel installed successfully so can use those in the meantime
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mortonjt
commented on August 15, 2024
You're installing within a conda environment, so don't use pip.
On a good note, I recently froze a conda environment for a workshop.
You can install this via
wget https://raw.githubusercontent.com/mortonjt/q2stats-workshops/master/environment.yml
conda env create -n qiime2-2019.7-plus --file environment.yml
This environment has the fixed tensorflow version for both songbird / tensorflow (and deicode and qurro). Let me know if this works for you and I can post this into the readme as an alternative install option.
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mortonjt
commented on August 15, 2024
Looking at the message more carefully, I'm seeing a GLIBC error popping up your barnacle install.
I remember seeing those in the past with conda installs - I bet a conda install will not work on that machine.
For this sort of thing, I'd recommend using virtual environments instead, namely
virtualenv mmvec_env
source activate mmvec_env/bin/activate
pip install tensorflow==1.14.0
pip install mmvec
I'd recommend using the latest mmvec version, since the outputs are a bit more readable.
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mortonjt
commented on August 15, 2024
Hi @afvrbanac , great! I'm closing this issue - feel free to follow up if there are further installation issues.
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dacuotecuo111
commented on August 15, 2024
Hi, mortonjt.
I am a postdoc at the University of Arkansas. I want to do some microbiome-metabolites analysis with mmvec and I found some useful information from the github website. I installed mmvec under qiime2-2020.02. When I try running the mmvec with provided tables, it says "No module named 'tensorflow'". However, when I try to install this module (with different versions), none of them works.
I am not a professional bioinformatic person, so I am not familiar with any "environments".
Could you please provide me with any advice?
I attached the error information below. Looking forward your response.
(qiime2-2020.2) xxxxxx@x86_64-apple-darwin13 omicsstudio % mmvec paired-omics --microbe-file otus_nt.biom --metabolite-file lcms_nt.biom --summary-dir summary
Traceback (most recent call last):
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/bin/mmvec", line 17, in
import tensorflow as tf
ModuleNotFoundError: No module named 'tensorflow'
(qiime2-2020.2) xxxxxxx@x86_64-apple-darwin13 omicsstudio %
from mmvec.
mortonjt
commented on August 15, 2024
I’m assuming that you installed MMvec with conda correct?
I’d next try
conda install tensorflow=1.15 -c conda-forge
Otherwise I’d try installing MMvec with pip
Let me know if one of those works, I’ll update the readme with updated
instructions
…On Sat, Nov 13, 2021 at 4:45 AM dacuotecuo111 ***@***.***> wrote:
Hi, mortonjt.
I am a postdoc at the University of Arkansas. I want to do some
microbiome-metabolites analysis with mmvec and I found some useful
information from the github website. I installed mmvec under
qiime2-2020.02. When I try running the mmvec with provided tables, it says
"No module named 'tensorflow'". However, when I try to install this module
(with different versions), none of them works.
I am not a professional bioinformatic person, so I am not familiar with
any "environments".
Could you please provide me with any advice?
I attached the error information below. Looking forward your response.
(qiime2-2020.2) ***@***.***_64-apple-darwin13 omicsstudio % mmvec
paired-omics --microbe-file otus_nt.biom --metabolite-file lcms_nt.biom
--summary-dir summary
Traceback (most recent call last):
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/bin/mmvec",
line 17, in
import tensorflow as tf
ModuleNotFoundError: No module named 'tensorflow'
(qiime2-2020.2) ***@***.***_64-apple-darwin13 omicsstudio %
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dacuotecuo111
commented on August 15, 2024
Hi,
I appreciate your quick response. I installed the tensorflow 1.15.0 and encountered another problem. I pasted the error below. BTW, I am using a Mac air M1 (version 11.6).
--------------
(qiime2-2020.2) ***@***.***_64-apple-darwin13 omicsstudio % mmvec paired-omics --microbe-file otus_nt.biom --metabolite-file lcms_nt.biom --summary-dir summary
Traceback (most recent call last):
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/bin/mmvec", line 18, in <module>
from tensorflow.contrib.distributions import Multinomial, Normal
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow/__init__.py", line 50, in __getattr__
module = self._load()
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow/__init__.py", line 44, in _load
module = _importlib.import_module(self.__name__)
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_core/contrib/__init__.py", line 39, in <module>
from tensorflow.contrib import compiler
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_core/contrib/compiler/__init__.py", line 21, in <module>
from tensorflow.contrib.compiler import jit
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_core/contrib/compiler/__init__.py", line 22, in <module>
from tensorflow.contrib.compiler import xla
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_core/contrib/compiler/xla.py", line 22, in <module>
from tensorflow.python.estimator import model_fn as model_fn_lib
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_core/python/estimator/model_fn.py", line 26, in <module>
from tensorflow_estimator.python.estimator import model_fn
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_estimator/__init__.py", line 10, in <module>
from tensorflow_estimator._api.v1 import estimator
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_estimator/_api/v1/estimator/__init__.py", line 10, in <module>
from tensorflow_estimator._api.v1.estimator import experimental
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_estimator/_api/v1/estimator/experimental/__init__.py", line 10, in <module>
from tensorflow_estimator.python.estimator.canned.dnn import dnn_logit_fn_builder
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/canned/dnn.py", line 27, in <module>
from tensorflow_estimator.python.estimator import estimator
File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/estimator.py", line 36, in <module>
from tensorflow.python.profiler import trace
ImportError: cannot import name 'trace'
…----------------------------------------
Thank you
Xiaofan
------------------ 原始邮件 ------------------
发件人: "biocore/mmvec" ***@***.***>;
发送时间: 2021年11月14日(星期天) 凌晨0:41
***@***.***>;
抄送: "Xiaofan ***@***.******@***.***>;
主题: Re: [biocore/mmvec] Unable to install both in Qiime2 environments and as standalone (#97)
I’m assuming that you installed MMvec with conda correct?
I’d next try
conda install tensorflow=1.15 -c conda-forge
Otherwise I’d try installing MMvec with pip
Let me know if one of those works, I’ll update the readme with updated
instructions
On Sat, Nov 13, 2021 at 4:45 AM dacuotecuo111 ***@***.***>
wrote:
> Hi, mortonjt.
>
> I am a postdoc at the University of Arkansas. I want to do some
> microbiome-metabolites analysis with mmvec and I found some useful
> information from the github website. I installed mmvec under
> qiime2-2020.02. When I try running the mmvec with provided tables, it says
> "No module named 'tensorflow'". However, when I try to install this module
> (with different versions), none of them works.
>
> I am not a professional bioinformatic person, so I am not familiar with
> any "environments".
>
> Could you please provide me with any advice?
> I attached the error information below. Looking forward your response.
>
> (qiime2-2020.2) ***@***.***_64-apple-darwin13 omicsstudio % mmvec
> paired-omics --microbe-file otus_nt.biom --metabolite-file lcms_nt.biom
> --summary-dir summary
>
> Traceback (most recent call last):
>
> File "/Users/xiaofanwang/opt/miniconda3/envs/qiime2-2020.2/bin/mmvec",
> line 17, in
>
> import tensorflow as tf
>
> ModuleNotFoundError: No module named 'tensorflow'
>
> (qiime2-2020.2) ***@***.***_64-apple-darwin13 omicsstudio %
> ------------------------------
>
> —
> You are receiving this because you modified the open/close state.
>
>
> Reply to this email directly, view it on GitHub
> <#97 (comment)>, or
> unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AA75VXITL7EOCWZ3RTK52NTULZFUPANCNFSM4I7SBD5A>
> .
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mortonjt
commented on August 15, 2024
hmm, I'm getting confused on what is going on. How exactly did you install mmvec?
There are 2 options that I see moving forward
- Uninstall mmvec (either
pip uninstall mmvecorconda uninstall mmvec) and reinstall. You've got some missing packages and you may need to just reinstall to get all of the packages you need - Build a new qiime2 environment from scratch. There could be something weird going on with mmvec and qiime2. I do have a qiime2 mmvec conda recipe that you can build from scratch here. That can be installed via
conda create -n q2-mmvec -f environment.ymlusing the environment file here. But do note that this is for a linux build, which won't work on your mac.
from mmvec.
dacuotecuo111
commented on August 15, 2024
Hi, Jamie
Thank you for your patience.
I had qiime2-2021.4 installed and download the qiime2-2020.2 because it said mmvec only work with 2020.6 and before. Then under the qiime2-2020.2 environment, I downloaded "mmvec" with conda install mmvec -c conda-forge; I think this step succeed. But when I run the mmvec with provided tables (examples), there is an error pop up saying I do not have the tensorflow module. I downloaded the tensorflow 1.15.0
Then I rerun the mmvec. Another error come out as I showed you in the last email "from tensorflow.python.profiler import trace
ImportError: cannot import name 'trace'". I tried uninstalled the mmvec and reinstalled but it doesn't work for me. Same error messages came out. I also tried the option 2 but it didn't go through.
I basically do not know what should I do next. I am in a hurry to figure this thing out because I think this software will favor my study very well. Please help me on the installation and I can provide any error information if needed.
Thank so for helping.
Xiaofan
…------------------ 原始邮件 ------------------
发件人: "biocore/mmvec" ***@***.***>;
发送时间: 2021年11月14日(星期天) 中午11:11
***@***.***>;
抄送: "Xiaofan ***@***.******@***.***>;
主题: Re: [biocore/mmvec] Unable to install both in Qiime2 environments and as standalone (#97)
hmm, I'm getting confused on what is going on. How exactly did you install mmvec?
There are 2 options that I see moving forward
Uninstall mmvec (either pip uninstall mmvec or conda uninstall mmvec) and reinstall. You've got some missing packages and you may need to just reinstall to get all of the packages you need
Build a new qiime2 environment from scratch. There could be something weird going on with mmvec and qiime2. I do have a qiime2 mmvec conda recipe that you can build from scratch here. That can be installed via conda create -n q2-mmvec -f envrionment.yml using the environment file here.
—
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mortonjt
commented on August 15, 2024
Have you tried pip install mmvec?
I’m sorry that you are going through this, it looks like the conda recipe
is misbehaving, so the recipe will need to be updated. I recommend first
having MMvec installed by itself in a standalone environment, it’ll make
it much easier to debug. I haven’t seen this particular tensorflow error
before, so I’ll need more information to help debug this.
You can also try out the GNPS tutorial of everything fails - but I’d try to
get this working first
https://ccms-ucsd.github.io/GNPSDocumentation/mmvec/
…On Sun, Nov 14, 2021 at 7:27 AM dacuotecuo111 ***@***.***> wrote:
Hi, Jamie
Thank you for your patience.
I had qiime2-2021.4 installed and download the qiime2-2020.2 because
it said mmvec only work with 2020.6 and before. Then under the
qiime2-2020.2 environment, I downloaded "mmvec" with conda install
mmvec -c conda-forge; I think this step succeed. But when I run the mmvec
with provided tables (examples), there is an error pop up saying I do not
have the tensorflow module. I downloaded the tensorflow 1.15.0
Then I rerun the mmvec. Another error come out as I showed you in the last
email "from tensorflow.python.profiler import trace
ImportError: cannot import name 'trace'". I tried uninstalled the mmvec
and reinstalled but it doesn't work for me. Same error messages came out. I
also tried the option 2 but it didn't go through.
I basically do not know what should I do next. I am in a hurry to figure
this thing out because I think this software will favor my study very well.
Please help me on the installation and I can provide any error information
if needed.
Thank so for helping.
Xiaofan
------------------ 原始邮件 ------------------
发件人: "biocore/mmvec" ***@***.***>;
发送时间: 2021年11月14日(星期天) 中午11:11
***@***.***>;
抄送: "Xiaofan ***@***.******@***.***>;
主题: Re: [biocore/mmvec] Unable to install both in Qiime2 environments
and as standalone (#97)
hmm, I'm getting confused on what is going on. How exactly did you install
mmvec?
There are 2 options that I see moving forward
Uninstall mmvec (either pip uninstall mmvec or conda uninstall mmvec) and
reinstall. You've got some missing packages and you may need to just
reinstall to get all of the packages you need
Build a new qiime2 environment from scratch. There could be something
weird going on with mmvec and qiime2. I do have a qiime2 mmvec conda recipe
that you can build from scratch here. That can be installed via conda
create -n q2-mmvec -f envrionment.yml using the environment file here.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub, or unsubscribe.
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from mmvec.
dacuotecuo111
commented on August 15, 2024
I just downloaded virtualenv with and created an environment.
pip3 install virtualenv==16.7.9Mac:~ michael$ mkdir myproject Mac:~ michael$ cd myproject/ Mac:myproject michael$Mac:myproject michael$ virtualenv --no-site-packages venvsource venv/bin/activate
pip install mmvec
Then some error come out:
Downloading scikit-bio-0.5.1.tar.gz (8.2 MB)
|████████████████████████████████| 8.2 MB 22.0 MB/s
Preparing metadata (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Users/xiaofanwang/myproject1/venv/bin/python3.9 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/r5/h2rgz5x53h182z3869f9vwr80000gn/T/pip-install-gleqc2od/scikit-bio_00e249145c294cf78ec779eb3018c4a6/setup.py'"'"'; __file__='"'"'/private/var/folders/r5/h2rgz5x53h182z3869f9vwr80000gn/T/pip-install-gleqc2od/scikit-bio_00e249145c294cf78ec779eb3018c4a6/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/r5/h2rgz5x53h182z3869f9vwr80000gn/T/pip-pip-egg-info-tf39a5ff
cwd: /private/var/folders/r5/h2rgz5x53h182z3869f9vwr80000gn/T/pip-install-gleqc2od/scikit-bio_00e249145c294cf78ec779eb3018c4a6/
Complete output (5 lines):
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/r5/h2rgz5x53h182z3869f9vwr80000gn/T/pip-install-gleqc2od/scikit-bio_00e249145c294cf78ec779eb3018c4a6/setup.py", line 20, in <module>
import numpy as np
ModuleNotFoundError: No module named 'numpy'
----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/e5/7e/cf03a7e53da18ae6a847894384838e9a36a98b48909a3f347ff6077c7304/scikit-bio-0.5.1.tar.gz#sha256=2d606f0bbd50df3e5814c10260d0e1a35484ecf141e5e5c809d9c9dbf87a3655 (from https://pypi.org/simple/scikit-bio/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Collecting mmvec
Downloading mmvec-1.0.5.tar.gz (33 kB)
Preparing metadata (setup.py) ... done
Downloading mmvec-1.0.4.tar.gz (33 kB)
Preparing metadata (setup.py) ... done
Downloading mmvec-1.0.3.tar.gz (32 kB)
Preparing metadata (setup.py) ... done
Collecting pandas>=0.18.0
Downloading pandas-1.3.4-cp39-cp39-macosx_10_9_x86_64.whl (11.6 MB)
|████████████████████████████████| 11.6 MB 10.1 MB/s
Collecting mmvec
Downloading mmvec-1.0.2.tar.gz (32 kB)
Preparing metadata (setup.py) ... done
Downloading mmvec-1.0.1.tar.gz (32 kB)
Preparing metadata (setup.py) ... done
Downloading mmvec-1.0.0.tar.gz (31 kB)
Preparing metadata (setup.py) ... done
Downloading mmvec-0.6.0.tar.gz (26 kB)
Preparing metadata (setup.py) ... done
Downloading mmvec-0.5.0.tar.gz (18 kB)
Preparing metadata (setup.py) ... done
ERROR: Cannot install mmvec==0.5.0, mmvec==0.6.0, mmvec==1.0.0, mmvec==1.0.1, mmvec==1.0.2, mmvec==1.0.3, mmvec==1.0.4, mmvec==1.0.5 and mmvec==1.0.6 because these package versions have conflicting dependencies.
The conflict is caused by:
mmvec 1.0.6 depends on scikit-bio>=0.5.1
mmvec 1.0.5 depends on scikit-bio>=0.5.1
mmvec 1.0.4 depends on scikit-bio>=0.5.1
mmvec 1.0.3 depends on scikit-bio>=0.5.1
mmvec 1.0.2 depends on scikit-bio>=0.5.1
mmvec 1.0.1 depends on scikit-bio>=0.5.1
mmvec 1.0.0 depends on scikit-bio>=0.5.1
mmvec 0.6.0 depends on scikit-bio>=0.5.1
mmvec 0.5.0 depends on scikit-bio>=0.5.1
To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
…________________
Not sure if I am doing anything useful. . I usded the old verison of virtualenv to be able to use the --no-site-packages option.
Do you know why it return an error this time?
Thanks
------------------ 原始邮件 ------------------
发件人: "biocore/mmvec" ***@***.***>;
发送时间: 2021年11月14日(星期天) 晚上10:40
***@***.***>;
抄送: "Xiaofan ***@***.******@***.***>;
主题: Re: [biocore/mmvec] Unable to install both in Qiime2 environments and as standalone (#97)
Have you tried pip install mmvec?
I’m sorry that you are going through this, it looks like the conda recipe
is misbehaving, so the recipe will need to be updated. I recommend first
having MMvec installed by itself in a standalone environment, it’ll make
it much easier to debug. I haven’t seen this particular tensorflow error
before, so I’ll need more information to help debug this.
You can also try out the GNPS tutorial of everything fails - but I’d try to
get this working first
https://ccms-ucsd.github.io/GNPSDocumentation/mmvec/
On Sun, Nov 14, 2021 at 7:27 AM dacuotecuo111 ***@***.***>
wrote:
> Hi, Jamie
>
> Thank you for your patience.
>
> &nbsp;I had qiime2-2021.4 installed and download the qiime2-2020.2 because
> it said mmvec only work with 2020.6 and before. Then under the
> qiime2-2020.2 environment, I downloaded "mmvec" with&nbsp;conda install
> mmvec -c conda-forge; I think this step succeed. But when I run the mmvec
> with provided tables (examples), there is an error pop up saying I do not
> have the tensorflow module. I downloaded the tensorflow 1.15.0
>
> Then I rerun the mmvec. Another error come out as I showed you in the last
> email "from tensorflow.python.profiler import trace
>
> ImportError: cannot import name 'trace'". I tried uninstalled the mmvec
> and reinstalled but it doesn't work for me. Same error messages came out. I
> also tried the option 2 but it didn't go through.
>
> I basically do not know what should I do next. I am in a hurry to figure
> this thing out because I think this software will favor my study very well.
> Please help me on the installation and I can provide any error information
> if needed.
>
> Thank so for helping.
>
> Xiaofan
>
>
>
>
>
>
>
>
>
>
> ------------------ 原始邮件 ------------------
> 发件人: "biocore/mmvec" ***@***.***&gt;;
> 发送时间:&nbsp;2021年11月14日(星期天) 中午11:11
> ***@***.***&gt;;
> 抄送:&nbsp;"Xiaofan ***@***.******@***.***&gt;;
> 主题:&nbsp;Re: [biocore/mmvec] Unable to install both in Qiime2 environments
> and as standalone (#97)
>
>
>
>
>
>
> hmm, I'm getting confused on what is going on. How exactly did you install
> mmvec?
>
> There are 2 options that I see moving forward
>
> Uninstall mmvec (either pip uninstall mmvec or conda uninstall mmvec) and
> reinstall. You've got some missing packages and you may need to just
> reinstall to get all of the packages you need
>
> Build a new qiime2 environment from scratch. There could be something
> weird going on with mmvec and qiime2. I do have a qiime2 mmvec conda recipe
> that you can build from scratch here. That can be installed via conda
> create -n q2-mmvec -f envrionment.yml using the environment file here.
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub, or unsubscribe.
> Triage notifications on the go with GitHub Mobile for iOS or Android.
>
> —
> You are receiving this because you modified the open/close state.
>
>
> Reply to this email directly, view it on GitHub
> <#97 (comment)>, or
> unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AA75VXMOMQJTMQJALOTEUCTUL7BLJANCNFSM4I7SBD5A>
> .
>
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You are receiving this because you commented.
Reply to this email directly, view it on GitHub, or unsubscribe.
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from mmvec.
mortonjt
commented on August 15, 2024
um, no don't install virtualenv
Just conda uninstall mmvec, and pip install mmvec within your conda environment.
I've just created a fresh qiime2-2020.6 environment on my macbook and confirmed that pip installing mmvec works.
The conda recipe does appear broken though do to tensorflow though ...
from mmvec.
dacuotecuo111
commented on August 15, 2024
Hi, Morton
I am using biocore/mmvec to study the co-occurance of microbes and metabolites. Everything works fine but I found the qiime metadata tabulate command generated different results every time. How should I deal with the inconsistency? Is there any option that I can use to fix the results and move forward?
Looking forward of your responses urgently.
Thank you so much
Xiaofan
Original
From:"Jamie Morton"< ***@***.*** >;
Date:2021/11/15 2:45
To:"biocore/mmvec"< ***@***.*** >;
CC:"dacuotecuo111"< ***@***.*** >;"Comment"< ***@***.*** >;
Subject:Re: [biocore/mmvec] Unable to install both in Qiime2 environments andas standalone (#97)
um, no don't install virtualenv
Just conda uninstall mmvec, and pip install mmvec within your conda environment.
I've just created a fresh qiime2-2020.6 environment on my macbook and confirmed that pip installing mmvec works.
The conda recipe does appear broken though do to tensorflow though ...
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub, or unsubscribe.
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from mmvec.
mortonjt
commented on August 15, 2024
Hi, see the issuetracker, since there are other resolved issues that had
similar issues. If you are still running into problems - can you open a new
issue? Otherwise this thread is going to be buried
…On Tue, Dec 27, 2022 at 9:58 PM dacuotecuo111 ***@***.***> wrote:
Hi, Morton
I am using biocore/mmvec to study the co-occurance of microbes and
metabolites. Everything works fine but I found the qiime metadata
tabulate command generated different results every time. How should I deal
with the inconsistency? Is there any option that I can use to fix the
results and move forward?
Looking forward of your responses urgently.
Thank you so much
Xiaofan
Original
From:"Jamie Morton"< ***@***.*** >;
Date:2021/11/15 2:45
To:"biocore/mmvec"< ***@***.*** >;
CC:"dacuotecuo111"< ***@***.*** >;"Comment"< ***@***.*** >;
Subject:Re: [biocore/mmvec] Unable to install both in Qiime2 environments
andas standalone (#97)
um, no don't install virtualenv
Just conda uninstall mmvec, and pip install mmvec within your conda
environment.
I've just created a fresh qiime2-2020.6 environment on my macbook and
confirmed that pip installing mmvec works.
The conda recipe does appear broken though do to tensorflow though ...
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub, or unsubscribe.
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Reply to this email directly, view it on GitHub
<#97 (comment)>, or
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.
You are receiving this because you modified the open/close state.Message
ID: ***@***.***>
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Related Issues (20)
- Error from biom table in wrong orientation and some manual suggestions HOT 5
- ranks.qza file for heatmap HOT 7
- paired_omics error - 'arm_the_gpu' HOT 5
- heatmap change "--p-x-labels " size HOT 3
- Error: QIIME 2 has no plugin/command named 'mmvec'. HOT 3
- ranks with full taxonomic hierarqui rather than featureid HOT 2
- Plugin error from mmvec HOT 14
- help with heatmap conditionals to create ranks.qza file HOT 1
- what is the role of example? HOT 4
- Could mmvec measure the consumption of metabolites? HOT 1
- Why 13 metabolites as ground truth in soil dataset? HOT 2
- Tips and Tricks to speed up training
- MMvec refactor HOT 6
- tensorflow.contrib HOT 1
- Plugin error from mmvec: index 0 is out of bounds for axis 0 with size 0
- An qiime2 error has occurred HOT 5
- error: no such option: --o-model-stats HOT 10
- Different results HOT 4
- docs: specify abundance vs frequency HOT 1
- Compatibility issues on macbook pro with M1 chip HOT 4
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