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问题[anaconda](computer)

Martin Hope
bmv
Asked: 2020-09-02 11:45:33 +0800 CST
  • 6

我想运行一个带有奇点的 conda 命令。命令是：

singularity exec ~/dockerimage.sif conda

它产生一个错误：

/.singularity.d/actions/exec: 9: exec: conda: Permission denied

这是我的码头文件：

FROM ubuntu:20.04

ARG DEBIAN_FRONTEND=noninteractive

RUN apt-get update && apt-get install -y apt-utils wget=1.20.3-1ubuntu1 python3.8=3.8.2-1ubuntu1.2 python3-pip=20.0.2-5ubuntu1 python3-yaml=5.3.1-1  git=1:2.25.1-1ubuntu3
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-py38_4.8.3-Linux-x86_64.sh && chmod +x Miniconda3-py38_4.8.3-Linux-x86_64.sh && ./Miniconda3-py38_4.8.3-Linux-x86_64.sh -b && cp /root/miniconda3/bin/conda /usr/bin/conda
RUN wget https://data.qiime2.org/distro/core/qiime2-2020.8-py36-linux-conda.yml && conda env create -n qiime2-2020.8 --file qiime2-2020.8-py36-linux-conda.yml && conda install -y -n qiime2-2020.8 -c conda-forge -c bioconda -c qiime2 -c defaults q2cli q2template q2-types q2-feature-table q2-metadata vsearch snakemake

我应该在 Dockerfile 中添加什么？它将如何运作？

docker anaconda
Martin Hope
Sayan Dey
Asked: 2020-08-17 05:52:07 +0800 CST
  • 7

我是双启动用户，我使用 Ubuntu18.04 和 Windows 10。我还有一个鹦鹉 Linux 在 ubuntu 内的 VM 中运行。很明显，我在这些平台上同步工具时遇到了问题。

我在这方面有持续的需求。我想同步我所有的 anaconda 安装，即我需要一个选项来登记和触发我的 anaconda windows 包以在 Ubuntu 中自动安装，反之亦然。

我在互联网上搜索了一下，但没有找到相关的东西。有什么办法吗？

sync anaconda
Martin Hope
chelwin
Asked: 2019-08-07 04:45:14 +0800 CST
  • 7

我过去创建了 conda 环境，没有任何问题。所以，即使这一次我也着手创造了一个。
conda create -n astropython anaconda

接下来，文档建议通过运行卸载任何以前的 astropy 副本： conda uninstall astropy 我做到了，现在我的 conda 坏了。如果我使用 conda 运行任何命令，我会收到以下错误回溯。

Traceback (most recent call last):
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/common/serialize.py", line 19, in get_yaml
    import ruamel_yaml as yaml
ModuleNotFoundError: No module named 'ruamel_yaml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/common/serialize.py", line 22, in get_yaml
    import ruamel.yaml as yaml
ModuleNotFoundError: No module named 'ruamel'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1062, in __call__
    return func(*args, **kwargs)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/cli/main.py", line 74, in _main
    from ..base.context import context
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/base/context.py", line 28, in <module>
    from ..common.configuration import (Configuration, ConfigurationLoadError, MapParameter,
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/common/configuration.py", line 40, in <module>
    from .serialize import yaml_load
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/common/serialize.py", line 30, in <module>
    yaml = get_yaml()
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/_vendor/auxlib/decorators.py", line 59, in _memoized_func
    result = func(*args, **kwargs)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/common/serialize.py", line 24, in get_yaml
    raise ImportError("No yaml library available.\n"
ImportError: No yaml library available.
To proceed, conda install ruamel_yaml

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/common/serialize.py", line 19, in get_yaml
    import ruamel_yaml as yaml
ModuleNotFoundError: No module named 'ruamel_yaml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/common/serialize.py", line 22, in get_yaml
    import ruamel.yaml as yaml
ModuleNotFoundError: No module named 'ruamel'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/vsanc/anaconda3/bin/conda", line 13, in <module>
    sys.exit(main())
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/cli/main.py", line 150, in main
    return conda_exception_handler(_main, *args, **kwargs)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1354, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1065, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1109, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1120, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1175, in print_unexpected_error_report
    from .base.context import context
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/base/context.py", line 28, in <module>
    from ..common.configuration import (Configuration, ConfigurationLoadError, MapParameter,
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/common/configuration.py", line 40, in <module>
    from .serialize import yaml_load
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/common/serialize.py", line 30, in <module>
    yaml = get_yaml()
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/_vendor/auxlib/decorators.py", line 59, in _memoized_func
    result = func(*args, **kwargs)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/common/serialize.py", line 24, in get_yaml
    raise ImportError("No yaml library available.\n"
ImportError: No yaml library available.
To proceed, conda install ruamel_yaml

再次运行conda install ruamel_yaml会吐出相同的回溯。我的 $PATH 是正确的，No module named ruamel的解决方案没有解决问题。

因此，我查看了这些文件，发现 site-packages 目录中没有 ruamel_yaml 文件夹。我将 ruamel_yaml 文件夹从复制$HOME/anaconda3/pkgs/ruamel_yaml0.15.71/到$HOME/anaconda3/lib/python3.6/site-packages/. 现在，当我运行任何 conda 命令时，都会出现以下错误：

Traceback (most recent call last):
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1062, in __call__
    return func(*args, **kwargs)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 80, in do_call
    module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
  File "/Users/vsanc/anaconda3/lib/python3.6/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 994, in _gcd_import
  File "<frozen importlib._bootstrap>", line 971, in _find_and_load
  File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/cli/main_update.py", line 8, in <module>
    from .install import install
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/cli/install.py", line 19, in <module>
    from ..core.index import calculate_channel_urls, get_index
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/core/package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda_package_handling/api.py", line 3, in <module>
    from libarchive.exception import ArchiveError as _LibarchiveArchiveError
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/libarchive/__init__.py", line 1, in <module>
    from .entry import ArchiveEntry
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/libarchive/entry.py", line 4, in <module>
    from ctypes import c_char_p, create_string_buffer
  File "/Users/vsanc/anaconda3/lib/python3.6/ctypes/__init__.py", line 7, in <module>
    from _ctypes import Union, Structure, Array
ImportError: dlopen(/Users/vsanc/anaconda3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libffi.6.dylib
  Referenced from: /Users/vsanc/anaconda3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-darwin.so
  Reason: image not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/vsanc/anaconda3/bin/conda", line 13, in <module>
    sys.exit(main())
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/cli/main.py", line 150, in main
    return conda_exception_handler(_main, *args, **kwargs)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1354, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1065, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1109, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1120, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1190, in print_unexpected_error_report
    from .cli.main_info import get_env_vars_str, get_main_info_str
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/cli/main_info.py", line 19, in <module>
    from ..core.index import _supplement_index_with_system
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda/core/package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/conda_package_handling/api.py", line 3, in <module>
    from libarchive.exception import ArchiveError as _LibarchiveArchiveError
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/libarchive/__init__.py", line 1, in <module>
    from .entry import ArchiveEntry
  File "/Users/vsanc/anaconda3/lib/python3.6/site-packages/libarchive/entry.py", line 4, in <module>
    from ctypes import c_char_p, create_string_buffer
  File "/Users/vsanc/anaconda3/lib/python3.6/ctypes/__init__.py", line 7, in <module>
    from _ctypes import Union, Structure, Array
ImportError: dlopen(/Users/vsanc/anaconda3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libffi.6.dylib
  Referenced from: /Users/vsanc/anaconda3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-darwin.so
  Reason: image not found
anaconda
Martin Hope
Marcel
Asked: 2019-07-19 23:35:00 +0800 CST
  • 7

我在 Windows 上，下载新版本的 anaconda（64 位）并安装。当我执行“conda update conda”时，我得到了一条奇怪的额外行： 在此处输入图像描述 请注意“(base) C:\Users\marcelha>ET _sysp=%~dpA”我没有输入（显然），但 conda 做到了。

当我执行“conda update --all”时，我的体验与Conda update all 一样想要删除所有包

当我这样做时，Anaconda Prompt 甚至从我的计算机上消失了，并且 Jupyter Lab 中的终端不再有输入线。

anaconda
Martin Hope
SammyC
Asked: 2019-06-30 16:31:27 +0800 CST
  • 5

我安装了 Anaconda 和 Pycharm。我想访问 Pycharm 中的 Anaconda 库（现在我无法将 numpy、sklearn 等导入 Pycharm）。我去了设置和项目解释器并选择了 conda。现在它说它正在加载，但它会永远持续下去，我不确定是否发生了什么（见屏幕打印）请任何人帮助我，以便我可以访问 pycharm 中的 anaconda 库？谢谢你！！

在此处输入图像描述

如果我仍然单击“确定”以加载项目解释器，我仍然无法在之后导入 numpy。（请参阅第二个屏幕打印）如您所见，未找到 numpy，我收到错误消息。

在此处输入图像描述

python anaconda
Martin Hope
Alexandru Bucur
Asked: 2019-06-25 10:33:28 +0800 CST
  • 5

我已经为 Windows 10 安装了 Anaconda，我想从 Docker 导入一些旧的笔记本。我使用 Anaconda Prompt 在新环境中安装了 tweepy

conda install -c conda-forge tweepy

并使用 import tweepy 在命令行中检查

我一直留在名为“twitter_api”的新环境中，在 Anaconda Prompt 中，并在 Anaconda Navigator 中切换到这个环境。在这里，我安装了 Jupiter Notebooks，并将旧笔记复制到一个新文件夹中。但是当我尝试运行它们时，出现错误：

ModuleNotFoundError: No module named 'tweepy'

截屏

python anaconda
Martin Hope
hokage555
Asked: 2019-04-14 06:34:32 +0800 CST
  • 0

我正在努力将我的 conda 版本更新到最新版本的 4.6.12。

使用conda update conda 表示所有包都是最新的。

conda update conda=4.6.12并在 PackagesNotFoundError 中使用结果。因此，打字conda -V仍然给出 4.6.11。还有什么我可以尝试的吗？

谢谢你的帮助。

最好的问候，火影

python updates anaconda
Martin Hope
Nemo
Asked: 2019-04-05 18:00:02 +0800 CST
  • 0

我在 Windows 7 64 位中安装了带有 python 3 的 anaconda。由于经验不足，我不知道为什么我最终得到了如图所示的自定义版本的anaconda

# Name                    Version                   Build  Channel
anaconda                  custom           py36h363777c_0

当我运行时conda list，我可以看到pillow如图所示安装的包

pep8                      1.7.1                    py36_0
pickleshare               0.7.5                    py36_0
pillow                    5.4.1            py36hdc69c19_0
pip                       18.1                     pypi_0    pypi
pluggy                    0.9.0                    py36_0

但是，当我运行import pillow或import Pillow在 Jupyterlab 中时，出现错误

ModuleNotFoundError: No module named 'pillow'

令人困惑的是，我可以import PIL在 Jupyterlab 中运行，尽管我看不到PIL安装的包。

然后我看到下面的说明似乎与 Pillow 和 PIL 之间的冲突相矛盾

你能告诉我发生了什么事吗？提前致谢。

python3 anaconda jupyter-notebook