Troubleshooting

Permission denied errors during installation

Cause

The umask command determines the mask settings that control how file permissions are set for newly created files. If you have a very restrictive umask, such as 077, you get “permission denied” errors.

Solution

Set a less restrictive umask before calling conda commands. Conda was intended as a user space tool, but often users need to use it in a global environment. One place this can go awry is with restrictive file permissions. Conda creates links when you install files that have to be read by others on the system.

To give yourself full permissions for files and directories, but prevent the group and other users from having access:

  1. Before installing, set the umask to 007.

  2. Install conda.

  3. Return the umask to the original setting:

    umask 007
    conda install
    umask 077
    

For more information on umask, see http://en.wikipedia.org/wiki/Umask.

Permission denied errors after using sudo conda command

Solution

Once you run conda with sudo, you must use sudo forever. We recommend that you NEVER run conda with sudo.

Already installed error message

Cause

If you are trying to fix conda problems without removing the current installation and you try to reinstall Miniconda or Anaconda to fix it, you get an error message that Miniconda or Anaconda is already installed, and you cannot continue.

Solution

Install using the –force option.

Download and install the appropriate Miniconda for your operating system from the Miniconda download page using the force option --force or -f:

bash Miniconda3-latest-MacOSX-x86_64.sh -f

NOTE: Substitute the appropriate filename and version for your operating system.

NOTE: Be sure that you install to the same install location as your existing install so it overwrites the core conda files and does not install a duplicate in a new folder.

Conda reports that a package is installed, but it appears not to be

Sometimes conda claims that a package is already installed, but it does not appear to be, for example, a Python package that gives ImportError.

There are several possible causes for this problem, each with its own solution.

Cause

You are not in the same conda environment as your package.

Solution

  1. Make sure that you are in the same conda environment as your package. The conda info command tells you what environment is currently active—under default environment.

  2. Verify that you are using the Python from the correct environment by running:

    import sys
    print(sys.prefix)
    

Cause

For Python packages, you have set the PYTHONPATH or PYTHONHOME variable. These environment variables cause Python to load files from locations other than the standard ones. Conda works best when these environment variables are not set, as their typical use cases are obviated by conda environments and a common issue is that they cause Python to pick up the wrong versions or broken versions of a library.

Solution

For Python packages, make sure you have not set the PYTHONPATH or PYTHONHOME variables. The command conda info -a displays the values of these environment variables.

  • To unset these environment variables temporarily for the current Terminal session, run unset PYTHONPATH.
  • To unset them permanently, check for lines in the files:
    • If you use bash—~/.bashrc, ~/.bash_profile, ~/.profile.
    • If you use zsh—~/.zshrc`.
    • If you use PowerShell on Windows, the file output by $PROFILE .

Cause

You have site-specific directories or, for Python, you have so-called site-specific files. These are typically located in ~/.local on Linux and macOS. For a full description of the locations of site-specific packages, see PEP 370. As with PYTHONPATH, Python may try importing packages from this directory, which can cause issues.

Solution

For Python packages, remove site-specific directories and site-specific files.

Cause

For C libraries, the following environment variables have been set:

  • macOS—DYLD_LIBRARY_PATH.
  • Linux—LD_LIBRARY_PATH.

These act similarly to PYTHONPATH for Python. If they are set, they can cause libraries to be loaded from locations other than the conda environment. Conda environments obviate most use cases for these variables. The command conda info -a shows what these are set to.

Solution

Unset DYLD_LIBRARY_PATH or LD_LIBRARY_PATH.

Cause

Occasionally, an installed package becomes corrupted. Conda works by unpacking the packages in the pkgs directory and then hard-linking them to the environment. Sometimes these get corrupted, breaking all environments that use them, and also any additional environments, since the same files are hard-linked each time.

Solution

Run the command conda install -f to unarchive the package again and relink it. It also does an md5 verification on the package. Usually if this is different, it is because your channels have changed and there is a different package with the same name, version, and build number.

NOTE: This breaks the links to any other environments that already had this package installed, so you have to reinstall it there, too. It also means that running conda install -f a lot can use up a lot of disk space if you have a lot of environments.

NOTE: The -f flag to conda install (--force) implies --no-deps, so conda install -f package does not reinstall any of the dependencies of package.

pkg_resources.DistributionNotFound: conda==3.6.1-6-gb31b0d4-dirty

Cause

The local version of conda needs updating.

Solution

Force reinstall conda. A useful way to work off the development version of conda is to run python setup.py develop on a checkout of the conda git repository. However, if you are not regularly running git pull, it is a good idea to un-develop, as you will otherwise not get any regular updates to conda. The normal way to do this is to run python setup.py develop -u.

However, this command does not replace the conda script itself. With other packages, this is not an issue, as you can just reinstall them with conda, but conda cannot be used if conda is installed.

The fix is to use the ./bin/conda executable in the conda git repository to force reinstall conda, that is, run ./bin/conda install -f conda. You can then verify with conda info that you have the latest version of conda, and not a git checkout—the version should not include any hashes.

macOS error “ValueError unknown locale: UTF-8”

Cause

This is a bug in the macOS Terminal app that shows up only in certain locales. Locales are country-language combinations.

Solution

  1. Open Terminal in /Applications/Utilities

  2. Clear the Set locale environment variables on startup checkbox.

    ../_images/conda_locale.jpg

This sets your LANG environment variable to be empty. This may cause Terminal use to incorrect settings for your locale. The locale command in Terminal tells you what settings are used.

To use the correct language, add a line to your bash profile, which is typically ~/.profile:

export LANG=your-lang

NOTE: Replace your-lang with the correct locale specifier for your language.

The command locale -a displays all the specifiers. For example, the language code for US English is en_US.UTF-8. The locale affects what translations are used when they are available and also how dates, currencies and decimals are formatted.

AttributeError or missing getproxies

When running a command such as conda update ipython, you may get an AttributeError: 'module' object has no attribute 'getproxies'.

Cause

This can be caused by an old version of requests or by having the PYTHONPATH environment variable set.

Solution

Update requests and be sure PYTHONPATH is not set:

  1. Run conda info -a to show the requests version and various environment variables such as PYTHONPATH.
  2. Update the requests version with pip install -U requests.
  3. Clear PYTHONPATH:
    • On Windows, clear it the environment variable settings.
    • On macOS and Linux, clear it by removing it from the bash profile and restarting the shell.

Shell commands open from the wrong location

When you run a command within a conda environment, conda does not access the correct package executable.

Cause

In both bash and zsh, when you enter a command, the shell searches the paths in PATH one by one until it finds the command. The shell then caches the location, which is called hashing in shell terminology. When you run command again, the shell does not have to search the PATH again.

The problem is that before you installed the program, you ran a command which loaded and hashed another version of that program in some other location on the PATH, such as /usr/bin. Then you installed the program using conda install, but the shell still had the old instance hashed.

Solution

Reactivate the environment or run hash -r (in bash) or rehash (in zsh).

When you run source activate, conda automatically runs hash -r in bash and rehash in zsh to clear the hashed commands, so conda finds things in the new path on the PATH. But there is no way to do this when conda install is run because the command must be run inside the shell itself, meaning either you have to run the command yourself or use source a file that contains the command.

This is a relatively rare problem, since this happens only in the following circumstances:

  1. You activate an environment or use the root environment, and then run a command from somewhere else.
  2. Then you conda install a program, and then try to run the program again without running activate or deactivate.

The command type command_name always tells you exactly what is being run. This is better than which command_name, which ignores hashed commands and searches the PATH directly. The hash is reset by source activate, or by hash -r in bash or rehash in zsh.

Programs fail due to invoking conda Python instead of system Python

Cause

After installing Anaconda or Miniconda, programs that run python switch from invoking the system Python to invoking the Python in the root conda environment. If these programs rely on the system Python to have certain configurations or dependencies that are not in the root conda environment Python, the programs may crash. For example, some users of the Cinnamon desktop environment on Linux Mint have reported these crashes.

Solution

Edit your .bash_profile and .bashrc files so that the conda binary directory, such as ~/miniconda3/bin, is no longer added to the PATH environment variable. You can still run conda activate and deactivate by using their full path names, such as ~/miniconda3/bin/conda.

You may also create a folder with symbolic links to conda, activate and deactivate, and then edit your .bash_profile or .bashrc file to add this folder to your PATH. If you do this, running python will invoke the system Python, but running conda commands, source activate MyEnv, source activate root, or source deactivate will work normally.

After running source activate to activate any environment, including after running source activate root, running python will invoke the Python in the active conda environment.

UnsatisfiableSpecifications error

Cause

Some conda package installation specifications are impossible to satisfy. For example, conda create -n tmp python=3 wxpython=3 produces an “Unsatisfiable Specifications” error because wxPython 3 depends on Python 2.7, so the specification to install Python 3 conflicts with the specification to install wxPython 3.

When an unsatisfiable request is made to conda, conda shows a message such as this one:

The following specifications were found to be in conflict:
- python 3*
- wxpython 3* -> python 2.7*
Use "conda info <package>" to see the dependencies for each package.

This indicates that the specification to install wxpython 3 depends on installing Python 2.7, which conflicts with the specification to install python 3.

Solution

Use “conda info wxpython” or “conda info wxpython=3” to show information about this package and its dependencies:

wxpython 3.0 py27_0
-------------------
file name   : wxpython-3.0-py27_0.tar.bz2
name        : wxpython
version     : 3.0
build number: 0
build string: py27_0
channel     : defaults
size        : 34.1 MB
date        : 2014-01-10
fn          : wxpython-3.0-py27_0.tar.bz2
license_family: Other
md5         : adc6285edfd29a28224c410a39d4bdad
priority    : 2
schannel    : defaults
url         : https://repo.continuum.io/pkgs/free/osx-64/wxpython-3.0-py27_0.tar.bz2
dependencies:
    python 2.7*
    python.app

By examining the dependencies of each package, you should be able to determine why the installation request produced a conflict and modify the request so it can be satisfied without conflicts. In this example, you could install wxPython with Python 2.7:

conda create -n tmp python=2.7 wxpython=3

Package installation fails from a specific channel

Cause

Sometimes it is necessary to install a specific version from a specific channel because that version is not available from the default channel.

Solution

The following example describes the problem in detail and its solution.

Suppose you have a specific need to install the Python cx_freeze module with Python 3.4. A first step is to create a Python 3.4 environment:

conda create -n py34 python=3.4

Using this environment you should first attempt:

conda install -n py34 cx_freeze

However, when you do this you get the following error:

Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata .........
Solving package specifications: .
Error: Package missing in current osx-64 channels:
- cx_freeze

You can search for packages on anaconda.org with

  anaconda search -t conda cx_freeze

The message indicates that cx_freeze cannot be found in the default package channels. However, there may be a community-created version available and you can search for it by running the following command:

$ anaconda search -t conda cx_freeze
Using Anaconda Cloud api site https://api.anaconda.org
Run 'anaconda show <USER/PACKAGE>' to get more details:
Packages:
     Name                      |  Version | Package Types   | Platforms
     ------------------------- |   ------ | --------------- | ---------------
     inso/cx_freeze            |    4.3.3 | conda           | linux-64
     pyzo/cx_freeze            |    4.3.3 | conda           | linux-64, win-32, win-64, linux-32, osx-64
                                          : http://cx-freeze.sourceforge.net/
     silg2/cx_freeze           |    4.3.4 | conda           | linux-64
                                          : create standalone executables from Python scripts
     takluyver/cx_freeze       |    4.3.3 | conda           | linux-64
Found 4 packages

In this example, there are 4 different places that you could try to get the package. None of them are officially supported or endorsed by Anaconda, but members of the conda community have provided many valuable packages. If you want to go with public opinion, then the web interface provides more information:

cx_freeze packages on anaconda.org

Notice that the pyzo organization has by far the most downloads, so you might choose to use their package. If so, you can add their organization’s channel by specifying it on the command line:

$ conda create -c pyzo -n cxfreeze_py34 cx_freeze python=3.4
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ..........
Solving package specifications: .........

Package plan for installation in environment /Users/ijstokes/anaconda/envs/cxfreeze_py34:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    cx_freeze-4.3.3            |           py34_4         1.8 MB
    setuptools-20.7.0          |           py34_0         459 KB
    ------------------------------------------------------------
                                           Total:         2.3 MB

The following NEW packages will be INSTALLED:

    cx_freeze:  4.3.3-py34_4
    openssl:    1.0.2h-0
    pip:        8.1.1-py34_1
    python:     3.4.4-0
    readline:   6.2-2
    setuptools: 20.7.0-py34_0
    sqlite:     3.9.2-0
    tk:         8.5.18-0
    wheel:      0.29.0-py34_0
    xz:         5.0.5-1
    zlib:       1.2.8-0

Now you have a software environment sandbox created with Python 3.4 and cx_freeze.

Conda automatically upgrades to unwanted version

When making a python package for an app, you create an environment for the app from a file req.txt that sets a certain version, such as python=2.7.9. However, when you conda install your package, it automatically upgrades to a later version, such as 2.7.10.

Cause

If you make a conda package for the app using conda build, you can set dependencies with specific version numbers. In this example, the requirements lines that say - python could be - python ==2.7.9 instead. It is important to have 1 space before the == operator and no space after.

Solution

Exercise caution when coding version requirements.

ValidationError: Invalid value for timestamp

Cause

This happens when certain packages are installed with conda 4.3.28, and then conda is downgraded to 4.3.27 or earlier.