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📝 Add conda channels troubleshoot
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Tania Allard
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# Troubleshooting Common Problems
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When troubleshooting, you may see unexpected behaviors or receive an error message. This section provides advice on
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how to identify and mitigate the cause of the problem and how to resolve it (for the most commonly encountered issues).
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how to identify and fix some of the most commonly encountered issues.
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Most of the `docker run` flags used in this document are explained in detail in the [Common Features, Docker Options section](../using/common.html#Docker-Options) of the documentation.
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@@ -28,8 +28,8 @@ $ touch stagingarea/kale.txt
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touch: cannot touch 'stagingarea/kale.txt': Permission denied
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```
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In this case the user of the container (`jovyan`) and the owner of the mounted volume (`root`) have different permission levels and ownership over the container's directories and mounts.
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The following sections cover a few of these scenarios and suggestions to fix these problems.
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In this case, the user of the container (`jovyan`) and the owner of the mounted volume (`root`) have different permission levels and ownership over the container's directories and mounts.
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The following sections cover a few of these scenarios and how to fix them.
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**Some things to try:**
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@@ -118,7 +118,7 @@ The following sections cover a few of these scenarios and suggestions to fix the
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## Permission issues after changing the UID/GIU and USER in the container
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If on top of changing the UID and GID you also **need to create a new user**, you might be experiencing any of the following issues:
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If you have also **created a new user**, you might be experiencing any of the following issues:
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- `root` is the owner of `/home` or a mounted volume
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- when starting the container, you get an error such as `Failed to change ownership of the home directory.`
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@@ -163,7 +163,7 @@ If on top of changing the UID and GID you also **need to create a new user**, yo
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- `-w "/home/${NB_USER}"` sets the working directory to be the new user's home
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```{admonition} Additional notes
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In the example above, the `-v` flag is used to mount the local volume onto the `/home` directory of the new user.
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In the example above, the `-v` flag is used to mount the local volume onto the new user's `/home` directory.
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However, if you are mounting a volume elsewhere, you also need to use the `-e CHOWN_EXTRA=<some-dir>` flag to avoid any permission
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issues (see the section [Permission denied when mounting volumes](../using/troubleshooting.html#permission-denied-when-mounting-volumes) in this page).
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@@ -200,7 +200,7 @@ If on top of changing the UID and GID you also **need to create a new user**, yo
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-v $(PWD)/<my-vol>:/home/jovyan/work
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```
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In this example, we use the syntax `$(PWD)`, which is replaced with the full path to the current directory at runtime. The destination
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This example uses the syntax `$(PWD)`, which is replaced with the full path to the current directory at runtime. The destination
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path should also be an absolute path starting with a `/` such as `home/jovyan/work`.
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- You might want to consider using the Docker native `--user <UID>` and `--group-add users` flags instead of `-e NB_GID` and `-e NB_UID`:
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@@ -215,7 +215,7 @@ If on top of changing the UID and GID you also **need to create a new user**, yo
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-v <my-vol>:/home/jovyan/work jupyter/datascience-notebook
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```
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This command will launch the container with a specific user UID and add that user to the `users` group so that it can modify the files in the default `/home` and `/opt/conda` directories.
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This command will launch the container with a specific user UID and add that user to the `users` group to modify the files in the default `/home` and `/opt/conda` directories.
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Further avoiding issues when trying to `conda install` additional packages.
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- Use `docker inspect <container_id>` and look for the [`Mounts` section](https://docs.docker.com/storage/volumes/#start-a-container-with-a-volume) to verify that the volume was created and mounted accordingly:
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],
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```
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## Problems installing conda packages from specific channels
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By default, the docker-stacks images have the conda channels priority set to `strict`. This may cause problems when trying to install packages from a channel with lower priority.
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```bash
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$ conda config --show | grep priority
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# channel_priority: strict
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# to see its meaning
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$ conda config --describe channel_priority
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# checking the current channels
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$ conda config --show default_channels
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# default_channels:
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# - https://repo.anaconda.com/pkgs/main
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# - https://repo.anaconda.com/pkgs/r
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```
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**Installing packages from alternative channels:**
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You can install packages from other conda channels (e.g. bioconda) by disabling the `channel_priority` setting:
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```bash
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# install by disabling channel priority at command level
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$ conda install --no-channel-priority -c bioconda bioconductor-geoquery
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```
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## Tokens are being rejected
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If you are a regular user of VSCode and the Jupyter extension you might experience either of these issues when using any of the docker-stacks images:
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If you are a regular user of VSCode and the Jupyter extension, you might experience either of these issues when using any of the docker-stacks images:
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- when clicking on the URL displayed on your command line logs, you face a "This site cannot be reached" page on your web browser
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- using the produced token and/or URL results in an "Invalid credentials" error on the Jupyter "Token authentication is enabled" page
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- when clicking on the URL displayed on your command line logs you face a "This site cannot be reached" page on your web browser
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```bash
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# example log output from the docker run command
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[...]
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Or copy and paste one of these URLs:
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http://3d4cf3809e3f:8888/?token=996426e890f8dc22fa6835a44442b6026cba02ee61fee6a2
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or http://127.0.0.1:8888/?token=996426e890f8dc22fa6835a44442b6026cba02ee61fee6a2
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```
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**Some things to try:**
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1. The first thing you want to try is to check that there are no other Jupyter processes running in the background:
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1. **Find lingering Jupyter processes in the background**
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The first thing you want to try is to check that no other Jupyter processes are running in the background:
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```bash
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ps aux | grep jupyter
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@@ -263,8 +301,10 @@ If you are a regular user of VSCode and the Jupyter extension you might experien
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kill 3412
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```
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2. Alternatively - you might want to ensure that the "Jupyter: Auto Start" setting is turned off to avoid this issue in the future.
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2. **Turn off Jupyter auto start in VSCode**
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Alternatively - you might want to ensure that the `Jupyter: Auto Start` setting is turned off to avoid this issue in the future.
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You can achieve this from the `Preferences > Jupyter` menu in VScode:
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