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(faq)=
Frequently Asked Questions (FAQ)
A collection of frequently asked questions with answers. If you have a question and have found an answer, send a PR to add it here!
Why is my repository failing to build with ResolvePackageNotFound ?
If you used conda env export to generate your environment.yml it will generate a list of packages and versions of packages that is pinned to platform specific versions.
These very specific versions are not available in the Linux Docker image used by repo2docker. A typical error message will look like the following:
Step 39/44 : RUN conda env update -n root -f "environment.yml" && conda clean -tipsy && conda list -n root
---> Running in ebe9a67762e4
Solving environment: ...working... failed
ResolvePackageNotFound:
- jsonschema==2.6.0=py36hb385e00_0
- libedit==3.1.20181209=hb402a30_0
- tornado==5.1.1=py36h1de35cc_0
...
We recommend to use conda env export --no-builds -f environment.yml to export
your environment and then edit the file by hand to remove platform specific
packages like appnope.
See {ref}export-environment for a recipe on how to create strict exports of
your environment that will work with repo2docker.
Can I add executable files to the user's PATH?
Yes! With a file, you can place any files that should be called from the command line in the folder ~/.local/bin.
This folder will be available in a user's PATH, and can be run from the command line (or as a subsequent build step.)
Can I use repo2docker to bootstrap my own Dockerfile to edit by hand?
No, you can't.
If you pass the --debug flag to repo2docker, it outputs the
intermediate Dockerfile that is used to build the Docker image. While
it is tempting to copy this as a base for your own Dockerfile, that is
not supported & in most cases will not work. The --debug output is
just our intermediate generated Dockerfile, and is meant to be built
in a very specific way. Hence the output of --debug can not be
built with a normal docker build -t . or similar traditional
Docker command.
Check out the binder-examples GitHub organization for example repositories you can copy & modify for your own use!
Can I use repo2docker to edit a local host repository within a Docker environment?
Yes: use the --editable or -E flag (don't confuse this with
the -e flag for environment variables), and run repo2docker on a
local repository:
repo2docker -E my-repository/
This builds a Docker container from the files in that repository
(using, for example, a requirements.txt or install.R file),
then runs that container, while connecting the working directory
inside the container to the local repository outside the
container. For example, in case there is a notebook file (.ipynb),
this will open in a local web browser, and one can edit it and save
it. The resulting notebook is updated in both the Docker container and
the local repository. Once the container is exited, the changed file
will still be in the local repository.
This allows for easy testing of the container while debugging some items, as well as using a fully customizable container to edit notebooks (among others).
:::{note}
Editable mode is a convenience option that will bind the
repository to the container working directory (usually
$HOME). If you need to mount to a different location in
the container, use the --volumes option instead. Similarly,
for a fully customized user Dockerfile, this option is not
guaranteed to work.
:::
Why is my R shiny app not launching?
If you are trying to run an R shiny app using the /shiny/folder_containing_shiny
url option, but the launch returns "The application exited during initialization.",
there might be something wrong with the specification of the app. One way of debugging
the app in the container is by running the rstudio url, open either the ui or
server file for the app, and run the app in the container rstudio. This way you can
see the rstudio logs as it tries to initialize the shiny app. If you are missing a
package or other dependency for the container, this will be obvious at this stage.
Why does repo2docker need to exist? Why not use tool like source2image?
The Jupyter community believes strongly in building on top of pre-existing tools whenever possible (this is why repo2docker buildpacks largely build off of patterns that already exist in the data analytics community). We try to perform due-diligence and search for other communities to leverage and help, but sometimes it makes the most sense to build our own new tool. In the case of repo2docker, we spent time integrating with a pre-existing tool called source2image. This is an excellent open tool for containerization, but we ultimately decided that it did not fit the use-case we wanted to address. For more information, read our blog post about why we built repo2docker.