Skip to content

FAQ.md

Latest commit

 

History

History
70 lines (53 loc) · 2.95 KB

FAQ.md

File metadata and controls

70 lines (53 loc) · 2.95 KB

Frequently Asked Questions

Why am I getting the error "libmamba Could not solve for environment specs"?

This indicates that micromamba was unable to find a set of packages which met all the constraints that were set for the environment.

This can happen if you forgot to include a channel that is the source for a required package.

This error sometimes occurs when moving from one CPU architecture to another, such as when moving from x86 to a ARM-based CPUs (such as Apple M1 and M2 CPUs). Some conda repositories do a good job of supporting multiple architectures (such as Conda Forge), but others only support x86 CPUs (Bioconda). You can work around this by forcing docker build ... to emulate another CPU architecture by appending --platform=linux/amd64 to the FROM line of your Dockerfile. However, emulation can result in significantly slower builds.

Why do I get errors when building the example Dockerfiles?

Docker Desktop has a configuration setting for how much disk space to use. When this limit is reached, the error messages thrown by the container may not seem related to disk space. For example:

  • micromamba install ... may give the error `libmamba Non-writable cache error``
  • apt-get install ... may give the error At least one invalid signature was encountered.

To free up some of the disk space allocated to Docker, execute docker system prune --all. Then attempt the docker build ... command again.

Why am I getting the error critical libmamba Subprocess call failed. Aborting.?

docker had a change in how ulimit values are set within containers starting in docker v22.10. By passing docker build or docker run the flag --ulimit nofile=65536:65536 you can increase the nofile limit within the container.

How do I install software using apt/apt-get/apk?

The default user in mambaorg/micromamba does not have root-level permissions. Therefore you need to switch to user root before installing software using the system package manager. After installing the software you should switch back to $MAMBA_USER.

Here is an example Dockerfile:

FROM mambaorg/micromamba:1.4.4

COPY --chown=$MAMBA_USER:$MAMBA_USER env.yaml /tmp/env.yaml
RUN micromamba install -y -n base -f /tmp/env.yaml && \
    micromamba clean --all --yes

USER root
RUN apt-get update && apt-get install -y \
    bluetooth \
    && rm -rf /var/lib/apt/lists/*
USER $MAMBA_USER