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Questions tagged [mamba]

Mamba is a Python-based CLI conceived as a drop-in replacement for conda, offering higher speed and more reliable environment solutions.

Mamba is a fast, robust, and cross-platform package manager.

It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda’s commands.

https://github.com/mamba-org/mamba

109 questions
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conda wants to remove half my packages if I try to update just one (on a fresh Anaconda installation)

The issue Today (31-Mar-2023) I downloaded Anaconda, uninstalled an older version and installed today's version on a Windows PC (private PC, no corporate firewall). As suggested in another question Conda very slow and downloading only from conda…
Pythonista anonymous
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Conda environments' name missing after mamba installation

After installing mamba and creating an environment, all the names of my previous conda environments are missing. I can see their path and even activate them if I do: conda activate /environment/path this is what it looks like when I do: conda env…
Ebert Alvares
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Snakemake cannot activate an existing conda environment

I understood from the Snakemake docs that the conda directive can take the name of an existing conda environment. However, I am faced with the error EnvironmentNameNotFound: Could not find conda environment. Why can Snakemake not find the existing…
Ezra Herman
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mamba upgrade to 1.x

I have mamba 0.27 installed on my mac OS. How can I upgrade to mamba 1.x? Can I simply do a fresh re-installation of the newer version, if I want to keep my existing mamba environments and settings? I checked mamba's documentation, and I searched in…
Cahit
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Use micromamba virtual environment in VS Code

We have to use micromamba for our app because conda is prohibitively slow for installing our packages. We use a devcontainer to install micromamba and its packages. This works for the VS Code terminal but the editor still cannot find my packages. I…
twinlakes
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Issues When Installing Openpyxl

I was trying to install openpyxl and I got the following error message: Traceback (most recent call last): File "C:\Users\XXXXXXX\anaconda3\Scripts\mamba-script.py", line 10, in sys.exit(main()) File…
Lash360
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Using R in a Snakemake workflow with Mambaforge

I'm building a pipeline with Snakemake. One rule involves an R script that reads a CSV file using readr. I get this error when I run the pipeline with --use-singularity and --use-conda Error: Unknown TZ UTC In addition: Warning message: In…
Tomas Bencomo
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Mamba env throws "AttributeError: 'Namespace' object has no attribute 'func'"

I'm suddenly getting the following error when running mamba env export: $ mamba env export Traceback (most recent call last): File "/scicore/home/neher/roemer0001/miniconda3/lib/python3.9/site-packages/conda/exception_handler.py", line 17, in…
Cornelius Roemer
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Micromamba install gets stuck when run in docker container on ARM mac

When using micromamba install in an amd64 docker container run on M1 ARM macOS 13.5, the installation hangs indefinitely after the extraction step. The following docker file, built with docker build . --platform linux/amd64 FROM…
Cornelius Roemer
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How can I get IJulia working inside a mamba environment?

I am having trouble installing IJulia in Julia 1.9.1 inside a mamba environment. The crux of the issue seems to be the compiler not being able to find MbedTLS even though it is installed Looking for: ['mbedtls'] conda-forge/noarch …
Sudoh
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print all unmet dependencies in conda

I'm trying to install a package via conda on an M1 mac. This package has a lot of dependencies, some of which seem to be un-satisfiable due to lack of pre-built packages in conda-forge. I know I can trigger building of packages in conda-forge by…
PejoPhylo
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Getting 'GLIBCXX_3.4.30 not found' error in RStudio after creating new R environment with mamba on Ubuntu 20.04 - How to fix it?

I just installed mamba to create a new R environment. So, I ran mamba create -n myenv -c conda-forge -c bioconda r-seurat=4* "bioconductor-genomeinfodbdata=1.2.7" bioconductor-deseq2. On the other hand, I installed the RStudio version 2022.02.0…
Zeke
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Error loading r package within conda environment: libproj.so.15: cannot open shared object file

I am creating the following conda environment: $ mamba create -n mexico -c conda-forge -c bioconda -c R r-base=4.2.3 r-data.table=1.14.8 r-terra=1.5_21 __ __ __ __ / \ / \ / \ / \ …
Gonzalo Rizzo
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conda environments in team and shared Linux environment - best practices?

Conda is great, but it assumes that people code completely independently much like the complete lack of namespace hierarchy in public python modules. Looking for best practices with 6 people all developing in largely the same conda environment.…
Sean Blanton
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How to install package with apt-get in Gitlab CI pipeline using micromamba image

I'm using the micromamba image in a Gitlab CI pipeline. I need to install an additional package with apt-get (libgl1-mesa-glx). With the miniconda image this was working: image: continuumio/miniconda3:latest before_script: - apt-get update &&…
Daniel
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