Having issues with one of the RUN in the docker file
Open
@byee4 is already working on this.
Since Jun 7, 2023.
- Dominant language
- Dockerfile
- Stars
- 0
- Forks
- 1
- Avg merge
- 2h
- Merged PRs (30d)
- 4
Description
Hi Brian, I'm having issues with RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt in the docker file. Now I'm just using a copy of deseq2/1.39's files and only added one line in conda-packages.txt file, bioconductor-ensdb.hsapiens.v79.
But when I try to build it, I always encounter issues with the error below:
(base) shuhaoxu@Shuhaos-MBP 1.39.3 % docker build -t deseq2/1.39.3 .
[+] Building 617.1s (10/12)
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 1.62kB 0.0s
=> [internal] load metadata for docker.io/jupyter/datascience-notebook:hub-2.2.2 1.1s
=> [auth] jupyter/datascience-notebook:pull token for registry-1.docker.io 0.0s
=> [1/7] FROM docker.io/jupyter/datascience-notebook:hub-2.2.2@sha256:f5984966ed1024e70369860 0.0s
=> [internal] load build context 0.0s
=> => transferring context: 825B 0.0s
=> CACHED [2/7] COPY apt-packages.txt /tmp/apt-packages.txt 0.0s
=> [3/7] COPY conda-packages.txt /tmp/conda-packages.txt 0.0s
=> [4/7] RUN apt-get update && xargs apt-get install -y < /tmp/apt-packages.txt 231.7s
=> ERROR [5/7] RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.t 384.7s
------
> [5/7] RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt:
------
Dockerfile:26
--------------------
24 |
25 | # Install additional R packages from conda-forge using mamba
26 | >>> RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt
27 |
28 | RUN Rscript -e 'install.packages("devtools", repos = "https://cran.us.r-project.org")'
--------------------
ERROR: failed to solve: process "/bin/bash -o pipefail -c mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt" did not complete successfully: exit code: 137
I also tried to just switch using mamda to conda , which did not work neither.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Assessment
This issue has not been assessed yet.