Merck / Merck/TraceTrack

Unable to build Docker image using instructions

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Dominant language
Python
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Forks
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Description

I have an Ubuntu 22.04 vm and want to build Tracetrack
I'm following instructions but Docker image build fails due to incompatible anaconda and python packages.
Has anyone built this recently and can point me to changes needed for build?
``
```
$ sudo make docker-build
docker-compose build
[+] Building 1813.7s (12/30) docker:default
=> [monitor internal] load build definition from Dockerfile 0.2s
=> => transferring dockerfile: 994B 0.1s
=> [monitor internal] load .dockerignore 0.2s
=> => transferring context: 2B 0.1s
=> [worker internal] load build definition from Dockerfile 0.2s
=> => transferring dockerfile: 994B 0.1s
=> [worker internal] load .dockerignore 0.2s
=> => transferring context: 2B 0.0s
=> [worker internal] load metadata for docker.io/continuumio/miniconda3:latest 0.6s
=> [worker 1/13] FROM docker.io/continuumio/miniconda3@sha256:15f887d74b3ffe0fa21a741bfeaec8ccc8947b527acfb7542eff84ae1bfdd6bf 0.0s
=> [monitor internal] load build context 0.1s
=> => transferring context: 2.91kB 0.1s
=> [worker internal] load build context 0.1s
=> => transferring context: 2.91kB 0.1s
=> CACHED [monitor 2/13] RUN apt-get update -y && apt-get install -y --no-install-recommends libgtextutils 0.0s
=> CACHED [monitor 3/13] WORKDIR /tmp 0.0s
=> CACHED [monitor 4/13] COPY environment.yml environment.yml 0.0s
=> ERROR [monitor 5/13] RUN conda env update -n base -f environment.yml && rm -rf /tmp/* && conda clean --all & 1809.7s
------
> [monitor 5/13] RUN conda env update -n base -f environment.yml && rm -rf /tmp/* && conda clean --all && rm -r /opt/miniconda/lib/python3.7/site-packages/future/backports/test/ /opt/miniconda/pkgs/*:
2.102 /opt/conda/lib/python3.12/argparse.py:2006: FutureWarning: `remote_definition` is deprecated and will be removed in 25.9. Use `conda env create --file=URL` instead.
2.102 action(self, namespace, argument_values, option_string)
3.750 Channels:
3.750 - bioconda
3.750 - conda-forge
3.750 - defaults
3.750 Platform: linux-64
3.750 Collecting package metadata (repodata.json): ...working... done
92.57 Solving environment: ...working... failed
1324.8 Channels:
1324.8 - bioconda
1324.8 - conda-forge
1324.8 - defaults
1324.8 Platform: linux-64
1324.8 Collecting package metadata (repodata.json): ...working... done
1360.8 Solving environment: ...working... failed
1805.7
1805.7 LibMambaUnsatisfiableError: Encountered problems while solving:
1805.7 - package anaconda-anon-usage-0.4.4-py311hc06175d_0 requires python >=3.11,<3.12.0a0, but none of the providers can be installed
1805.7
1805.7 Could not solve for environment specs
1805.7 The following packages are incompatible
1805.7 ├─ anaconda-anon-usage is installable with the potential options
1805.7 │ ├─ anaconda-anon-usage [0.2.0|0.3.0|...|0.4.4] would require
1805.7 │ │ └─ python >=3.11,<3.12.0a0 , which can be installed;
1805.7 │ ├─ anaconda-anon-usage [0.4.3|0.4.4] would require
1805.7 │ │ └─ python >=3.12,<3.13.0a0 , which can be installed;
1805.7 │ ├─ anaconda-anon-usage [0.2.0|0.3.0|...|0.4.4] would require
1805.7 │ │ └─ python >=3.10,<3.11.0a0 , which can be installed;
1805.7 │ ├─ anaconda-anon-usage [0.2.0|0.3.0|...|0.4.4] would require
1805.7 │ │ └─ python >=3.8,<3.9.0a0 , which can be installed;
1805.7 │ └─ anaconda-anon-usage [0.2.0|0.3.0|...|0.4.4] would require
1805.7 │ └─ python >=3.9,<3.10.0a0 , which can be installed;
1805.7 ├─ menuinst is installable with the potential options
1805.7 │ ├─ menuinst [2.0.0|2.0.1|...|2.2.0] would require
1805.7 │ │ └─ python >=3.12,<3.13.0a0 , which can be installed;
1805.7 │ ├─ menuinst [2.0.0|2.0.1|...|2.2.0] would require
1805.7 │ │ ├─ python >=3.10,<3.11.0a0 , which can be installed;
1805.7 │ │ └─ python_abi 3.10.* *_cp310, which can be installed;
1805.7 │ ├─ menuinst [2.0.0|2.0.1|...|2.2.0] would require
1805.7 │ │ ├─ python >=3.11,<3.12.0a0 , which can be installed;
1805.7 │ │ └─ python_abi 3.11.* *_cp311, which can be installed;
1805.7 │ ├─ menuinst [2.0.0|2.0.1|...|2.2.0] would require
1805.7 │ │ └─ python_abi 3.12.* *_cp312, which can be installed;
1805.7 │ ├─ menuinst [2.0.0|2.0.1|...|2.1.2] would require
1805.7 │ │ ├─ python >=3.8,<3.9.0a0 , which can be installed;
1805.7 │ │ └─ python_abi 3.8.* *_cp38, which can be installed;
1805.7 │ ├─ menuinst 2.0.0 would require
1805.7 │ │ ├─ pypy3.9 >=7.3.12 with the potential options
1805.7 │ │ │ ├─ pypy3.9 7.3.12 would require
1805.7 │ │ │ │ └─ python 3.9.* *_7.3_pypy, which can be installed;
1805.7 │ │ │ ├─ pypy3.9 7.3.12, which can be installed;
1805.7 │ │ │ ├─ pypy3.9 7.3.13, which can be installed;
1805.7 │ │ │ └─ pypy3.9 [7.3.15|7.3.16], which can be installed;
1805.7 │ │ └─ python_abi 3.9 *_pypy39_pp73, which can be installed;
1805.7 │ ├─ menuinst [2.0.0|2.0.1|...|2.2.0] would require
1805.7 │ │ ├─ python >=3.9,<3.10.0a0 , which can be installed;
1805.7 │ │ └─ python_abi 3.9.* *_cp39, which can be installed;
1805.7 │ ├─ menuinst [2.0.1|2.0.2] would require
1805.7 │ │ ├─ pypy3.9 >=7.3.13 , which can be installed;
1805.7 │ │ └─ python_abi 3.9 *_pypy39_pp73, which can be installed;
1805.7 │ ├─ menuinst [2.1.0|2.1.1|2.1.2] would require
1805.7 │ │ ├─ pypy3.9 >=7.3.15 , which can be installed;
1805.7 │ │ └─ python_abi 3.9 *_pypy39_pp73, which can be installed;
1805.7 │ ├─ menuinst [2.1.2|2.2.0] would require
1805.7 │ │ └─ python_abi 3.13.* *_cp313, which can be installed;
1805.7 │ ├─ menuinst [2.0.0|2.0.1|...|2.2.0] would require
1805.7 │ │ └─ python >=3.10,<3.11.0a0 , which can be installed;
1805.7 │ ├─ menuinst [2.0.0|2.0.1|...|2.2.0] would require
1805.7 │ │ └─ python >=3.11,<3.12.0a0 , which can be installed;
1805.7 │ ├─ menuinst [2.0.0|2.0.1|...|2.2.0] would require
1805.7 │ │ └─ python >=3.8,<3.9.0a0 , which can be installed;
1805.7 │ └─ menuinst [2.0.0|2.0.1|...|2.2.0] would require
1805.7 │ └─ python >=3.9,<3.10.0a0 , which can be installed;
1805.7 └─ python >=3.7,<3.8 is not installable because there are no viable options
1805.7 ├─ python [3.7.0|3.7.1|3.7.2|3.7.3|3.7.6] would require
1805.7 │ └─ python_abi * *_cp37m, which conflicts with any installable versions previously reported;
1805.7 ├─ python [3.7.0|3.7.1|...|3.7.9] conflicts with any installable versions previously reported;
1805.7 └─ python [3.7.10|3.7.12|...|3.7.9] would require

```

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the Dockerfile and environment.yml used by make docker-build, then reproduce the failure on Ubuntu 22.04 with sudo make docker-build. Investigate the Conda solver error involving Python 3.7, anaconda-anon-usage, and menuinst. Done means the Docker image builds successfully for both monitor and worker services.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, docker-compose, python
Domain
build-system, devops
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
32/100

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