Comments (4)
joverlee521
commented on September 28, 2024
1
Tracked the underlying issue in nextstrain/conda-base#38, but there should still be better messages from the CLI if the runtime was not actually updated.
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joverlee521
commented on September 28, 2024
1
Ah, this could be as simple as updating the version of micromamba we are using for our conda runtime.
I overrode the default version with NEXTSTRAIN_CONDA_MICROMAMBA_VERSION=1.1.0 nextstrain setup conda --force and now it produces the expected error:
$ nextstrain update conda
Checking for newer versions of Nextstrain CLI…
nextstrain-cli is up to date!
Updating conda runtime…
Updating Conda package nextstrain-base from 20230615T171309Z to 20230717T174555Z…
Updating Conda packages in /Users/jlee2346/.nextstrain/runtimes/conda/env…
- nextstrain-base ==20230717T174555Z
__
__ ______ ___ ____ _____ ___ / /_ ____ _
/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
bioconda/osx-64 Using cache
bioconda/noarch Using cache
nextstrain/noarch No change
nextstrain/osx-64 No change
error libmamba Could not solve for environment specs
Encountered problems while solving:
- package nextstrain-base-20230717T174555Z-h0dc7051_0_locked requires nodejs ==18.16.1 h46e3395_0, but none of the providers can be installed
The environment can't be solved, aborting the operation
critical libmamba Could not solve for environment specs
Error running ('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'update', 'nextstrain-base ==20230717T174555Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin')
Traceback (most recent call last):
File "/Users/jlee2346/Repos/nextstrain/cli/nextstrain/cli/runner/conda.py", line 347, in micromamba
subprocess.run(argv, env = env, check = True)
File "/Users/jlee2346/.pyenv/versions/3.6.5/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'update', 'nextstrain-base ==20230717T174555Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin')' returned non-zero exit status 1.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/jlee2346/Repos/nextstrain/cli/nextstrain/cli/runner/conda.py", line 486, in update
micromamba("update", update_spec)
File "/Users/jlee2346/Repos/nextstrain/cli/nextstrain/cli/runner/conda.py", line 349, in micromamba
raise InternalError(f"Error running {argv!r}") from err
nextstrain.cli.errors.InternalError: Error running ('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'update', 'nextstrain-base ==20230717T174555Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin')
Updating failed!
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joverlee521
commented on September 28, 2024
This also fails to update when I try to install specific versions with the NEXTSTRAIN_* envvars:
$ NEXTSTRAIN_CONDA_CHANNEL=nextstrain/label/main \
NEXTSTRAIN_CONDA_BASE_PACKAGE="nextstrain-base ==20230628T211222Z" \
nextstrain update conda
Checking for newer versions of Nextstrain CLI…
nextstrain-cli is up to date!
Updating conda runtime…
Updating nextstrain-base from 20230615T171309Z to ==20230628T211222Z…
Updating Conda packages in /Users/jlee2346/.nextstrain/runtimes/conda/env…
- nextstrain-base ==20230628T211222Z
__
__ ______ ___ ____ _____ ___ / /_ ____ _
/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
nextstrain/label/main/noarch 130.0 B @ 231.0 B/s 0.6s
nextstrain/label/main/osx-64 30.2kB @ 34.1kB/s 0.9s
bioconda/osx-64 4.2MB @ 1.5MB/s 3.1s
bioconda/noarch 4.6MB @ 1.1MB/s 4.0s
conda-forge/noarch 13.4MB @ 1.7MB/s 8.8s
conda-forge/osx-64 29.8MB @ 2.7MB/s 13.0s
Transaction
Prefix: /Users/jlee2346/.nextstrain/runtimes/conda/env
All requested packages already installed
Transaction starting
Transaction finished
Cleaning up…
__
__ ______ ___ ____ _____ ___ / /_ ____ _
/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
Collect information..
Cleaning index cache..
Cleaning lock files..
Cleaning tarballs..
Cleaning packages..
Runtime updated!
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joverlee521
commented on September 28, 2024
Running the forced setup with NEXTSTRAIN_* envvars produces an actual error:
$ NEXTSTRAIN_CONDA_CHANNEL=nextstrain/label/main \
NEXTSTRAIN_CONDA_BASE_PACKAGE="nextstrain-base ==20230628T211222Z" \
nextstrain setup --force conda
Setting up conda…
Removing existing directory /Users/jlee2346/.nextstrain/runtimes/conda/micromamba to start fresh…
Requesting Micromamba from https://api.anaconda.org/download/conda-forge/micromamba/1.0.0/osx-64/micromamba-1.0.0-1.tar.bz2…
Downloading and extracting Micromamba to /Users/jlee2346/.nextstrain/runtimes/conda/micromamba…
Removing existing directory /Users/jlee2346/.nextstrain/runtimes/conda/env to start fresh…
Installing Conda packages into /Users/jlee2346/.nextstrain/runtimes/conda/env…
- nextstrain-base ==20230628T211222Z
__
__ ______ ___ ____ _____ ___ / /_ ____ _
/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
nextstrain/label/main/osx-64 30.2kB @ 79.6kB/s 0.4s
nextstrain/label/main/noarch 135.0 B @ 278.0 B/s 0.5s
bioconda/osx-64 4.2MB @ 2.1MB/s 2.2s
bioconda/noarch 4.6MB @ 1.5MB/s 3.1s
conda-forge/noarch 13.4MB @ 2.4MB/s 6.3s
conda-forge/osx-64 29.8MB @ 3.0MB/s 11.6s
Encountered problems while solving:
- package nextstrain-base-20230628T211222Z-h0dc7051_0_locked requires git ==2.41.0 pl5321h5c607e1_0, but none of the providers can be installed
The environment can't be solved, aborting the operation
error libmamba Could not solve for environment specs
critical libmamba UnsatisfiableError
Error running ('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20230628T211222Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain/label/main', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')
Traceback (most recent call last):
File "nextstrain.cli.runner.conda", line 347, in micromamba
subprocess.run(argv, env = env, check = True)
File "subprocess", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20230628T211222Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain/label/main', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')' returned non-zero exit status 1.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "nextstrain.cli.runner.conda", line 233, in setup_prefix
micromamba("create", *packages)
File "nextstrain.cli.runner.conda", line 349, in micromamba
raise InternalError(f"Error running {argv!r}") from err
nextstrain.cli.errors.InternalError: Error running ('/Users/jlee2346/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20230628T211222Z', '--prefix', '/Users/jlee2346/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain/label/main', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')
Set up failed!
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Related Issues (20)
- Installation fails when there is a space in the path HOT 1
- Docker runner assumes the Docker Hub (docker.io) registry HOT 4
- ENH: Detect and warn user if their environment deviates from nextstrain-base HOT 1
- Pyright failures with 1.1.309
- `nextstrain update conda` in 7.0.0 can error with "Invalid version" HOT 13
- Improve runtime documentation HOT 1
- pyparsing 3.1.0 causing test failures in Markdown image inlining HOT 4
- [batch] ZIP archive of build dir is stored without compression HOT 1
- Integrate AWS Batch set up and usage doc with runtime doc
- Uncaught ImmatureSignatureError: The token is not yet valid (iat) HOT 3
- Python user site directory leaks into Conda runtime HOT 5
- Test compatibility with SingularityCE 4.x series
- nextstrain view can't connect to host on a Mac inside a Conda environment HOT 8
- Use same version resolution method in `nextstrain setup conda` as `nextstrain update conda` HOT 1
- Invalid `~/.shrc` file named in standalone installer instructions HOT 5
- Broken CI due to upstream release; mypy implicated HOT 1
- Consider UI/UX for AWS Batch runtime without Docker runtime HOT 1
- Singularity/Apptainer Version HOT 4
- remote/s3 should instantiate its own MimeTypes instance
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