tsibley
commented
4 months ago This works locally for me now, but the very first time I ran it (after I pushed my updates), I ran into this error:
$ nextstrain setup --force conda
Setting up conda…
Removing existing directory /home/tom/.nextstrain/runtimes/conda/micromamba to start fresh…
Requesting Micromamba from https://api.anaconda.org/download/conda-forge/micromamba/1.5.8/linux-64/micromamba-1.5.8-0.tar.bz2…
Downloading and extracting Micromamba to /home/tom/.nextstrain/runtimes/conda/micromamba…
Removing existing directory /home/tom/.nextstrain/runtimes/conda/env to start fresh…
Installing Conda packages into /home/tom/.nextstrain/runtimes/conda/env…
- nextstrain-base ==20240501T220407Z
bioconda/noarch (check zst) Checked 0.1s
bioconda/linux-64 (check zst) Checked 0.2s
nextstrain/linux-64 (check zst) Checked 0.2s
nextstrain/noarch 116.0 B @ 566.0 B/s 0.2s
conda-forge/noarch 14.6MB @ 32.8MB/s 0.6s
conda-forge/linux-64 34.2MB @ 38.5MB/s 1.0s
bioconda/linux-64 5.4MB @ 4.6MB/s 1.2s
bioconda/noarch 5.2MB @ 3.9MB/s 1.2s
nextstrain/linux-64 25.2kB @ 14.7kB/s 1.7s
Transaction
Prefix: /home/tom/.nextstrain/runtimes/conda/env
Updating specs:
- nextstrain-base==20240501T220407Z
Package Version Build Channel Size
──────────────────────────────────────────────────────────────────────────────────────────────
Install:
──────────────────────────────────────────────────────────────────────────────────────────────
+ _libgcc_mutex 0.1 conda_forge conda-forge 3kB
+ ca-certificates 2024.2.2 hbcca054_0 conda-forge 155kB
+ ld_impl_linux-64 2.40 h55db66e_0 conda-forge 713kB
[…]
Summary:
Install: 314 packages
Total download: 466MB
──────────────────────────────────────────────────────────────────────────────────────────────
Transaction starting
ld_impl_linux-64 713.3kB @ 9.9MB/s 0.1s
python_abi 6.4kB @ 88.4kB/s 0.1s
_libgcc_mutex 2.6kB @ 28.7kB/s 0.1s
[+] 0.1s
Downloading (5) ╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 877.7kB / 465.9MB libstdcxx-ng 0.0s
Extracting (4) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0 / 314 _libgcc_mutex 0.0sterminate called after throwing an instance of 'std::logic_error'
what(): basic_string: construction from null is not valid
Error running ('/home/tom/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/home/tom/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20240501T220407Z', '--prefix', '/home/tom/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')
Traceback (most recent call last):
File "/home/tom/nextstrain/cli/nextstrain/cli/runner/conda.py", line 389, in micromamba
subprocess.run(argv, env = env, check = True)
File "/home/tom/.pyenv/versions/3.11.4/lib/python3.11/subprocess.py", line 571, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '('/home/tom/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/home/tom/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20240501T220407Z', '--prefix', '/home/tom/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')' died with <Signals.SIGABRT: 6>.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/tom/nextstrain/cli/nextstrain/cli/runner/conda.py", line 275, in setup_prefix
micromamba("create", install_spec)
File "/home/tom/nextstrain/cli/nextstrain/cli/runner/conda.py", line 391, in micromamba
raise InternalError(f"Error running {argv!r}") from err
nextstrain.cli.errors.InternalError: Error running ('/home/tom/.nextstrain/runtimes/conda/micromamba/bin/micromamba', '--root-prefix', '/home/tom/.nextstrain/runtimes/conda/micromamba', '--no-rc', '--no-env', '--yes', 'create', 'nextstrain-base ==20240501T220407Z', '--prefix', '/home/tom/.nextstrain/runtimes/conda/env', '--override-channels', '--strict-channel-priority', '--channel', 'nextstrain', '--channel', 'conda-forge', '--channel', 'bioconda', '--no-py-pin', '--allow-uninstall', '--allow-downgrade')
Set up failed!This is an error inside micromamba. I have not been able to replicate it with either a) repeated invocations or b) downgrading back to 1.1.0 and trying the upgrade again.
Resolves #366
Mirrors #301
Description of proposed changes
Related issue(s)
Checklist