karllandheer
commented
12 months ago Hello, this was resolved on its own. My guess is a conda update broke something. Leaving it here incase this happens again
Open karllandheer opened 12 months ago
karllandheer
commented
12 months ago Hello, this was resolved on its own. My guess is a conda update broke something. Leaving it here incase this happens again
Error when running fslinstaller.py file conda on Ubuntu 20.04.6 LTS. Was working fine yesterday, my guess is conda updated something? Version FSL 6.0.7.6 is being selected
last part of Log file here
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── 17:04:34 fslinstaller.py: 937: [stdout]: 17:04:34 fslinstaller.py: 937: [stdout]: 17:12:31 fslinstaller.py: 937: [stdout]: 17:12:31 fslinstaller.py: 937: [stdout]: Downloading and Extracting Packages 17:12:31 fslinstaller.py: 937: [stdout]: 17:12:37 fslinstaller.py: 937: [stdout]: Preparing transaction: ...working... done 17:13:18 fslinstaller.py: 937: [stdout]: Verifying transaction: ...working... done 17:16:13 fslinstaller.py: 937: [stdout]: Executing transaction: ...working... 17:16:13 fslinstaller.py: 937: [stdout]: 17:16:13 fslinstaller.py: 937: [stdout]: done 17:16:14 fslinstaller.py: 937: [stdout]: # 17:16:14 fslinstaller.py: 937: [stdout]: # To activate this environment, use 17:16:14 fslinstaller.py: 937: [stdout]: # 17:16:14 fslinstaller.py: 937: [stdout]: # $ conda activate base 17:16:14 fslinstaller.py: 937: [stdout]: # 17:16:14 fslinstaller.py: 937: [stdout]: # To deactivate an active environment, use 17:16:14 fslinstaller.py: 937: [stdout]: # 17:16:14 fslinstaller.py: 937: [stdout]: # $ conda deactivate 17:16:14 fslinstaller.py: 937: [stdout]: 17:16:15 fslinstaller.py: 768: Running cp fslversion /usr/local/fsl/etc [as admin: False] 17:16:15 fslinstaller.py: 768: Running cp /tmp/tmp4onmsein/fsl-6.0.7.6_linux-64.yml /usr/local/fsl/etc [as admin: False] 17:16:15 fslinstaller.py: 768: Running /usr/local/fsl/bin/mamba clean -y --all [as admin: False] 17:16:16 fslinstaller.py: 937: [stderr]: No module named 'conda.cliconda' 17:16:17 fslinstaller.py: 937: [stderr]: 17:16:17 fslinstaller.py: 937: [stderr]: # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<< 17:16:17 fslinstaller.py: 937: [stderr]: 17:16:17 fslinstaller.py: 937: [stderr]: Traceback (most recent call last): 17:16:17 fslinstaller.py: 937: [stderr]: File "/usr/local/fsl/lib/python3.11/site-packages/conda/exception_handler.py", line 17, in call 17:16:17 fslinstaller.py: 937: [stderr]: return func(*args, *kwargs) 17:16:17 fslinstaller.py: 937: [stderr]: ^^^^^^^^^^^^^^^^^^^^^ 17:16:17 fslinstaller.py: 937: [stderr]: File "/usr/local/fsl/lib/python3.11/site-packages/mamba/mamba.py", line 956, in exception_converter 17:16:17 fslinstaller.py: 937: [stderr]: raise e 17:16:17 fslinstaller.py: 937: [stderr]: File "/usr/local/fsl/lib/python3.11/site-packages/mamba/mamba.py", line 949, in exception_converter 17:16:17 fslinstaller.py: 937: [stderr]: exit_code = _wrapped_main(args, **kwargs) 17:16:17 fslinstaller.py: 937: [stderr]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 17:16:17 fslinstaller.py: 937: [stderr]: File "/usr/local/fsl/lib/python3.11/site-packages/mamba/mamba.py", line 895, in _wrapped_main 17:16:17 fslinstaller.py: 937: [stderr]: result = do_call(parsed_args, p) 17:16:17 fslinstaller.py: 937: [stderr]: ^^^^^^^^^^^^^^^^^^^^^^^ 17:16:17 fslinstaller.py: 937: [stderr]: File "/usr/local/fsl/lib/python3.11/site-packages/mamba/mamba.py", line 758, in do_call 17:16:17 fslinstaller.py: 937: [stderr]: exit_code = clean(args, parser) 17:16:17 fslinstaller.py: 937: [stderr]: ^^^^^^^^^^^^^^^^^^^ 17:16:17 fslinstaller.py: 937: [stderr]: File "/usr/local/fsl/lib/python3.11/site-packages/mamba/mamba.py", line 701, in clean 17:16:17 fslinstaller.py: 937: [stderr]: module = import_module("conda.cli" + relative_mod, name.rsplit(".", 1)[0]) 17:16:17 fslinstaller.py: 937: [stderr]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 17:16:17 fslinstaller.py: 937: [stderr]: File "/usr/local/fsl/lib/python3.11/importlib/init.py", line 126, in import_module 17:16:17 fslinstaller.py: 937: [stderr]: return _bootstrap._gcd_import(name[level:], package, level) 17:16:17 fslinstaller.py: 937: [stderr]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 17:16:17 fslinstaller.py: 937: [stderr]: File "", line 1204, in _gcd_import
17:16:17 fslinstaller.py: 937: [stderr]: File "", line 1176, in _find_and_load
17:16:17 fslinstaller.py: 937: [stderr]: File "", line 1126, in _find_and_load_unlocked
17:16:17 fslinstaller.py: 937: [stderr]: File "", line 241, in _call_with_frames_removed
17:16:17 fslinstaller.py: 937: [stderr]: File "", line 1204, in _gcd_import
17:16:17 fslinstaller.py: 937: [stderr]: File "", line 1176, in _find_and_load
17:16:17 fslinstaller.py: 937: [stderr]: File "", line 1126, in _find_and_load_unlocked
17:16:17 fslinstaller.py: 937: [stderr]: File "", line 241, in _call_with_frames_removed
17:16:17 fslinstaller.py: 937: [stderr]: File "", line 1204, in _gcd_import
17:16:17 fslinstaller.py: 937: [stderr]: File "", line 1176, in _find_and_load
17:16:17 fslinstaller.py: 937: [stderr]: File "", line 1140, in _find_and_load_unlocked
17:16:17 fslinstaller.py: 937: [stderr]: ModuleNotFoundError: No module named 'conda.cliconda'
17:16:17 fslinstaller.py: 937: [stderr]:
17:16:17 fslinstaller.py: 937: [stderr]:
17:16:17 fslinstaller.py: 937: [stderr]: CONDA_ROOT=/usr/local/fsl
17:16:17 fslinstaller.py: 937: [stderr]: CURL_CA_BUNDLE=
17:16:17 fslinstaller.py: 937: [stderr]: LD_PRELOAD=
17:16:17 fslinstaller.py: 937: [stderr]: PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
17:16:17 fslinstaller.py: 937: [stderr]: REQUESTS_CA_BUNDLE=
17:16:17 fslinstaller.py: 937: [stderr]: SSL_CERT_FILE=
17:16:17 fslinstaller.py: 937: [stderr]: SUDO_COMMAND=/usr/bin/bash
17:16:17 fslinstaller.py: 937: [stderr]: SUDO_GID=0
17:16:17 fslinstaller.py: 937: [stderr]: SUDO_UID=0
17:16:17 fslinstaller.py: 937: [stderr]: SUDO_USER=root
17:16:17 fslinstaller.py: 937: [stderr]:
17:16:17 fslinstaller.py: 937: [stderr]: active environment : None
17:16:17 fslinstaller.py: 937: [stderr]: user config file : /home/dnanexus/.condarc
17:16:17 fslinstaller.py: 937: [stderr]: populated config files : /usr/local/fsl/.condarc
17:16:17 fslinstaller.py: 937: [stderr]: conda version : 23.11.0
17:16:17 fslinstaller.py: 937: [stderr]: conda-build version : not installed
17:16:17 fslinstaller.py: 937: [stderr]: python version : 3.11.6.final.0
17:16:17 fslinstaller.py: 937: [stderr]: solver : libmamba (default)
17:16:17 fslinstaller.py: 937: [stderr]: virtual packages : __archspec=1=skylake_avx512
17:16:17 fslinstaller.py: 937: [stderr]: conda=23.11.0=0
17:16:17 fslinstaller.py: 937: [stderr]: glibc=2.31=0
17:16:17 fslinstaller.py: 937: [stderr]: linux=5.15.0=0
17:16:17 fslinstaller.py: 937: [stderr]: unix=0=0
17:16:17 fslinstaller.py: 937: [stderr]: base environment : /usr/local/fsl (writable)
17:16:17 fslinstaller.py: 937: [stderr]: conda av data dir : /usr/local/fsl/etc/conda
17:16:17 fslinstaller.py: 937: [stderr]: conda av metadata url : None
17:16:17 fslinstaller.py: 937: [stderr]: channel URLs : https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64
17:16:17 fslinstaller.py: 937: [stderr]: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/noarch
17:16:17 fslinstaller.py: 937: [stderr]: https://conda.anaconda.org/conda-forge/linux-64
17:16:17 fslinstaller.py: 937: [stderr]: https://conda.anaconda.org/conda-forge/noarch
17:16:17 fslinstaller.py: 937: [stderr]: package cache : /usr/local/fsl/pkgs
17:16:17 fslinstaller.py: 937: [stderr]: envs directories : /usr/local/fsl/envs
17:16:17 fslinstaller.py: 937: [stderr]: /home/dnanexus/.conda/envs
17:16:17 fslinstaller.py: 937: [stderr]: platform : linux-64
17:16:17 fslinstaller.py: 937: [stderr]: user-agent : conda/23.11.0 requests/2.31.0 CPython/3.11.6 Linux/5.15.0-1050-aws ubuntu/20.04.6 glibc/2.31 solver/libmamba conda-libmamba-solver/23.11.1 libmambapy/1.5.4
17:16:17 fslinstaller.py: 937: [stderr]: UID:GID : 0:0
17:16:17 fslinstaller.py: 937: [stderr]: netrc file : None
17:16:17 fslinstaller.py: 937: [stderr]: offline mode : False
17:16:17 fslinstaller.py: 937: [stderr]:
17:16:17 fslinstaller.py: 937: [stderr]:
17:16:17 fslinstaller.py: 937: [stderr]: An unexpected error has occurred. Conda has prepared the above report.
17:16:17 fslinstaller.py: 937: [stderr]: If you suspect this error is being caused by a malfunctioning plugin,
17:16:17 fslinstaller.py: 937: [stderr]: consider using the --no-plugins option to turn off plugins.
17:16:17 fslinstaller.py: 937: [stderr]:
17:16:17 fslinstaller.py: 937: [stderr]: Example: conda --no-plugins install
17:16:17 fslinstaller.py: 937: [stderr]:
17:16:17 fslinstaller.py: 937: [stderr]: Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
17:16:17 fslinstaller.py: 937: [stderr]: the command line to run the command without plugins enabled.
17:16:17 fslinstaller.py: 937: [stderr]:
17:16:17 fslinstaller.py: 937: [stderr]: Example: CONDA_NO_PLUGINS=true conda install
17:16:17 fslinstaller.py: 937: [stderr]:
17:16:17 fslinstaller.py: 167:
ERROR occurred during installation!
17:16:17 fslinstaller.py: 167: This command returned an error: /usr/local/fsl/bin/mamba clean -y --all
$ /usr/local/fsl/bin/mamba clean -y --all17:16:17 fslinstaller.py: 937: [stderr]: 17:16:17 fslinstaller.py: 937: [stderr]: environment variables: 17:16:17 fslinstaller.py: 937: [stderr]: CIO_TEST=17:16:17 fslinstaller.py:2309: File "/tmp/fslinstaller.py", line 2301, in handle_error yield File "/tmp/fslinstaller.py", line 2401, in main post_install_cleanup(ctx, tmpdir) File "/tmp/fslinstaller.py", line 1824, in post_install_cleanup ctx.run(Process.check_call, cmd) File "/tmp/fslinstaller.py", line 1384, in run return process_func(admin=self.need_admin, File "/tmp/fslinstaller.py", line 845, in check_call raise RuntimeError('This command returned an error: ' + cmd)
17:16:17 fslinstaller.py: 167: Removing failed installation directory /usr/local/fsl 17:16:17 fslinstaller.py: 768: Running rm -r /usr/local/fsl [as admin: False]