open-discussion > RE: FSL Error in Mac Ventura 13.1
Jul 17, 2023  04:07 PM | Alex P
RE: FSL Error in Mac Ventura 13.1

Has anyone any clue about this error?


I encountered the same error on a macbook m1 Ventura 13.4.1, installing the fsl-6.0.7_macos-M1. 


The log is as it follows: "


21:06:27 fslinstaller.py: 933:  [stderr]: # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]:     Traceback (most recent call last):
21:06:27 fslinstaller.py: 933:  [stderr]:       File "/Users/$Usern/fsl/lib/python3.10/site-packages/conda/exceptions.py", line 1124, in __call__
21:06:27 fslinstaller.py: 933:  [stderr]:         return func(*args, **kwargs)
21:06:27 fslinstaller.py: 933:  [stderr]:       File "/Users/$User/fsl/lib/python3.10/site-packages/conda_env/cli/main.py", line 78, in do_call
21:06:27 fslinstaller.py: 933:  [stderr]:         exit_code = getattr(module, func_name)(args, parser)
21:06:27 fslinstaller.py: 933:  [stderr]:       File "/Users/$User/fsl/lib/python3.10/site-packages/conda/notices/core.py", line 109, in wrapper
21:06:27 fslinstaller.py: 933:  [stderr]:         return func(*args, **kwargs)
21:06:27 fslinstaller.py: 933:  [stderr]:       File "/Users/$User/fsl/lib/python3.10/site-packages/conda_env/cli/main_update.py", line 132, in execute
21:06:27 fslinstaller.py: 933:  [stderr]:         result[installer_type] = installer.install(prefix, specs, args, env)
21:06:27 fslinstaller.py: 933:  [stderr]:       File "/Users/$User/fsl/lib/python3.10/site-packages/mamba/mamba_env.py", line 153, in mamba_install
21:06:27 fslinstaller.py: 933:  [stderr]:         transaction.fetch_extract_packages()
21:06:27 fslinstaller.py: 933:  [stderr]:     RuntimeError: Download error (28) Timeout was reached [https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/osx-arm64/fsl-basisfield-2203.1-hcb8d3e5_4.tar.bz2]
21:06:27 fslinstaller.py: 933:  [stderr]:     SSL connection timeout
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]: `$ /Users/$User/fsl/bin/mamba update -n base -f /private/var/folders/8x/3s_r17r166jgs59n1tl1zvhh0000gn/T/tmp316qp81t/fsl-6.0.7_macos-M1.yml`
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]:   environment variables:
21:06:27 fslinstaller.py: 933:  [stderr]:                  CIO_TEST=<not set>
21:06:27 fslinstaller.py: 933:  [stderr]:   CONDA_AUTO_UPDATE_CONDA=false
21:06:27 fslinstaller.py: 933:  [stderr]:                CONDA_ROOT=/Users/$User/fsl
21:06:27 fslinstaller.py: 933:  [stderr]:                     CPATH=/usr/local/include
21:06:27 fslinstaller.py: 933:  [stderr]:            CURL_CA_BUNDLE=<not set>
21:06:27 fslinstaller.py: 933:  [stderr]:                  INFOPATH=/opt/homebrew/share/info:
21:06:27 fslinstaller.py: 933:  [stderr]:                LD_PRELOAD=<not set>
21:06:27 fslinstaller.py: 933:  [stderr]:              LIBRARY_PATH=/usr/local/lib
21:06:27 fslinstaller.py: 933:  [stderr]:                   MANPATH=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/share/man:/Lib
21:06:27 fslinstaller.py: 933:  [stderr]:                           rary/Developer/CommandLineTools/usr/share/man:/Library/Developer/Comma
21:06:27 fslinstaller.py: 933:  [stderr]:                           ndLineTools/Toolchains/XcodeDefault.xctoolchain/usr/share/man:/opt/hom
21:06:27 fslinstaller.py: 933:  [stderr]:                           ebrew/share/man::
21:06:27 fslinstaller.py: 933:  [stderr]:                      PATH=/Library/Frameworks/Python.framework/Versions/2.7/bin:/opt/homebrew/bi
21:06:27 fslinstaller.py: 933:  [stderr]:                           n:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr
21:06:27 fslinstaller.py: 933:  [stderr]:                           /bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/var/run/com.apple.security.cry
21:06:27 fslinstaller.py: 933:  [stderr]:                           ptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security
21:06:27 fslinstaller.py: 933:  [stderr]:                           .cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.c
21:06:27 fslinstaller.py: 933:  [stderr]:                           ryptexd/codex.system/bootstrap/usr/appleinternal/bin
21:06:27 fslinstaller.py: 933:  [stderr]:        REQUESTS_CA_BUNDLE=<not set>
21:06:27 fslinstaller.py: 933:  [stderr]:             SSL_CERT_FILE=<not set>
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]:      active environment : None
21:06:27 fslinstaller.py: 933:  [stderr]:        user config file : /Users/$User/.condarc
21:06:27 fslinstaller.py: 933:  [stderr]:  populated config files : /Users/$User/fsl/.condarc
21:06:27 fslinstaller.py: 933:  [stderr]:           conda version : 23.1.0
21:06:27 fslinstaller.py: 933:  [stderr]:     conda-build version : not installed
21:06:27 fslinstaller.py: 933:  [stderr]:          python version : 3.10.12.final.0
21:06:27 fslinstaller.py: 933:  [stderr]:        virtual packages : __archspec=1=arm64
21:06:27 fslinstaller.py: 933:  [stderr]:                           __osx=13.4.1=0
21:06:27 fslinstaller.py: 933:  [stderr]:                           __unix=0=0
21:06:27 fslinstaller.py: 933:  [stderr]:        base environment : /Users/$User/fsl  (writable)
21:06:27 fslinstaller.py: 933:  [stderr]:       conda av data dir : /Users/$User/fsl/etc/conda
21:06:27 fslinstaller.py: 933:  [stderr]:   conda av metadata url : None
21:06:27 fslinstaller.py: 933:  [stderr]:            channel URLs : https://fsl.fmrib.ox.ac.uk/fsldownloads/...
21:06:27 fslinstaller.py: 933:  [stderr]:                           https://fsl.fmrib.ox.ac.uk/fsldownloads/...
21:06:27 fslinstaller.py: 933:  [stderr]:                           https://conda.anaconda.org/conda-forge/o...
21:06:27 fslinstaller.py: 933:  [stderr]:                           https://conda.anaconda.org/conda-forge/n...
21:06:27 fslinstaller.py: 933:  [stderr]:           package cache : /Users/$User/fsl/pkgs
21:06:27 fslinstaller.py: 933:  [stderr]:        envs directories : /Users/$User/fsl/envs
21:06:27 fslinstaller.py: 933:  [stderr]:                           /Users/$User/.conda/envs
21:06:27 fslinstaller.py: 933:  [stderr]:                platform : osx-arm64
21:06:27 fslinstaller.py: 933:  [stderr]:              user-agent : conda/23.1.0 requests/2.31.0 CPython/3.10.12 Darwin/22.5.0 OSX/13.4.1
21:06:27 fslinstaller.py: 933:  [stderr]:                 UID:GID : 501:20
21:06:27 fslinstaller.py: 933:  [stderr]:              netrc file : None
21:06:27 fslinstaller.py: 933:  [stderr]:            offline mode : False
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:27 fslinstaller.py: 933:  [stderr]: An unexpected error has occurred. Conda has prepared the above report.
21:06:27 fslinstaller.py: 933:  [stderr]: 
21:06:28 fslinstaller.py: 167: 
ERROR occurred during installation!
21:06:28 fslinstaller.py: 167:     This command returned an error: /Users/$User/fsl/bin/mamba env update -n base -f /private/var/folders/8x/3s_r17r166jgs59n1tl1zvhh0000gn/T/tmp316qp81t/fsl-6.0.7_macos-M1.yml


21:06:28 fslinstaller.py:2297:   File "/Users/$User/Downloads/fslinstaller.py", line 2289, in handle_error
    yield
  File "/Users/$User/Downloads/fslinstaller.py", line 2387, in main
    install_fsl(ctx)
  File "/Users/$User/Downloads/fslinstaller.py", line 1786, in install_fsl
    ctx.run(Process.monitor_progress, cmd,
  File "/Users/$User/Downloads/fslinstaller.py", line 1377, in run
    return process_func(admin=self.need_admin,
  File "/Users/$User/Downloads/fslinstaller.py", line 905, in monitor_progress
    raise RuntimeError('This command returned '


21:06:28 fslinstaller.py: 167: Removing failed installation directory /Users/$User/fsl
21:06:28 fslinstaller.py: 764: Running rm -r /Users/$User/fsl [as admin: False]


".


I tried using Python3 (different versions) and Python2.7.


Thank you for any suggestion.

Threaded View

TitleAuthorDate
nsav Jan 23, 2023
nora mila Dec 25, 2023
Chris Klink Nov 30, 2023
RE: FSL Error in Mac Ventura 13.1
Alex P Jul 17, 2023
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