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Conda install nf-core cli on mac arm64 fails #3303

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swingingsimian opened this issue Nov 28, 2024 · 0 comments
Open

Conda install nf-core cli on mac arm64 fails #3303

swingingsimian opened this issue Nov 28, 2024 · 0 comments
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swingingsimian commented Nov 28, 2024

Description of the bug

Following the instructions here: https://nf-co.re/docs/nf-core-tools/installation#bioconda i.e. conda install nf-core, fails with the following error:

Error while loading conda entry point: conda-libmamba-solver (dlopen(/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/bindings.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.20.dylib                                                                                                                                                              
  Referenced from: <496442DC-0EDE-3705-A2B5-401A4FC0D733> /Users/nathanjohnson/miniconda3/lib/libmamba.2.0.0.dylib                                                                               
  Reason: tried: '/Users/nathanjohnson/miniconda3/lib/libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/../../../libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/../../../libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/bin/../lib/libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/bin/../lib/libarchive.20.dylib' (no such file), '/usr/local/lib/libarchive.20.dylib' (no such file), '/usr/lib/libarchive.20.dylib' (no such file, not in dyld cache))  

A little googling led me to try the following to force install of the dependencies from the same channel, this takes a while to find a successful resolution, but does eventually work:

conda install --solver=classic conda-forge::conda-libmamba-solver conda-forge::libmamba conda-forge::libmambapy conda-forge::libarchive

This is on a very new M4 mac:

uname -a
Darwin Nathans-MBP.fritz.box 24.1.0 Darwin Kernel Version 24.1.0: Thu Nov 14 18:15:21 PST 2024; root:xnu-11215.41.3~13/RELEASE_ARM64_T6041 arm64 arm Darwin

Command used and terminal output

conda install nf-core
...
Error while loading conda entry point: conda-libmamba-solver (dlopen(/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/bindings.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.20.dylib                                                                                                                                                              
  Referenced from: <496442DC-0EDE-3705-A2B5-401A4FC0D733> /Users/nathanjohnson/miniconda3/lib/libmamba.2.0.0.dylib                                                                               
  Reason: tried: '/Users/nathanjohnson/miniconda3/lib/libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/../../../libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/lib/python3.12/site-packages/libmambapy/../../../libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/bin/../lib/libarchive.20.dylib' (no such file), '/Users/nathanjohnson/miniconda3/bin/../lib/libarchive.20.dylib' (no such file), '/usr/local/lib/libarchive.20.dylib' (no such file), '/usr/lib/libarchive.20.dylib' (no such file, not in dyld cache))  

System information

No response

@swingingsimian swingingsimian added the bug Something isn't working label Nov 28, 2024
@swingingsimian swingingsimian changed the title Conda install on mac arm64 fails Conda install nf-core cli on mac arm64 fails Nov 28, 2024
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