Installation not working on ARM based mac

[stephanbitterwolf]

Hello and thanks for your time,

I tried installing eggnog-mapper locally on my M1 Mac but have been getting an error code that I was hoping someone here could help to resolve.

I run the command pip install eggnog-mapper and got the following error:

"-I/opt/homebrew/Caskroom/miniconda/base/include/python3.11 -c Bio/triemodule.c -o build/temp.macosx-11.1-arm64-cpython-311/Bio/triemodule.o Bio/triemodule.c:837:25: error: expression is not assignable Py_TYPE(&Trie_Type) = &PyType_Type;

      1 error generated.
      error: command '/usr/bin/clang' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for biopython
"

I'm sure this is because I am trying to install the program on the ARM-based M1 mac. I'd love if eggnog-mapper could run natively on my computer without needing to use Rosetta. Is Eggnog-mapper compatible with M1? 

[Cantalapiedra]

Hi @stephanbitterwolf ,

I cannot help you, because I don't own a Mac. Hopefully someone else may help you. Sorry for the inconveniences.

Best, Carlos

[iframst]

I'm encountering the same issue. Ill let you know if I solve it.

[Gr1m3y]

I have run into the same issue, failed to build wheel for biopython. Biopython installs fine on its own. M1 Mac as well, using Python 3.11.8. I will keep trying to figure it out, but up to this point, I am stumped.

[Gr1m3y]

I managed to get it running. Turns out to be an issue with the version in Biopython it seems. I downloaded the source from the repository and updated requirements.txt and setup.py to use Biopython v1.83 and installed with pip directly from the source code. I will try to run it to make sure that there are not other issues, but this seems to be the fix.

[iframst]

I managed to get it running. Turns out to be an issue with the version in Biopython it seems. I downloaded the source from the repository and updated requirements.txt and setup.py to use Biopython v1.83 and installed with pip directly from the source code. I will try to run it to make sure that there are not other issues, but this seems to be the fix.

I’ll try that this afternoon too and report back

[Cantalapiedra]

Was this issue solved? If so, I could try to document this on the eggnog-mapper's wiki

[Gr1m3y]

Was this issue solved? If so, I could try to document this on the eggnog-mapper's wiki

My solution bumping the Biopython version seems to have fixed it for me. At least so far, I haven't run into any issues and the annotations seemed to work fine.

[Chatchamew]

I have upgraded Biopython to version 1.83 using " pip install --upgrade biopython " and I still have the same problems with wheels for Biopython when I try to install eggnog-mapper. What should I do?