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Error while installing Bonito.

Open AzlanNI opened this issue 2 years ago • 1 comments

Hello everyone!

I am currently trying to install bonito on my Mac and on the HPC of our University.

If i try the Developer Quickstart way :

$ git clone https://github.com/nanoporetech/bonito.git # or fork first and clone that $ cd bonito $ python3 -m venv venv3 $ source venv3/bin/activate (venv3) $ pip install --upgrade pip (venv3) $ pip install -r requirements.txt (venv3) $ python setup.py develop

On my Mac i get an Error while installing requirements.txt which looks like:

Collecting requests==2.25.1 Using cached requests-2.25.1-py2.py3-none-any.whl (61 kB) ERROR: Could not find a version that satisfies the requirement ont-koi==0.0.9 (from versions: none) ERROR: No matching distribution found for ont-koi==0.0.9

Maybe someone has seen a similar Error and can help me out.

Also if i try to use the PyPi Mirror of our HPC to install bonito i always get the Error :

  ############################
  # Package would be ignored #
  ############################
  Python recognizes 'remora.trained_models' as an importable package, however it is
  included in the distribution as "data".
  This behavior is likely to change in future versions of setuptools (and
  therefore is considered deprecated).

  Please make sure that 'remora.trained_models' is included as a package by using
  setuptools' `packages` configuration field or the proper discovery methods
  (for example by using `find_namespace_packages(...)`/`find_namespace:`
  instead of `find_packages(...)`/`find:`).

  You can read more about "package discovery" and "data files" on setuptools
  documentation page.

!!

check.warn(importable)

error: command 'icc' failed: No such file or directory [end of output]

I would appreciate some help!

Kind regards,

Azlan

AzlanNI avatar Jun 01 '22 12:06 AzlanNI

I have the same issue, any update on it?

jmbreda avatar Aug 15 '22 11:08 jmbreda

Bonito does not support Mac - please use dorado instead https://github.com/nanoporetech/dorado

iiSeymour avatar May 31 '23 14:05 iiSeymour