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etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
773 stars 216 forks source link

M1 MacBook Pro Installation Problem (osx-arm64?) #656

Open VeritatemAmo opened 1 year ago

VeritatemAmo commented 1 year ago

I have recently gotten a M1 MacBook Pro as a work computer and tried to install ete3 on it. However, running the commend in terminal: conda install -c etetoolkit ete3_external_apps or conda install -c etetoolkit ete_toolchain gives me the error message:

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels:

I didn't have a problem installing ete3 with my old MacBook Pro with intel i5 chips. I wonder if it is because ete_toolchain only exist in osx-64 conda channel but not osx-arm64 channel? BTW, I also don't see a ete_toolchain on pypi.org.

VeritatemAmo commented 1 year ago

I found a solution to the problem: run pip install -I ete3 instead of installing from conda. This seems to install the dependents as well (maybe, since it's working now).

Neato-Nick commented 1 year ago

Also on an M1 chip, unfortunately this did not work for me. I get this dreaded error

Traceback (most recent call last):
  File "/Users/nick/miniconda3/bin/ete3", line 5, in <module>
    from ete3.tools.ete import main
  File "/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/tools/ete.py", line 55, in <module>
    from . import (ete_split, ete_expand, ete_annotate, ete_ncbiquery, ete_view,
  File "/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/tools/ete_view.py", line 48, in <module>
    from .. import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle, CircleFace, AttrFace,
ImportError: cannot import name 'TextFace' from 'ete3' (/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/__init__.py)

And I did try this https://github.com/etetoolkit/ete/issues/354

VeritatemAmo commented 1 year ago

Also on an M1 chip, unfortunately this did not work for me. I get this dreaded error

Traceback (most recent call last):
  File "/Users/nick/miniconda3/bin/ete3", line 5, in <module>
    from ete3.tools.ete import main
  File "/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/tools/ete.py", line 55, in <module>
    from . import (ete_split, ete_expand, ete_annotate, ete_ncbiquery, ete_view,
  File "/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/tools/ete_view.py", line 48, in <module>
    from .. import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle, CircleFace, AttrFace,
ImportError: cannot import name 'TextFace' from 'ete3' (/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/__init__.py)

And I did try this #354

This might help: https://github.com/etetoolkit/ete/issues/195

Neato-Nick commented 1 year ago

I went down that road as well but pyqt4 doesn't compile because of its SIPS dependency, which is no longer available. Pyqt6 is on conda and did install successfully but did not fix the issue

On Tue, Feb 14, 2023, 8:58 PM Linhe Xu @.***> wrote:

Also on an M1 chip, unfortunately this did not work for me. I get this dreaded error

Traceback (most recent call last): File "/Users/nick/miniconda3/bin/ete3", line 5, in from ete3.tools.ete import main File "/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/tools/ete.py", line 55, in from . import (ete_split, ete_expand, ete_annotate, ete_ncbiquery, ete_view, File "/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/tools/ete_view.py", line 48, in from .. import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle, CircleFace, AttrFace, ImportError: cannot import name 'TextFace' from 'ete3' (/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/init.py)

And I did try this #354 https://github.com/etetoolkit/ete/issues/354

This might help: #195 https://github.com/etetoolkit/ete/issues/195

— Reply to this email directly, view it on GitHub https://github.com/etetoolkit/ete/issues/656#issuecomment-1430756249, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMUDUXJX7TXKVZK4VF7W5LWXRPAPANCNFSM6AAAAAASYMQFXA . You are receiving this because you commented.Message ID: @.***>

VeritatemAmo commented 1 year ago

I went down that road as well but pyqt4 doesn't compile because of its SIPS dependency, which is no longer available. Pyqt6 is on conda and did install successfully but did not fix the issue … On Tue, Feb 14, 2023, 8:58 PM Linhe Xu @.> wrote: Also on an M1 chip, unfortunately this did not work for me. I get this dreaded error Traceback (most recent call last): File "/Users/nick/miniconda3/bin/ete3", line 5, in from ete3.tools.ete import main File "/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/tools/ete.py", line 55, in from . import (ete_split, ete_expand, ete_annotate, ete_ncbiquery, ete_view, File "/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/tools/ete_view.py", line 48, in from .. import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle, CircleFace, AttrFace, ImportError: cannot import name 'TextFace' from 'ete3' (/Users/nick/miniconda3/lib/python3.10/site-packages/ete3/init.py) And I did try this #354 <#354> This might help: #195 <#195> — Reply to this email directly, view it on GitHub <#656 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABMUDUXJX7TXKVZK4VF7W5LWXRPAPANCNFSM6AAAAAASYMQFXA . You are receiving this because you commented.Message ID: @.>

Let me reopen this issue then.