search

mapping-commons / sssom-py

Python toolkit for SSSOM mapping format
https://mapping-commons.github.io/sssom-py/index.html#
MIT License
48 stars 10 forks source link

`poetry install` `arm64` architecture err #524

Closed joeflack4 closed 3 months ago

joeflack4 commented 3 months ago

Overview

I'm using Apple Silicon (arm64), and I'm trying to create a fresh environment but getting an error.

To replicate

  1. Have an arm64 based machine
  2. virtualenv env
  3. source env/bin/activate
  4. poetry install
  5. Observe error

The error

incompatible architecture (have 'x86_64', need 'arm64')

Log

``` poetry install Installing dependencies from lock file Package operations: 54 installs, 8 updates, 0 removals • Installing attrs (23.2.0) • Installing exceptiongroup (1.2.0) • Installing iniconfig (2.0.0) • Updating packaging (21.3 -> 23.2) • Updating pluggy (1.0.0 -> 1.3.0) • Installing rpds-py (0.16.2) • Installing tomli (2.0.1) • Installing typing-extensions (4.9.0) • Installing annotated-types (0.6.0) • Installing certifi (2023.11.17) • Installing charset-normalizer (3.3.2) • Installing idna (3.6) • Installing pydantic-core (2.14.6) • Installing pytest (7.4.4) • Installing referencing (0.32.1) • Installing sortedcontainers (2.4.0) • Installing urllib3 (2.1.0) • Installing zipp (3.17.0) • Installing click (8.1.7) • Installing greenlet (2.0.1): Failed ImportError dlopen(/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/_cffi_backend.cpython-310-darwin.so, 0x0002): tried: '/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/_cffi_backend.cpython-310-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/_cffi_backend.cpython-310-darwin.so' (no such file), '/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/_cffi_backend.cpython-310-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')) at ~/Library/Python/3.10/lib/python/site-packages/xattr/lib.py:7 in 3│ 4│ from .compat import fs_encode 5│ 6│ try: → 7│ from ._lib import lib, ffi 8│ except ImportError: 9│ from .lib_build import ffi, c_source 10│ lib = ffi.verify(c_source) 11│ The following error occurred when trying to handle this error: FileNotFoundError [Errno 2] No such file or directory: '/Users/joeflack4/Library/Python/3.10/lib/python/site-packages/xattr/lib_build.h' at ~/Library/Python/3.10/lib/python/site-packages/xattr/lib_build.py:7 in 3│ from cffi import FFI 4│ 5│ PATH = os.path.dirname(__file__) 6│ → 7│ with open(os.path.join(PATH, 'lib_build.h')) as hf: 8│ c_header = hf.read() 9│ with open(os.path.join(PATH, 'lib_build.c')) as cf: 10│ c_source = cf.read() 11│ Cannot install greenlet. • Installing hbreader (0.9.1) • Installing importlib-metadata (7.0.1) • Installing isodate (0.6.1) • Installing jsonschema-specifications (2023.12.1) • Installing pydantic (2.5.3) • Updating pyparsing (3.0.9 -> 3.1.1) • Installing pytest-logging (2015.11.4) • Installing pytrie (0.4.0) • Installing pyyaml (6.0.1) • Installing requests (2.31.0) • Installing wrapt (1.16.0) ```

Possible solutions

Somehow, I think pyproject.toml and/or poetry.lock has to have some change to accommodate multiple architectures.

What I tried

I think I hacked around this issue temporarily by:

  1. Deleting poetry.lock
  2. poetry install
  3. Restoring the original poetry.lock (not committing the new one created)
matentzn commented 3 months ago

Let's hope this is temporary - I have so far not ever had that problem, maybe this is a temporarily broken dependencies

cmungall commented 3 months ago

Looks like no one has used poetry update on this repo for a while. The lock has an old version of greenlet that didn’t distribute the wheel you need.

See also https://github.com/mapping-commons/sssom-py/issues/343

On Sun, Apr 28, 2024 at 2:55 AM Nico Matentzoglu @.***> wrote:

Let's hope this is temporary - I have so far not ever had that problem, maybe this is a temporarily broken dependencies

— Reply to this email directly, view it on GitHub https://github.com/mapping-commons/sssom-py/issues/524#issuecomment-2081416650, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOOABLYPKUOGJCKHO4TY7TBQXAVCNFSM6AAAAABG4O2EACVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBRGQYTMNRVGA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

matentzn commented 3 months ago

Try again @joeflack4, made a new release

joeflack4 commented 3 months ago

@Chris yeah I figured it was either removed or just that that version was never released for arm64. I see you encountered a similar / same issue.

@matentzn I tried poetry install w/ your new update on master and it worked! Thanks!

Gonna close this now, but this is also a good time to bring up a similar issue I'm experiencing: sssom is not a package. I brought it up on slack first, but perhaps it should also be a GH issue.