support for arm64 or work around

[harshameghadri]

Hi,

Firstly, thank you for creating the package and the effort it requires to maintain it.

I have recently switched from intel mac to a m1 mac with arm64. As I see now that there is no native package for pyranges/ncls for arm64. is there a work around so I can try it out on m1?

I don't have access to an intel or x86_64 system for the project I am working on.

---

ImportError Traceback (most recent call last)
Cell In [19], line 1
----> 1 import pyranges as pr

File /opt/homebrew/lib/python3.9/site-packages/pyranges/init.py:17
15 from pyranges.methods.concat import concat
16 from pyranges.multioverlap import count_overlaps
---> 17 from pyranges.pyranges_main import PyRanges
18 from pyranges.readers import read_bam, read_bed, read_bigwig, read_gff3, read_gtf # NOQA: F401
20 version = pkg_resources.get_distribution("pyranges").version

File /opt/homebrew/lib/python3.9/site-packages/pyranges/pyranges_main.py:8
5 from natsort import natsorted # type: ignore
7 import pyranges as pr
----> 8 from pyranges.methods.intersection import _intersection, _overlap
9 from pyranges.multithreaded import (
10 _extend,
11 _extend_grp,
(...)
16 pyrange_apply_single,
17 )
18 from pyranges.tostring2 import tostring

File /opt/homebrew/lib/python3.9/site-packages/pyranges/methods/intersection.py:3
1 import numpy as np
2 import pandas as pd
----> 3 from ncls import NCLS # type: ignore
6 def _intersection(scdf, ocdf, **kwargs):
7 how = kwargs["how"]

File ~/miniforge3/envs/torch-gpu/lib/python3.9/site-packages/ncls/init.py:1
----> 1 from ncls.src.ncls import NCLS64
2 from ncls.src.ncls32 import NCLS32
4 import numpy as np

ImportError: dlopen(/Users/sriharshameghadri/miniforge3/envs/torch-gpu/lib/python3.9/site-packages/ncls/src/ncls.cpython-39-darwin.so, 0x0002): tried: '/Users/sriharshameghadri/miniforge3/envs/torch-gpu/lib/python3.9/site-packages/ncls/src/ncls.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/sriharshameghadri/miniforge3/envs/torch-gpu/lib/python3.9/site-packages/ncls/src/ncls.cpython-39-darwin.so' (no such file), '/Users/sriharshameghadri/miniforge3/envs/torch-gpu/lib/python3.9/site-packages/ncls/src/ncls.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))

[marco-mariotti]

Hi, I routinely work with pyranges on my M2 mac. Do you have Rosetta2 installed? If not, install it. Normally the OS would ask you automatically to install it upon necessity, but probably this does not happen when the need arises through command line interactions. If the problem persists, try to install conda (miniconda) or mamba, and install pyranges from the bioconda channel. This is how it worked for me at the first attempt.

…

On Fri, Jul 21, 2023 at 11:09 AM Sri Harsha Meghadri < ***@***.***> wrote: Hi, Firstly, thank you for creating the package and the effort it requires to maintain it. I have recently switched from intel mac to a m1 mac with arm64. As I see now that there is no native package for pyranges/ncls for arm64. is there a work around so I can try it out on m1? I don't have access to an intel or x86_64 system for the project I am working on. ------------------------------ ImportError Traceback (most recent call last) Cell In [19], line 1 ----> 1 import pyranges as pr File /opt/homebrew/lib/python3.9/site-packages/pyranges/*init*.py:17 15 from pyranges.methods.concat import concat 16 from pyranges.multioverlap import count_overlaps ---> 17 from pyranges.pyranges_main import PyRanges 18 from pyranges.readers import read_bam, read_bed, read_bigwig, read_gff3, read_gtf # NOQA: F401 20 *version* = pkg_resources.get_distribution("pyranges").version File /opt/homebrew/lib/python3.9/site-packages/pyranges/pyranges_main.py:8 5 from natsort import natsorted # type: ignore 7 import pyranges as pr ----> 8 from pyranges.methods.intersection import _intersection, _overlap 9 from pyranges.multithreaded import ( 10 _extend, 11 _extend_grp, (...) 16 pyrange_apply_single, 17 ) 18 from pyranges.tostring2 import tostring File /opt/homebrew/lib/python3.9/site-packages/pyranges/methods/intersection.py:3 1 import numpy as np 2 import pandas as pd ----> 3 from ncls import NCLS # type: ignore 6 def _intersection(scdf, ocdf, **kwargs): 7 how = kwargs["how"] File ~/miniforge3/envs/torch-gpu/lib/python3.9/site-packages/ncls/*init* .py:1 ----> 1 from ncls.src.ncls import NCLS64 2 from ncls.src.ncls32 import NCLS32 4 import numpy as np ImportError: dlopen(/Users/sriharshameghadri/miniforge3/envs/torch-gpu/lib/python3.9/site-packages/ncls/src/ ncls.cpython-39-darwin.so, 0x0002): tried: '/Users/sriharshameghadri/miniforge3/envs/torch-gpu/lib/python3.9/site-packages/ncls/src/ ncls.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/sriharshameghadri/miniforge3/envs/torch-gpu/lib/python3.9/site-packages/ncls/src/ ncls.cpython-39-darwin.so' (no such file), '/Users/sriharshameghadri/miniforge3/envs/torch-gpu/lib/python3.9/site-packages/ncls/src/ ncls.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')) — Reply to this email directly, view it on GitHub <#346>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACTXRIFU5XNRGJGAY7E6Q7LXRJBMFANCNFSM6AAAAAA2SR5PXU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Marco Mariotti Ramón y Cajal Fellow, Group Leader Department of Genetics, Microbiology and Statistics Universitat de Barcelona