Import scib error "but is an incompatible architecture (have 'x86_64', need 'arm64e" MacOXS Monterrey 12.5.1 with Apple M1 ultra

[DRSEI]

Hello evenyone

I was able to install the scib without any issue but i can't import scib .
The full error is below

`OSError: cannot load library '/Library/Frameworks/R.framework/Resources/lib/libR.dylib': dlopen(/Library/Frameworks/R.framework/Resources/lib/libR.dylib, 0x0002): tried: 

'/Library/Frameworks/R.framework/Resources/lib/libR.dylib' (mach-o file, but is an incompatible architecture (have (x86_64), need (arm64e))), 

'/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libR.dylib' (mach-o file, but is an incompatible architecture (have (x86_64), need (arm64e)))`

These are the machine details.

_Session information _

Click to view session information
-----
harmony             0.1.7
numba               0.56.0
numpy               1.22.4
pandas              1.4.3
scanpy              1.9.1
sctoolkit           NA
session_info        1.0.0
sklearn             1.1.2
torchvision         0.13.1
tqdm                4.64.0
-----
Click to view modules imported as dependencies
PIL                 9.2.0
anndata             0.8.0
appnope             0.1.3
asttokens           NA
backcall            0.2.0
beta_ufunc          NA
binom_ufunc         NA
certifi             2022.06.15
cffi                1.15.1
charset_normalizer  2.1.1
cycler              0.10.0
cython_runtime      NA
dateutil            2.8.2
debugpy             1.6.2
decorator           5.1.1
defusedxml          0.7.1
entrypoints         0.4
executing           0.9.1
fontTools           4.35.0
h5py                3.7.0
hypergeom_ufunc     NA
idna                3.3
igraph              0.9.11
imageio             2.21.1
ipykernel           6.15.1
ipython_genutils    0.2.0
ipywidgets          7.7.1
jedi                0.18.1
joblib              1.1.0
kiwisolver          1.4.4
llvmlite            0.39.0
lxml                4.9.1
matplotlib          3.5.3
matplotlib_inline   NA
mizani              0.7.4
mpl_toolkits        NA
natsort             8.1.0
nbinom_ufunc        NA
ncf_ufunc           NA
packaging           21.3
palettable          3.3.0
parso               0.8.3
patsy               0.5.2
pexpect             4.8.0
pickleshare         0.7.5
pkg_resources       NA
plotnine            0.9.0
prompt_toolkit      3.0.30
psutil              5.9.1
ptyprocess          0.7.0
pure_eval           0.2.2
pydev_ipython       NA
pydevconsole        NA
pydevd              2.8.0
pydevd_file_utils   NA
pydevd_plugins      NA
pydevd_tracing      NA
pygments            2.12.0
pyparsing           3.0.9
pytz                2022.2.1
requests            2.28.1
rpy2                3.4.2
scipy               1.9.0
seaborn             0.11.2
six                 1.16.0
skimage             0.19.3
stack_data          0.3.0
statsmodels         0.13.2
texttable           1.6.4
threadpoolctl       3.1.0
tifffile            2022.8.12
torch               1.12.1
tornado             6.2
traitlets           5.3.0
typing_extensions   NA
urllib3             1.26.11
wcwidth             0.2.5
zmq                 23.2.1
-----
IPython             8.4.0
jupyter_client      7.3.4
jupyter_core        4.11.1
notebook            6.4.12
-----
Python 3.10.5 (v3.10.5:f377153967, Jun  6 2022, 12:36:10) [Clang 13.0.0 (clang-1300.0.29.30)]
macOS-12.5.1-arm64-arm-64bit
-----
Session information updated at 2022-08-21 20:34

Appriciated your help.

[mumichae]

Hi,
this might be related to rpy2. Could you check if you can install and use rpy2 as intended? You also need a fully functional R instance on your system (or through conda), if you haven't set it up already.

[mumichae]

If you're having issues with R and python, I suggest you use conda/mamba.
The scib pipeline has some ready-to-use conda environment yaml files.

A more minimal setup would be:

conda env create -n scib -c conda-forge python=3.9 r-base=4 r-devtools
conda activate scib
pip install scib

which worked for me on a M1 Macbook