# Debugging Issue for Introduction to scvi-tools juytper notebook tutorial

**URL:** <https://discourse.scverse.org/t/debugging-issue-for-introduction-to-scvi-tools-juytper-notebook-tutorial/1514>\
**Category:** scvi-tools\
**Tags:** scvi\
**Created:** [June 13, 2023, 8:18pm UTC](https://discourse.scverse.org/t/debugging-issue-for-introduction-to-scvi-tools-juytper-notebook-tutorial/1514 "2023-06-13T20:18:48Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![Bakar](https://avatars.discourse-cdn.com/v4/letter/b/74df32/32.png) [@Bakar](https://discourse.scverse.org/u/Bakar)\
**Post date:** [June 13, 2023, 8:18pm UTC](https://discourse.scverse.org/t/debugging-issue-for-introduction-to-scvi-tools-juytper-notebook-tutorial/1514/1 "2023-06-13T20:18:48Z")

</div>

I am having issues addressing a error when trying to go through the [Introduction to scvi-tools](https://docs.scvi-tools.org/en/stable/tutorials/notebooks/api_overview.html) notebook on my personal computer.

An error surfaces when I try to run the following cell block:

```auto
# neighbors were already computed using scVI
sc.tl.leiden(adata, key_added="leiden_scVI", resolution=0.5)

```

 ![image](https://canada1.discourse-cdn.com/flex035/uploads/forum11/original/1X/b31228060fb8d1cec1d72a4739539f96783b0c3f.png)

```auto
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
File ~/anaconda3/lib/python3.10/site-packages/scanpy/tools/_leiden.py:108, in leiden(adata, resolution, restrict_to, random_state, key_added, adjacency, directed, use_weights, n_iterations, partition_type, neighbors_key, obsp, copy, **partition_kwargs)
    107 try:
--> 108 import leidenalg
    109 except ImportError:

File ~/anaconda3/lib/python3.10/site-packages/leidenalg/ __init__.py:35
      2 r""" This package implements the Leiden algorithm in ``C++`` and exposes it to
      3 python. It relies on ``(python-)igraph`` for it to function. Besides the
      4 relative flexibility of the implementation, it also scales well, and can be run
   (...)
     33 not immediately available in :func:`leidenalg.find_partition`.
     34 """
---> 35 from .functions import ALL_COMMS
     36 from .functions import ALL_NEIGH_COMMS

File ~/anaconda3/lib/python3.10/site-packages/leidenalg/functions.py:2
      1 import sys
----> 2 import igraph as _ig
      3 from . import _c_leiden

File ~/anaconda3/lib/python3.10/site-packages/igraph/ __init__.py:25
      6 __license__ = """
      7 Copyright (C) 2006- The igraph development team
      8 
   (...)
     22 02110-1301 USA
     23 """
---> 25 from igraph._igraph import (
     26 ADJ_DIRECTED,
     27 ADJ_LOWER,
     28 ADJ_MAX,
     29 ADJ_MIN,
     30 ADJ_PLUS,
     31 ADJ_UNDIRECTED,
     32 ADJ_UPPER,
     33 ALL,
     34 ARPACKOptions,
     35 BFSIter,
     36 BLISS_F,
     37 BLISS_FL,
     38 BLISS_FLM,
     39 BLISS_FM,
     40 BLISS_FS,
     41 BLISS_FSM,
     42 DFSIter,
     43 Edge,
     44 GET_ADJACENCY_BOTH,
     45 GET_ADJACENCY_LOWER,
     46 GET_ADJACENCY_UPPER,
     47 GraphBase,
     48 IN,
     49 InternalError,
     50 OUT,
     51 REWIRING_SIMPLE,
     52 REWIRING_SIMPLE_LOOPS,
     53 STAR_IN,
     54 STAR_MUTUAL,
     55 STAR_OUT,
     56 STAR_UNDIRECTED,
     57 STRONG,
     58 TRANSITIVITY_NAN,
     59 TRANSITIVITY_ZERO,
     60 TREE_IN,
     61 TREE_OUT,
     62 TREE_UNDIRECTED,
     63 Vertex,
     64 WEAK,
     65 arpack_options as default_arpack_options,
     66 community_to_membership,
     67 convex_hull,
     68 is_degree_sequence,
     69 is_graphical,
     70 is_graphical_degree_sequence,
     71 set_progress_handler,
     72 set_random_number_generator,
     73 set_status_handler,
     74 umap_compute_weights,
     75 __igraph_version__ ,
     76 )
     77 from igraph.adjacency import (
     78 _get_adjacency,
     79 _get_adjacency_sparse,
   (...)
     82 _get_inclist,
     83 )

ImportError: dlopen(/Users/bak/anaconda3/lib/python3.10/site-packages/igraph/_igraph.abi3.so, 0x000A): Library not loaded: @rpath/libblas.3.dylib
  Referenced from: <96A36561-4C61-39A1-9787-F499FDD5FD0E> /Users/bak/anaconda3/lib/python3.10/site-packages/igraph/_igraph.abi3.so
  Reason: tried: '/Users/bak/anaconda3/lib/python3.10/site-packages/igraph/../../../libblas.3.dylib' (no such file), '/Users/bak/anaconda3/lib/python3.10/site-packages/igraph/../../../libblas.3.dylib' (no such file), '/Users/bak/anaconda3/bin/../lib/libblas.3.dylib' (no such file), '/Users/bak/anaconda3/bin/../lib/libblas.3.dylib' (no such file), '/usr/local/lib/libblas.3.dylib' (no such file), '/usr/lib/libblas.3.dylib' (no such file, not in dyld cache)

During handling of the above exception, another exception occurred:

ImportError Traceback (most recent call last)
Cell In[24], line 2
      1 # neighbors were already computed using scVI
----> 2 sc.tl.leiden(adata, key_added="leiden_scVI", resolution=0.5)

File ~/anaconda3/lib/python3.10/site-packages/scanpy/tools/_leiden.py:110, in leiden(adata, resolution, restrict_to, random_state, key_added, adjacency, directed, use_weights, n_iterations, partition_type, neighbors_key, obsp, copy, **partition_kwargs)
    108 import leidenalg
    109 except ImportError:
--> 110 raise ImportError(
    111 'Please install the leiden algorithm: `conda install -c conda-forge leidenalg` or `pip3 install leidenalg`.'
    112 )
    113 partition_kwargs = dict(partition_kwargs)
    115 start = logg.info('running Leiden clustering')

ImportError: Please install the leiden algorithm: `conda install -c conda-forge leidenalg` or `pip3 install leidenalg`.

```

Besides a few NumbaDeprecationWarning and UserWarning outputs, all former cell blocks ran succesfully.

I have followed the instructions for [installations](https://docs.scvi-tools.org/en/stable/installation.html#) and made sure everything was installed without error. I using a **Apple M2 MAX**. I made sure to run ‘brew install --cask mambaforge’ as mentioned in the instructions.

I have tried running `conda install -c conda-forge leidenalg` and `pip3 install leidenalg` via the terminal but the issue still surfaces when I re-run the cell block. I have also tried looking through past threads if this issue has surfaced before but could not find any former discussion regarding this issue.