Running skeletor example throws error

[mmc46]

Running the example in R in http://natverse.org/fafbseg/articles/articles/installing-cloudvolume-meshparty.html, after installing skeletor.

Blender is a requirement, though it is not currently mentioned in docs. It is installed in /Applications/blender.app. For python to see it, I added a symlink to a path reticulate was looking at, /usr/local/bin.

ln -s /Applications/blender.app/Contents/MacOS/Blender /usr/local/bin/blender

# Checking that reticulate finds Blender
reticulate::py_run_string("import os")
reticulate::py_run_string("from distutils.spawn import find_executable")
reticulate::py_run_string("blender_executable = find_executable('blender')")
reticulate::py_run_string("print('Blender executable:', blender_executable)")
Blender executable: /usr/local/bin/blender

# running example in docs
library(natverse)
#> Loading required package: elmr
#> Loading required package: catmaid
#> Loading required package: httr
#> Loading required package: nat
#> Loading required package: rgl
#> Registered S3 method overwritten by 'nat':
#>   method             from
#>   as.mesh3d.ashape3d rgl
#> 
#> Attaching package: 'nat'
#> The following object is masked from 'package:rgl':
#> 
#>     wire3d
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, union
#> Loading required package: nat.flybrains
#> Loading required package: nat.templatebrains
#> Loading required package: nat.nblast
library(fafbseg)
#> Run dr_fafbseg() for a status report on your installation
choose_segmentation("flywire")
nx=xform_brain(elmr::dense_core_neurons, ref="FlyWire", sample="FAFB14")
xyz =xyzmatrix(nx)
ids = unique(flywire_xyz2id(xyz[sample(1:nrow(xyz),100),]))
neurons = skeletor(ids)
#> Failed: 720575940634367221
#> Error in py_run_string_impl(code, local, convert): CalledProcessError: Command '['/usr/local/bin/blender', '--background', '--python', '/var/folders/by/vvm2pb4s4vlgp5bgqqny8kdm0000gn/T/tmpymlc5rct']' died with <Signals.SIGABRT: 6>.
#> 
#> Detailed traceback: 
#>   File "<string>", line 1, in <module>
#>   File "/opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/skeletor/preprocessing.py", line 230, in simplify
#>     result = blend.run(_blender_executable
#>   File "/opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/trimesh/interfaces/generic.py", line 87, in run
#>     check_call(command_run,
#>   File "/opt/miniconda3/envs/flywire_env/lib/python3.8/subprocess.py", line 364, in check_call
#>     raise CalledProcessError(retcode, cmd)
#> Failed: 720575940637192819
#> Error in py_run_string_impl(code, local, convert): CalledProcessError: Command '['/usr/local/bin/blender', '--background', '--python', '/var/folders/by/vvm2pb4s4vlgp5bgqqny8kdm0000gn/T/tmpov7cq59r']' died with <Signals.SIGABRT: 6>.
#> 
#> Detailed traceback: 
#>   File "<string>", line 1, in <module>
#>   File "/opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/skeletor/preprocessing.py", line 230, in simplify
#>     result = blend.run(_blender_executable
#>   File "/opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/trimesh/interfaces/generic.py", line 87, in run
#>     check_call(command_run,
#>   File "/opt/miniconda3/envs/flywire_env/lib/python3.8/subprocess.py", line 364, in check_call
#>     raise CalledProcessError(retcode, cmd)
#> Warning in skeletor(ids): 2 ids could not be read and converted to skeletons

With the error, I also get a prompt that Blender has crashed

I can run the python skeletor example without problems.

From dr_fafbseg()

Python
----
python:         /opt/miniconda3/envs/flywire_env/bin/python
libpython:      /opt/miniconda3/envs/flywire_env/lib/libpython3.8.dylib
pythonhome:     /opt/miniconda3/envs/flywire_env:/opt/miniconda3/envs/flywire_env
version:        3.8.5 (default, Sep  4 2020, 02:22:02)  [Clang 10.0.0 ]
numpy:          /opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/numpy
numpy_version:  1.19.2

NOTE: Python version was forced by RETICULATE_PYTHON

                     module available version
1               cloudvolume      TRUE   3.2.1
2                   DracoPy      TRUE        
3                 meshparty      TRUE   1.8.0
4                  skeletor      TRUE  0.2.10
5                  pykdtree      TRUE        
6                  pyembree      TRUE   0.1.6
7 annotationframeworkclient      TRUE   2.0.1
8            PyChunkedGraph     FALSE        
9                   igneous      TRUE        
                                                                                    path
1               /opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/cloudvolume
2                                                                                       
3                 /opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/meshparty
4                  /opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/skeletor
5                  /opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/pykdtree
6                  /opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/pyembree
7 /opt/miniconda3/envs/flywire_env/lib/python3.8/site-packages/annotationframeworkclient
8                                                                                       
9                                                           /Users/mmc46/igneous/igneous

Any ideas on how to fix this?