You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
# Checking that reticulate finds Blenderreticulate::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)")
Blenderexecutable:/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.
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
.With the error, I also get a prompt that Blender has crashed
I can run the python skeletor example without problems.
From
dr_fafbseg()
Any ideas on how to fix this?
The text was updated successfully, but these errors were encountered: