Issues reading meshes from Flywire in R with fafbseg library.

[Nilay Yapici]

Hi Greg, 

We have recently installed fafbseg and natverse to access Flywire segmentation data. 

We receive the error below when attempting to read meshes from Flywire via R with fafbseg.  

>pmn1.flywire=read_cloudvolume_meshes("720575940623979522")
  downloading meshes
Error in py_call_impl(callable, dots$args, dots$keywords) :
  AttributeError: 'GrapheneMeshMetadata' object has no attribute 'max_meshed_layer'

  parsing downloaded meshes 

> traceback()
No traceback available 

Here is the dr_fafbseg() results: 

> dr_fafbseg()
fafbseg package:
Version: 0.11.1
GithubSHA1: ae195ccd8282c39f14a1252973b4c52e0984b1a9
Packaged: 2022-11-12 20:25:40 UTC; nilayyapici

-- File:
FlyWire
----
Checking secrets folder for tokens from R: /Users/nilayyapici/.cloudvolume/secrets
Valid FlyWire ChunkedGraph token is set and found by R!
cloudvolume found a token at  /Users/nilayyapici/.cloudvolume/secrets/cave-secret.json
Flywire API access via python+cloudvolume is working.
1 FlyWire/CloudVolume credential files available at
/Users/nilayyapici/.cloudvolume/secrets
[1] "cave-secret.json"

Flywire cloudvolume URL: graphene://https://prodv1.flywire-daf.com/segmentation/table/fly_v31
Google FFN1 segmentation
----
• Set the `fafbseg.skelziproot` option:
   `options(fafbseg.skelziproot="/path/to/zips")`
  if you want to use FFN1 skeleton files!

Python
----
python:         /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/bin/python
libpython:      /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/libpython3.8.dylib
pythonhome:     /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate:/Users/nilayyapici/Library/r-miniconda/envs/r-reticulate
version:        3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:05:47)  [Clang 12.0.1 ]
numpy:          /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/numpy
numpy_version:  1.23.4

           module available version                                                                                                path
1     cloudvolume      TRUE  8.16.0    /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/cloudvolume
2         DracoPy      TRUE   1.2.0                                                                                                    
3       meshparty      TRUE   0.2.2      /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/meshparty
4        skeletor      TRUE   1.2.3       /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/skeletor
5        pykdtree      TRUE               /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/pykdtree
6        pyembree      TRUE   0.1.6       /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/pyembree
7      caveclient      TRUE  4.17.1     /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/caveclient
8  pychunkedgraph      TRUE 0.1.113 /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/pychunkedgraph
9         igneous      TRUE                /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/igneous
10        pyarrow      TRUE  10.0.0        /Users/nilayyapici/Library/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/pyarrow

rJava
----
The rJava package is linked to the following JVM
java.version: 1.8.0_333
java.home: /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home
java.class.version: 52.0

System java
----
(used as a fallback when rJava not available)
java run time found at: /usr/bin/java
java.version: 8.0

h5reg test
----
h5reg xform infrastructure OK!
xform test gave correct results

Thank you so much for your help in advance. 

Best 

Nilay 

[Nilay Yapici]

I actually fixed this issue. It was related to the miniconda dependency versions. Mine were set to default not latest updated versions. I seem to be able to read meshes now. 

N. 

[Greg Jefferis]

Great!