Open pm4564 opened 2 years ago
Hi @pm4564, It looks like this is down to your version of the datetime library which looks like it's coupled to your python version.
Can you report the output of dr_fafbseg()
?
Aslo can you check
dt=reticulate::import('datetime')
dt$sys$version
what this does.
Checking secrets folder for tokens from R: /Users/Myers/.cloudvolume/secrets
Valid FlyWire ChunkedGraph token is set and found by R!
cloudvolume found a token at /Users/Myers/.cloudvolume/secrets/cave-secret.json
Flywire API access via python+cloudvolume is working.
1 FlyWire/CloudVolume credential files available at
/Users/Myers/.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/Myers/Library/r-miniconda/envs/r-reticulate/bin/python
libpython: /Users/Myers/Library/r-miniconda/envs/r-reticulate/lib/libpython3.6m.dylib
pythonhome: /Users/Myers/Library/r-miniconda/envs/r-reticulate:/Users/Myers/Library/r-miniconda/envs/r-reticulate
version: 3.6.12 | packaged by conda-forge | (default, Dec 9 2020, 00:24:39) [GCC Clang 11.0.0]
numpy: /Users/Myers/Library/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/numpy
numpy_version: 1.19.5
module available version
1 cloudvolume TRUE 6.1.0
2 DracoPy TRUE
3 meshparty FALSE
4 skeletor TRUE 1.1.0
5 pykdtree FALSE
6 pyembree TRUE 0.1.6
7 caveclient TRUE 4.9.0
8 pychunkedgraph FALSE
9 igneous FALSE
10 pyarrow TRUE 6.0.1
path
1 /Users/Myers/Library/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/cloudvolume
2
3
4 /Users/Myers/Library/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/skeletor
5
6 /Users/Myers/Library/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/pyembree
7 /Users/Myers/Library/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/caveclient
8
9
10 /Users/Myers/Library/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/pyarrow
rJava
----
The rJava package is linked to the following JVM
java.version: 14.0.1
java.home: /Library/Java/JavaVirtualMachines/jdk-14.0.1.jdk/Contents/Home
java.class.version: 58.0
System java
----
(used as a fallback when rJava not available)
java run time found at: /usr/bin/java
java.version: 14.0.1
h5reg test
----
h5reg xform infrastructure OK!
xform test gave correct results
Aslo can you check
dt=reticulate::import('datetime') dt$sys$version
what this does.
[1] "3.6.12 | packaged by conda-forge | (default, Dec 9 2020, 00:26:39) \n[GCC Clang 11.0.0]"
Have just updated fafbseg and run into the following error when querying an annotation table: