jefferis
commented
11 months ago Dear Arthur, thanks for the report. I think that the error message associated with trying to import cloudvolume in your renv evnvironment may be hidden.
Can you try importing directly
reticulate::import(“cloudvolume”) And reporting any observed error message?
Sent from my iPhone
On 5 Oct 2023, at 21:37, ArthurZhao @.***> wrote:
I have fafbseg installed in the system library and it works fine. eg.
id = "720575940620061120" msh <- read_cloudvolume_meshes(id) I started a new project with renv, now read_cloudvolume_meshes() returns an error:
Error: Please install the python cloudvolume package: This should normally work: fafbseg::simple_python('basic') For more details see ?simple_python or the cloud-volume docshttps://github.com/seung-lab/cloud-volume#setup If you have already installed cloudvolume but it is not found then R probably can't find the relevant version of Python Do: usethis::edit_r_environ() to point to the right python e.g. RETICULATE_PYTHON="/opt/miniconda3/envs/r-reticulate/bin/python" 12. stop(call. = F, "Please install the python cloudvolume package:\n", "This should normally work:\n", "fafbseg::simple_python('basic')\n", "For more details see ?simple_python or the cloud-volume docs", "https://github.com/seung-lab/cloud-volume#setup\n", "If you have already installed cloudvolume but it is not found\n", ... at cloudvolume-reticulate.R#7 11. value[3L] 10. tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9. tryCatchList(expr, classes, parentenv, handlers) 8. tryCatch(cv <- reticulate::import("cloudvolume"), error = function(e) { message(as.character(e)) stop(call. = F, "Please install the python cloudvolume package:\n", "This should normally work:\n", "fafbseg::simple_python('basic')\n", ... at cloudvolume-reticulate.R#3 7. (function (min_version = NULL) { check_reticulate() tryCatch(cv <- reticulate::import("cloudvolume"), error = function(e) { ... 6. eval(mc, parent.frame()) 5. eval(mc, parent.frame()) 4. withVisible(eval(mc, parent.frame())) 3. check_cloudvolume_reticulate() at cloudvolume-reticulate.R#68 2. save_cloudvolume_meshes(segments, savedir = savedir, ..., cloudvolume.url = cloudvolume.url) at cloudvolume-reticulate.R#207 1. read_cloudvolume_meshes(id) dr_fafbseg() returns the following (omitting the long fafbseg package options section):
dr_fafbseg() R packages
fafbseg package: Version: 0.13 GithubSHA1: 379cb24d0b971392b37bfeb4394b3c94a2ea2567
-- File: R arrow package: 13.0.0.1 FlyWire
Checking secrets folder for tokens from R: C:/Users/artxz/.cloudvolume/secrets Valid FlyWire ChunkedGraph token is set and found by R! Please use simple_python to install python+cloudvolume for full access to flywire API!
1 FlyWire/CloudVolume credential files available at C:/Users/artxz/.cloudvolume/secrets [1] "cave-secret.json" Error : invalid version specification ‘NA’
Flywire cloudvolume URL: graphene://https://prod.flywire-daf.com/segmentation/table/fly_v31 Google FFN1 segmentation
- Set the
fafbseg.skelziprootoption:options(fafbseg.skelziproot="/path/to/zips")if you want to use FFN1 skeleton files!Python
python: C:/Users/artxz/AppData/Local/r-miniconda/envs/r-reticulate/python.exe libpython: C:/Users/artxz/AppData/Local/r-miniconda/envs/r-reticulate/python38.dll pythonhome: C:/Users/artxz/AppData/Local/r-miniconda/envs/r-reticulate version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 05:59:00) [MSC v.1929 64 bit (AMD64)] Architecture: 64bit numpy: C:/Users/artxz/AppData/Local/r-miniconda/envs/r-reticulate/Lib/site-packages/numpy numpy_version: 1.22.3
NOTE: Python version was forced by use_python() function
package version requirement channel installed core1 cloud-volume 8.5.4 cloud-volume=8.5.4 pypi TRUE TRUE 2 caveclient 4.12.5 caveclient=4.12.5 pypi TRUE TRUE 3 seatable-api 2.5.5 seatable-api=2.5.5 pypi TRUE TRUE 4 pyarrow 7.0.0 pyarrow=7.0.0 pypi TRUE FALSE 5 fafbseg
FALSE FALSE 6 DracoPy FALSE FALSE 7 meshparty FALSE FALSE 8 skeletor FALSE FALSE 9 pykdtree FALSE FALSE 10 pyembree FALSE FALSE 11 pychunkedgraph FALSE FALSE 12 igneous FALSE FALSE 13 fastremap 1.12.2 fastremap=1.12.2 pypi TRUE FALSE 14 ncollpyde FALSE FALSE cloud-volume seems available though there is an error at the beginning: Error : invalid version specification ‘NA’. Any ideas ?
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artxz
I have
fafbseginstalled in the system library and it works fine. eg.I started a new project with renv, now
read_cloudvolume_meshes()returns an error:dr_fafbseg()returns the following (omitting the longfafbseg package optionssection):cloud-volumeseems available though there is an error at the beginning:Error : invalid version specification ‘NA’.Any ideas ?