Problem with installation

[niming2]

Hi all,

I'm trying to use sjSDM to run joint species distribution model. But when I run the model it reminds:
Error: PyTorch not installed
I have tried all methods provided in installation_help, but they don't work. Hope advises from you. Here are reports from install_diagnostic() :

      name                                                                        python

1 base C:\Users\au734704\AppData\Local\anaconda3/python.exe
2 r-reticulate C:\Users\au734704\AppData\Local\anaconda3\envs\r-reticulate/python.exe
3 r-sjsdm C:\Users\au734704\AppData\Local\anaconda3\envs\r-sjsdm/python.exe

ENV: base

torch:

packages in environment at C:\Users\au734704\AppData\Local\ANACON~1:

Name Version Build Channel

numpy:

packages in environment at C:\Users\au734704\AppData\Local\ANACON~1:

Name Version Build Channel

numpy 1.24.3 py311hdab7c0b_1
numpy-base 1.24.3 py311hd01c5d8_1
numpydoc 1.5.0 py311haa95532_0

ENV: r-reticulate
torch:

packages in environment at C:\Users\au734704\AppData\Local\ANACON~1\envs\r-reticulate:

Name Version Build Channel

pytorch 2.0.1 py3.11_cpu_0 pytorch
pytorch-cuda 11.7 h16d0643_5 pytorch
pytorch-mutex 1.0 cpu pytorch
pytorch-ranger 0.1.1 pypi_0 pypi
torch-optimizer 0.3.0 pypi_0 pypi
torchaudio 2.0.2 py311_cpu pytorch
torchvision 0.15.2 py311_cpu pytorch

numpy:

packages in environment at C:\Users\au734704\AppData\Local\ANACON~1\envs\r-reticulate:

Name Version Build Channel

numpy 1.25.2 py311hdab7c0b_0
numpy-base 1.25.2 py311hd01c5d8_0

ENV: r-sjsdm

torch:

packages in environment at C:\Users\au734704\AppData\Local\ANACON~1\envs\r-sjsdm:

Name Version Build Channel

pytorch 2.0.1 py3.11_cpu_0 pytorch
pytorch-mutex 1.0 cpu pytorch
pytorch-ranger 0.1.1 pypi_0 pypi
torch-optimizer 0.3.0 pypi_0 pypi
torchvision 0.15.2 py311_cpu pytorch

numpy:

packages in environment at C:\Users\au734704\AppData\Local\ANACON~1\envs\r-sjsdm:

Name Version Build Channel

numpy 1.25.2 py311hdab7c0b_0
numpy-base 1.25.2 py311hd01c5d8_0

python: C:/Users/au734704/AppData/Local/anaconda3/envs/r-sjsdm/python.exe
libpython: C:/Users/au734704/AppData/Local/anaconda3/envs/r-sjsdm/python311.dll
pythonhome: C:/Users/au734704/AppData/Local/anaconda3/envs/r-sjsdm
version: 3.11.5 | packaged by Anaconda, Inc. | (main, Sep 11 2023, 13:26:23) [MSC v.1916 64 bit (AMD64)]
Architecture: 64bit
numpy: C:/Users/au734704/AppData/Local/anaconda3/envs/r-sjsdm/Lib/site-packages/numpy
numpy_version: 1.25.2
torch: C:\Users\au734704\AppData\Local\ANACON~1\envs\r-sjsdm\Lib\site-packages\torch

NOTE: Python version was forced by use_python() function

 active environment : None
   user config file : C:\Users\au734704\.condarc

populated config files : C:\Users\au734704.condarc
conda version : 23.7.2
conda-build version : 3.26.0
python version : 3.11.4.final.0
virtual packages : __archspec=1=x86_64
__win=0=0
base environment : C:\Users\au734704\AppData\Local\ANACON1 (writable)
conda av data dir : C:\Users\au734704\AppData\Local\ANACON1\etc\conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/win-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/msys2/win-64
https://repo.anaconda.com/pkgs/msys2/noarch
package cache : C:\Users\au734704\AppData\Local\ANACON1\pkgs
C:\Users\au734704.conda\pkgs
C:\Users\au734704\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\au734704\AppData\Local\ANACON1\envs
C:\Users\au734704.conda\envs
C:\Users\au734704\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/23.7.2 requests/2.31.0 CPython/3.11.4 Windows/10 Windows/10.0.22621
administrator : False
netrc file : None
offline mode : False

[MaximilianPi]

Hi @niming2,

1. You had already an existing anaconda3 installation on your system? If yes, let's get rid of it by deleting the following folder and then try to reinstall sjSDM using the install_sjSDM function

C:\Users\au734704\AppData\Local\anaconda3

2. If you have installed anaconda3 manually because the install_sjSDM() function was unable to install miniconda automatically, try to run the following commands (in R):

library(reticulate)
reticulate::conda_remove("r-reticulate")
reticulate::conda_remove("r-sjSDM")

reticulate::conda_create(envname = "r-sjsdm", python_version = "3.9")
# CPU Version:
reticulate::conda_install(envname = "r-sjsdm", 
                          packages =c("pytorch", "torchvision", "torchaudio", "cpuonly", "-c", "pytorch"))
# GPU Version:
reticulate::conda_install(envname = "r-sjsdm", 
                          packages =c("pytorch", "torchvision", "torchaudio", "pytorch-cuda=11.7", "-c", "pytorch", "-c" ,"nvidia"))

reticulate::conda_install(envname = "r-sjsdm",
                          packages = c("pyro-ppl", "torch_optimizer", "madgrad", "tqdm"), pip = TRUE)