Trouble shooting guide for the installation of the sjSDM package
We provide a function install_sjSDM to install automatically
all necessary python dependencies but it can fail sometimes because of
individual system settings or if other python/conda installations get into
the way.
A few notes before you start with the installation (skip this point if you do not know 'conda'):
existing 'conda' installations: make sure you have the latest conda3/miniconda3 version and remove unnecessary 'conda' installations.
existing 'conda'/'virtualenv' environments (skip this point if you do not know 'conda'): we currently enforce the usage of a specific environment called 'r-sjsdm', so if you want use a custom environment it should be named 'r-sjsdm'
Sometimes the automatic 'miniconda' installation
(via install_sjSDM) doesn't work because of white
spaces in the user's name. But you can easily download and install 'conda' on
your own:
Download and install the latest 'conda' version
Afterwards run:
install_sjSDM(version = c("gpu")) # or "cpu" if you do not have a proper gpu device
Reload the package and run the example , if this doesn't work:
Restart RStudio
Install manually 'pytorch', see the following section
Download and install the latest 'conda' version:
Install the latest 'conda' version
Open the command window (cmd.exe - hit windows key + r and write cmd)
Run in cmd.exe:
$ conda create --name r-sjsdm python=3.7
$ conda activate r-sjsdm
$ conda install pytorch torchvision cpuonly -c pytorch # cpu
$ conda install pytorch torchvision cudatoolkit=11.3 -c pytorch #gpu
$ python -m pip install pyro-ppl torch_optimizer madgrad
Restart R, try to run the example, and if this doesn't work:
Restart RStudio
See the 'Help and bugs' section
Run in R:
install_sjSDM(version = c("gpu")) # or "cpu" if
you do not have a proper 'gpu' device
Restart R try to run the example, if this doesn't work:
Restart RStudio
Install manually 'PyTorch', see the following section
We strongly advise to use a 'conda' environment but a virtual env should also work. The only requirement is that it is named 'r-sjsdm'
Download and install the latest 'conda' version:
Install the latest 'conda' version
Open your terminal
Run in your terminal:
$ conda create --name r-sjsdm python=3.7
$ conda activate r-sjsdm
$ conda install pytorch torchvision cpuonly -c pytorch # cpu
$ conda install pytorch torchvision cudatoolkit=11.3 -c pytorch #gpu
$ python -m pip install pyro-ppl torch_optimizer madgrad
Restart R try to run the example, if this doesn't work:
Restart RStudio
See the 'Help and bugs' section
Run in R:
install_sjSDM(version = c("cpu"))
Restart R try to run the example, if this doesn't work:
Restart RStudio
Install manually 'PyTorch', see the following section
Download and install the latest 'conda' version:
Install the latest 'conda' version
Open your terminal
Run in your terminal:
$ conda create --name r-sjsdm python=3.7
$ conda activate r-sjsdm
$ python -m pip install torch torchvision torchaudio
$ python -m pip install pyro-ppl torch_optimizer madgrad
Restart R try to run the example from, if this doesn't work:
Restart RStudio
See the 'Help and bugs' section
To report bugs or ask for help, post a
reproducible example
via the sjSDM issue tracker
with a copy of the install_diagnostic output as a quote.
Maintainer: Maximilian Pichler maximilian.pichler@biologie.uni-regensburg.de (ORCID)
Authors:
Florian Hartig florian.hartig@biologie.uni-regensburg.de (ORCID)
Other contributors:
Wang Cai caiwang0503@163.com [contributor]
Useful links: