Comments (4)
Could you pls post the output of sjSDM::install_diagnostic() here?
One solution could be to do a clean reinstall:
- remove the old environment completely:
i) reticulate::conda_remove("r-reticulate")
ii) restart session - reinstall via install_sjSDM()
I think the installation is still the bottleneck of the package and we have to find a way to improve it
from s-jsdm.
Ok, yeah I'll give that a go.
> > install_diagnostic()
>
> name
> 1 r-reticulate
> python
> 1 /home/k.taylor2/.local/share/r-miniconda/envs/r-reticulate/bin/python
>
> ENV: r-reticulate
>
> torch:
> # packages in environment at /home/k.taylor2/.local/share/r-miniconda/envs/r-reticulate:
> #
> # Name Version Build Channel
> pytorch 1.4.0 py3.6_cpu_0 [cpuonly] pytorch
> pytorch-ranger 0.1.1 pypi_0 pypi
> torch 1.9.0 pypi_0 pypi
> torch-optimizer 0.1.0 pypi_0 pypi
> torchaudio 0.4.0 py36 pytorch
> torchvision 0.5.0 py36_cpu [cpuonly] pytorch
>
>
> numpy:
> # packages in environment at /home/k.taylor2/.local/share/r-miniconda/envs/r-reticulate:
> #
> # Name Version Build Channel
> numpy 1.19.5 py36h2aa4a07_1 conda-forge
>
>
> python: /home/k.taylor2/.local/share/r-miniconda/envs/r-reticulate/bin/python
> libpython: /home/k.taylor2/.local/share/r-miniconda/envs/r-reticulate/lib/libpython3.6m.so
> pythonhome: /home/k.taylor2/.local/share/r-miniconda/envs/r-reticulate:/home/k.taylor2/.local/share/r-miniconda/envs/r-reticulate
> version: 3.6.12 |Anaconda, Inc.| (default, Sep 8 2020, 23:10:56) [GCC 7.3.0]
> numpy: /home/k.taylor2/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages/numpy
> numpy_version: 1.19.5
>
>
>
>
> active environment : None
> user config file : /home/k.taylor2/.condarc
> populated config files :
> conda version : 4.9.2
> conda-build version : not installed
> python version : 3.8.5.final.0
> virtual packages : __glibc=2.27=0
> __unix=0=0
> __archspec=1=x86_64
> base environment : /home/k.taylor2/.local/share/r-miniconda (writable)
> channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
> https://repo.anaconda.com/pkgs/main/noarch
> https://repo.anaconda.com/pkgs/r/linux-64
> https://repo.anaconda.com/pkgs/r/noarch
> package cache : /home/k.taylor2/.local/share/r-miniconda/pkgs
> /home/k.taylor2/.conda/pkgs
> envs directories : /home/k.taylor2/.local/share/r-miniconda/envs
> /home/k.taylor2/.conda/envs
> platform : linux-64
> user-agent : conda/4.9.2 requests/2.25.1 CPython/3.8.5 Linux/3.10.0-1062.18.1.el7.x86_64 ubuntu/18.04.5 glibc/2.27
> UID:GID : 4967:4034
> netrc file : None
> offline mode : False
from s-jsdm.
Ok, it took some finagling, but the clean re-install (after reticulate::conda_remove("r-reticulate")
AND remove.packages("sjSDM")
seemed to work.
from s-jsdm.
Great! Let's keep this issue open for other users with the same issue when upgrading to version 0.1.8
from s-jsdm.
Related Issues (20)
- CRAN Issue
- VENN diagram Anova HOT 1
- Problem with installation HOT 1
- Error in sjSDM_cv HOT 8
- PyTorch not installed HOT 13
- Is there a way to assess the significance (p-value?) of pairwise relationships in species associations? HOT 2
- ValueError: Expected parameter rate HOT 4
- Random factors HOT 19
- ValueError: Expected value argument HOT 3
- vp codist
- sjSDM on a remote server HOT 3
- sjSDM - memory issues of anova() HOT 6
- Installation error HOT 5
- Failing to run models on GPU
- Readme Files
- plotsjSDMcoef returns summary table / summary can't run invisible
- importance
- Exact VP definition HOT 1
- Internal structure set negative R2 to 0 or scale
- Bias in sjSDM::linear() coefficient estimates when including an intercept term. HOT 3
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from s-jsdm.