dependency installation issue in 0.1.8 - missing madgrad

[theoreticalecology]

dependency installation issue in 0.1.8 - missing madgrad

[MaximilianPi]

Could you pls post the output of sjSDM::install_diagnostic() here?

One solution could be to do a clean reinstall:

1. remove the old environment completely:
   i) reticulate::conda_remove("r-reticulate")
   ii) restart session
2. 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

[kjmtaylor22]

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 

[kjmtaylor22]

Ok, it took some finagling, but the clean re-install (after reticulate::conda_remove("r-reticulate") AND remove.packages("sjSDM") seemed to work.

[MaximilianPi]

Great! Let's keep this issue open for other users with the same issue when upgrading to version 0.1.8