Instalación kernel de R

Se siguen las instrucciones de instalación encontradas en este enlace irkernel.

Siendo root en deimos:

# /opt/tljh/user/bin/conda install r
# /opt/tljh/user/bin/conda install r-essentials


# R
> install.packages('IRkernel')
> IRkernel::installspec(user = FALSE)

En una sesión de jupyter, arriba a la derecha en 'new' aparece 'R'.

Instalación desde un entorno de mamba

# cd /opt/conda/mamba/
# mkdir Rnew
# cd Rnew
# /opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba create -n Rnew -c conda-forge r-base
# eval "$(/opt/conda/mamba/DE-global_hackathon/miniconda3/bin/mamba shell hook --shell bash)"
# mamba activate Rnew
(Rnew) # which R
/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/Rnew/bin/R

Instalando los paquetes para poder activarlo desde jupyterHUB

(Rnew) # R
> install.packages("IRKernel")
> system.file('kernelspec', package = 'IRkernel')
[1] "/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/Rnew/lib/R/library/IRkernel/kernelspec"
> quit()

Instalando kernel en jupyter

(Rnew) # mamba deactivate
# /opt/tljh/user/bin/jupyter kernelspec list
Available kernels:
  bash                    /opt/tljh/user/share/jupyter/kernels/bash
  python3                 /opt/tljh/user/share/jupyter/kernels/python3
  ir                      /usr/local/share/jupyter/kernels/ir
  py3_andex               /usr/local/share/jupyter/kernels/py3_andex
  python_atrackcs         /usr/local/share/jupyter/kernels/python_atrackcs
  python_digearth-hack    /usr/local/share/jupyter/kernels/python_digearth-hack
  python_esmvaltools      /usr/local/share/jupyter/kernels/python_esmvaltools
# /opt/tljh/user/bin/jupyter kernelspec install "/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/Rnew/lib/R/library/IRkernel/kernelspec" --name 'ir_new'
# /opt/tljh/user/bin/jupyter kernelspec listAvailable kernels:
  bash                    /opt/tljh/user/share/jupyter/kernels/bash
  python3                 /opt/tljh/user/share/jupyter/kernels/python3
  ir                      /usr/local/share/jupyter/kernels/ir
  ir_new                  /usr/local/share/jupyter/kernels/ir_new
  py3_andex               /usr/local/share/jupyter/kernels/py3_andex
  python_atrackcs         /usr/local/share/jupyter/kernels/python_atrackcs
  python_digearth-hack    /usr/local/share/jupyter/kernels/python_digearth-hack
  python_esmvaltools      /usr/local/share/jupyter/kernels/python_esmvaltools
# vim /usr/local/share/jupyter/kernels/ir_new/kernel.json
{"argv": ["R", "--slave", "-e", "IRkernel::main()", "--args", "{connection_file}"],
 "display_name":"R (new)",
 "env": {
  "MAMBA_PREFIX":"/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/Rnew",
  "MAMBA_DEFAULT_ENV":"Rnew",
  "PATH":"/opt/conda/mamba/DE-global_hackathon/miniconda3/envs/Rnew/bin:/opt/conda/mamba/DE-global_hackathon/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
 },
 "language":"R"
}

Instalando paquetes

Instalando paquetes (NOTA: la versión de R se ha ido degradando: 4.6.0, 4.5.3, 4.4.3)

# mamba activate Rnew
(Rnew) # mamba install -c conda-forge r-abind r-akima r-corrplot r-cowplot
(Rnew) # mamba install -c conda-forge r-egg r-evd r-extRemes r-factoextra r-fields r-fitdistrplus r-ggmap r-ggrepel r-ggsn r-ggspatial r-ggthemes r-jpeg
(Rnew) # mamba install -c conda-forge r-Kendall r-lubridate r-mapdata r-metR r-ncdf4 r-nortest r-openxlsx 
(Rnew) # mamba install -c conda-forge r-padr r-patchwork r-ppcor r-pracma r-RcolorBrewer r-reshape2 r-rgeos
(Rnew) # mamba install -c conda-forge r-rnaturalearth r-rnaturalearthdata r-scales r-sp 
(Rnew) # mamba install -c conda-forge r-terra r-tidyr r-trend r-WaveletComp r-zoo r-zyp