R Shiny Server Deployment in Hengrui Server¶

Server Info¶

shnvlshiny01    10.10.5.114  root/Hr@shiny0821        
shnvlshinyd01   10.10.13.56  root/Hr@shiny0821

Steps¶

shiny-server guide: https://docs.posit.co/shiny-server/
IT grant access to https://cran.rstudio.com/
yum install R
su - -c "R -e \"install.packages(c('shiny', 'rmarkdown', 'devtools', 'RJDBC'), repos='https://cran.rstudio.com/')\""
Download Shiny Server: https://posit.co/download/shiny-server/
yum install --nogpgcheck shiny-server-1.5.20.1002-x86_64.rpm
systemctl start shiny-server
systemctl enable shiny-server

Shiny Server Info¶

site_dir: /srv/shiny-server
log_dir: /var/log/shiny-server
config_dir: /etc/shiny-server/shiny-server.conf

Install prerequisite apps for R packages¶

yum install harfbuzz-devel fribidi-devel yum install freetype-devel libpng-devel libtiff-devel libjpeg-turbo-devel yum install poppler-cpp-devel

yum install libcurl-devel libxml2-devel openssl-devel libgit2-devel

Install R packages¶

su - -c "R -e \"install.packages(c('shiny', 'rmarkdown', 'devtools', 'RJDBC'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('DT'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('readxl'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('RSQLite'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('DBI'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('shinyjs'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('shinyWidgets'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('bslib'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('shinydisconnect'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('openxlsx'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('pdftools'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('shinyalert'), repos='https://cran.rstudio.com/')\""
su - -c "R -e \"install.packages(c('tidyverse'), repos='https://cran.rstudio.com/')\""

su - -c "R -e \"install.packages(c('config','golem'), repos='https://cran.rstudio.com/')\""

Deploy Shiny Apps¶

Save app folder in /srv/shiny-server, should have two files, ui.r and server.r

Deploy with golem¶

https://github.com/ThinkR-open/golem/issues/145

Install the package create by golem.

install.packages('/tmp/systemd-private-36b2a1fdf86c4a96acd80d08f2d0342c-chronyd.service-7hjinM/tmp/DefineHelper_1.0.tar.gz',lib = .libPaths()[length(.libPaths())],repos = NULL,dependencies = T)

Create a app.r file within the app folder, i.e. **/srv/shiny-server/define-helper**. Note that app.r must be saved with UTF-8 encoding

Sample app.r file:

options(shiny.maxRequestSize = 100*1024^2) #setting upload limit to 100MB
DefineHelper::run_app()

Add-on¶

Grant write access right to /srv/shiny-server, for the upload file of Shiny App

sudo chmod -R 777 define-helper

need investigation on how to configure a different location, such as /tmp/ for upload files, in server function of shiny app.

Emacs¶

quit: Ctrl-x Ctrl-c

save: Crtl-x Ctrl-s

R Shiny Configuration files¶

# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;
preserve_logs true;

# Define a server that listens on port 80
server {
  listen 80; 

  # Define a location at the base URL
  location / {

    # Host the directory of Shiny Apps stored in this directory
    site_dir /srv/shiny-server;

    # Log all Shiny output to files in this directory
    log_dir /var/log/shiny-server;

    # When a user visits the base URL rather than a particular application,
    # an index of the applications available in this directory will be shown.
    directory_index on;
  }
}

Https link¶

https://shinyapp.hengrui.com/

Other mirrors of R packages¶

https://cran.r-project.org/ https://cloud.r-project.org/ https://mirrors.tuna.tsinghua.edu.cn/CRAN/ https://mirrors.aliyun.com/CRAN/

Reference¶

netstat -lnpt