Today I upgraded to Shiny 1.3.0 and my Shiny server stopped rendering my apps correctly. Rstudio’s @winston and @jcheng came to my rescue and determined that it was a problem with my nginx proxy settings. That prompted me to write up these notes so next time I have to set up a server, I won’t be starting from scratch.
Install and configure Nginx
Here is the Rstudio article. Here is my corrected nginx.conf file:
/etc/nginx/nginx.conf
#user nobody;
worker_processes 1;
error_log /data/log/nginx_error.log debug;
pid /var/run/nginx.pid;
events {
worker_connections 1024;
}
http {
include mime.types;
default_type application/octet-stream;
access_log /data/log/nginx_access.log combined;
sendfile on;
#tcp_nopush on;
#keepalive_timeout 0;
keepalive_timeout 65;
#gzip on;
map $http_upgrade $connection_upgrade {
default upgrade;
'' close;
}
server {
# Open shiny server
location / {
proxy_pass http://127.0.0.1:3838/;
proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection $connection_upgrade;
proxy_read_timeout 20d;
proxy_buffering off;
}
# Open shiny server
location /apps/ {
proxy_pass http://127.0.0.1:3838/apps/;
proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection $connection_upgrade;
proxy_read_timeout 20d;
proxy_buffering off;
}
# Rstudio server
location /editor/ {
proxy_pass http://127.0.0.1:8787/;
proxy_http_version 1.1;
proxy_set_header Upgrade $http_upgrade;
proxy_set_header Connection $connection_upgrade;
proxy_read_timeout 20d;
proxy_buffering off;
}
listen 80;
server_name nycsa0204;
#charset koi8-r;
access_log /data/log/nginx_access.log;
error_log /data/log/nginx_error.log;
error_page 404 /404.html;
# redirect server error pages to the static page /50x.html
#
error_page 500 502 503 504 /50x.html;
location = /50x.html {
root /usr/share/nginx/html;
}
location ~ \.php$ {
try_files $uri =404;
fastcgi_pass unix:/var/run/php-fpm/php-fpm.sock;
fastcgi_index index.php;
fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
include fastcgi_params;
}
# deny access to .htaccess files, if Apache's document root
# concurs with nginx's one
#
location ~ /\.ht {
deny all;
}
}
}
What I like about the above nginx.conf file is that if I use servername as the URL it will show the shiny index and if I browse to the servername/editor it will open the Rstudio server IDE.
Rstudio server configuration
The only change I made here was to run it under my username:
/etc/rstudio/rserver.conf
# Server Configuration File
server-user=bosr
Shiny server configuration
Shiny runs as user shiny. You can also set where to want your log files:
/etc/shiny-server/shiny-server.conf
# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;
access_log /data/log/shiny-access.log combined;
sanitize_errors off;
# Define a server that listens on port 3838
server {
listen 3838 127.0.0.1;
# Define a location at the base URL
location / {
simple_scheduler 15;
# Host the directory of Shiny Apps stored in this directory
site_dir /data/shiny;
# Log all Shiny output to files in this directory
log_dir /data/log;
# 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;
}
}
Permissions
My shiny apps are located in /data/shiny, so I want both users (bosr and shiny) to have access to that location. This is done by creating a shiny-apps group and making both users a member of that group. That way I can use Rstudio server to develope apps (as user bosr) and users can run them on Shiny (as user shiny).
sudo groupadd shiny-apps
sudo usermod -aG shiny-apps bosr
sudo usermod -aG shiny-apps shiny
cd /data/shiny
sudo chown -R bosr:shiny-apps .
sudo chmod g+w .
sudo chmod g+s .
I also want to use the Rstudio Server IDE to install packages into the default library folder, so I need to change the ownership and permissions of that folder. Here it is based on my centOS server:
chmod 755 /usr/lib64/R/library
chown -v bosr:shiny-apps /usr/lib64/R/library
You can verify the changes by typing ls -l /usr/lib64/R/library.
To speed up package installs, configure R to use more than one core when compile source code.
/usr/lib64/R/etc/Renviron.site (create the file if it doesn’t already exist)
MAKEFLAGS=-j4
Set up automatic drive mappings as needed
/etc/fstab
# /etc/fstab
# Created by anaconda on Thu Feb 1 07:41:28 2018
#
# Accessible filesystems, by reference, are maintained under '/dev/disk'
# See man pages fstab(5), findfs(8), mount(8) and/or blkid(8) for more info
#
/dev/mapper/vg00-rootvol / xfs defaults 0 0
UUID=ba660186-313b-4482-82aa-23ce7ef7727b /boot xfs defaults 0 0
/dev/mapper/vg00-homevol /home xfs defaults 0 0
/dev/mapper/vg00-tmpvol /tmp xfs defaults 0 0
/dev/mapper/vg00-varvol /var xfs defaults 0 0
/dev/mapper/vg00-crashvol /var/crash xfs defaults 0 0
/dev/mapper/vg00-auditvol /var/log/audit xfs defaults 0 0
/dev/mapper/vg00-swapvol swap swap defaults 0 0
/dev/mapper/datafs-datafslv1 /data xfs defaults 0 0
//(server name)/research /media/research cifs credentials=/etc/fstab.cred,fil$
/etc/fstab.cred
Instead of putting your password in the fstab file, put it in a separate credential file with the proper premissions. They you only have to change the password in one place every time to change it.
username=bosr
password=(secret)
domain=(domain)
Troubleshooting
If you want to downgrade to an older version of a package, here is any easy way to do so:
library(devtools)
install_version("shiny", version = "1.2.0", repos = "http://cran.us.r-project.org")
If you want to start R without any automatic loading of packages:
R -vanilla