build/CentOS.md

In IsoplotRgui: Web Interface to 'IsoplotR'

Setting up your own online mirror using CRAN on CentOS

For Ubuntu instructions, go here

Install R and nginx, if required

If these packages are not installed on your system already, then you can add them with the following commands:

On CentOS 8 you can use, instead:

sudo dnf -y install epel-release dnf-plugins-core
sudo dnf config-manager --set-enabled powertools
sudo dnf -y install R
sudo dnf -y install nginx

If you get an 'unknown repo' error when trying to enable powertools, you may have better luck with sudo dnf config-manager --set-enabled PowerTools or sudo dnf config-manager --set-enabled codeready-builder-for-rhel-8-x86_64-rpms (if you are using RedHat 8) or sudo dnf config-manager --set-enabled codeready-builder-for-rhel-8-x86_64-rpms (if you are using RedHad on AWS).

On CentOS 7 you can use:

sudo yum -y install epel-release
sudo yum -y install R
sudo yum -y install nginx

Create a user to run IsoplotR

See the Ubuntu instructions.

Set up IsoplotRgui for this user

See the Ubuntu instructions.

Create a systemd service for IsoplotR

See the Ubuntu instructions.

Expose IsoplotR with nginx

Some distributions such as CentOS install nginx with a different default configuration. If you have a directory called /etc/nginx/default.d (and the /etc/nginx/nginx.conf file contains a server {...} block containing the line include /etc/nginx/default.d/*.conf;) then you can create a file called /etc/nginx/default.d/isoplotr.conf with the following contents:

location /isoplotr/ {
    proxy_pass http://127.0.0.1:3839/;
    proxy_http_version 1.1;
    proxy_set_header Upgrade $http_upgrade;
    proxy_set_header Connection "upgrade";
}

Restart nginx

See the Ubuntu instructions.

Set up auto-updating

See the Ubuntu instructions.

Maintenance

See the Ubuntu instructions.

Troubleshooting

If nginx serves up a '404' page telling you that it cannot find a page at localhost/isoplotr, you may have one of the following issues:

IsoplotRgui issues

Please ensure that IsoplotRgui is actually running. After attempting to start it with sudo systemctl start isoplotr systemctl does not necessarily report if this attempt failed. Read the logs to try to debug it:

journalctl -eu isoplotr

SELinux issues

If nginx tells you that it cannot find any page at localhost/isoplotr/ and you have a distribution (such as CentOS) based on SELinux, you may have a permissions issue.

Check the SELinux audit log:

sudo cat /var/log/audit/audit.log | grep nginx

If you see results like:

35528 comm="nginx" dest=3839 ...

It means that you are having an SELinux permissions issue, which you can try to solve like this:

sudo setsebool -P httpd_can_network_connect 1

And try browsing to http://localhost/isoplotr again.

IsoplotRgui documentation built on Nov. 10, 2023, 5:07 p.m.