Additional instructions for Linux

Here you'll find specific instructions to help you install and run Achilles on Linux. At the end of this page you'll find some details specifically for CentOS 6.

Installing on Linux

Make sure your distribution has libcurl-devel and libxml2-devel installed. If not, install as root (or sudo) using your distributions's software installation tool (e.g. yum, apt-get)

RCurl: "Cannot find curl-config": Install libcurl4-gnutls-dev or libcurl4-nss-dev, or libcurl4-openssl-dev

The R packages available on your distribution's standard repositories often are not the most recent. Follow the instructions at http://www.jason-french.com/blog/2013/03/11/installing-r-in-linux/ to install the latest R packages.
Ensure you have installed sun java Version 6 (the current Version 8 doesn't work). The open-source versions of Java do not seem to work. Each Linux distro has different instructions for how to do this.

For Centos: installing Java 6u45: http://www.if-not-true-then-false.com/2010/install-sun-oracle-java-jdk-jre-6-on-fedora-centos-red-hat-rhel/
For Ubuntu 14.04 & 18.04:
- Download jdk-6u45-linux-<system_architecture>.bin from Oracle webpage https://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase6-419409.html
- Follow these instructions: https://dzone.com/articles/installing-oracle-java6-ubuntu
{Other Linux users -- please add URL for installing Oracle/Sun java for your distro here}
After installation, run (from a shell):

sudo R CMD javareconf
Restart R
Getting around installation issues with rJava. Before loading from any of the github packages, execute the following command in R:

install.packages('rJava', .libPaths()[1], 'http://www.rforge.net/') There is a period in front of libPaths()
From: http://stackoverflow.com/questions/13375636/install-rjava-on-centos (last posting by purnendumaity on December 30, 2012)
See also (for Ubuntu): http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing

CentOS uses SELinux permission, which causes issues with "Permission Denied" to AchillesWeb files. See https://wiki.apache.org/httpd/13PermissionDenied

For how to fix: see http://wiki.centos.org/HowTos/SELinux

chmod -R +x /var/www/localhost
chcon -Rv --type=httpd_sys_content_t /var/www/localhost

Running Achilles on Linux

Full syntax for createConnectionDetails (for postgresql -- where database is omop, schema is omop, and user is achilles and password is achilles) is: connectionDetails <- createConnectionDetails(dbms="postgresql",server="localhost/omop",port="5432", schema="omop",user="achilles",password="achilles")

Type in R: ?createConnectionDetails for full syntax