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Servidor r.tiki.org - 2016

To be migrated from Ubuntu 12.04 & Tiki12 in a separate VM that UEB is paying in Dimensis, to an Ubuntu 14.04 VM within the http://ueb.vhir.org/Servidor+remot+uebvhir.org

Done by Xavier during March-April'2016.
VM 103
hostname: r
OS: Ubuntu 14.04 LTS 64bits
IP: 5.39.105.30
MAC Address: 02:00:00:0c:7d:89
cpu: 4
RAM: 4 Gb
Hard DIsk: 50 Gb
Intended use: R 3.x & Tiki 12.x & PluginR
standard iso or image for this OS

http://r.dimensis.com (currently serving pages as https://r.tiki.org )
https://r.uebvhir.org
(and also to test new tiki versions: nextr.seeds4c.org )

1.1. Introduction

See current setup (as of 2015): http://ueb.vhir.org/Servidor+r.dimensis.com+-+r.tiki.org

Server to host examples of PluginR applications, how to master Tiki + PluginR + R to create custom CMS's which include Web interfaces for R packages and scripts.

Based on ISPConfig, so that private spaces can be created for students for workshops, etc. It was initially created with such goal: an scheduled workshop at R Summer school in June-July 2013, and an approved workshop at the International UseR meeting in Albacete that 2013 (both of them just before Xavier's motorbike accident)

See:

1.2. ISPConfig installation

See:
https://www.howtoforge.com/perfect-server-ubuntu-14.04-apache2-php-mysql-pureftpd-bind-dovecot-ispconfig-3-p3
...

Access it at:
https://r.uebvhir.org:8080/

1.3. Add R & java repos

Command in a terminal on the server
sudo add-apt-repository ppa:marutter/rrutter
sudo apt-get update
sudo apt-get dist-upgrade

1.4. Add system R packages

Besides the usual, you can install these extra ones:

sudo apt-get install libdbd-mysql libmysqlclient-dev r-cran-rmysql libcurl4-openssl-dev libssl-dev

1.5. Tweak Java install

# Install Java extra packages
sudo apt-get install openjdk-7-jdk openjdk-7-jre-*
# Reconfigure Java in your system
sudo R CMD javareconf
# Choose Java openjdk-7 if you have more than one java install
sudo update-alternatives --config java
# Install rJava system package
sudo apt-get install r-cran-rjava

1.6. Update packages

Command in a terminal on the server
sudo su - -c "R -q -e \"update.packages(ask=F, repos='http://cran.rstudio.com/')\""

1.7. Install new packages

For instance, "tm" (needed for WordCloud type of charts), which was not available in R < 3.1, and Ubuntu 14.04 came with 3.0.x in it's default repositories.

Command in a terminal on the server
sudo su - -c "R -q -e \"install.packages('tm', repos='http://cran.rstudio.com/')\""


CairoDevice requires an special command with "no test load" on a server without the X windows:

Command in a terminal on the server
sudo su - -c "R -q -e \"install.packages('cairoDevice', INSTALL_opts='--no-test-load', repos='http://cran.rstudio.com/')\""

1.8. Install R Studio server

Command in a terminal on the server
sudo apt-get install gdebi-core
wget https://download2.rstudio.org/rstudio-server-0.99.902-amd64.deb
sudo gdebi rstudio-server-0.99.902-amd64.deb


To access it:
http://r.uebvhir.org:8787/

See also:
http://www.rstudio.com/ide/docs/server/getting_started

1.8.1. Install new php versions and switch between them

See: https://launchpad.net/~ondrej/+archive/ubuntu/php
It has php 5.5, 5.6, 7.0 etc.

commands in a terminal
sudo su
add-apt-repository ppa:ondrej/php
apt-get update
apt-get install php7.0 php5.6 php5.6-mysql php-gettext php5.6-mbstring libapache2-mod-php5.6 libapache2-mod-php7.0 php5.6-curl php5.6-gd php5.6-mcrypt php5.6-xml php5.6-xmlrpc libphp5.6-embed libphp7.0-embed php-memcache php5.6-intl php5.6-zip php7.0-curl php7.0-zip php7.0-xml php7.0-intl php7.0-mcrypt php7.0-mysql php7.0-mbstring php7.0-opcache php-apcu
exit


Installing both php5.6 & php7.0 might result in a lot of complaining from apt and lots of conflicts. The first suggested resolution was to remove all the stock php5 packages so that PHP 5.6 could be installed - so I just accepted the first suggestion.

The config files are all in /etc/php/5.6 and /etc/php/7.0 respectively - inside here is where you can configure which extensions are loaded, set the ini settings, and everything else for each version in isolation.

So to switch from php 5.6 to php 7.0 you need to do two things:

# For php in web apps
user@computer:/# sudo a2dismod php5.6; sudo a2enmod php7.0; sudo service apache2 restart
# For php-cli in the command line
user@computer:/# sudo ln -sfn /usr/bin/php7.0 /etc/alternatives/php
user@computer:/# php -v
# PHP 7.0.6-1+donate.sury.org~xenial+1 (cli) ( NTS )
# Copyright (c) 1997-2016 The PHP Group
# Zend Engine v3.0.0, Copyright (c) 1998-2016 Zend Technologies
#    with Zend OPcache v7.0.6-dev, Copyright (c) 1999-2016, by Zend Technologies
#    with Xdebug v2.4.0, Copyright (c) 2002-2016, by Derick Rethans
user@computer:/#


or from php7.0 to php5.6:

# For php in web apps
user@computer:/# sudo a2dismod php7.0 ; sudo a2enmod php5.6 ; sudo service apache2 restart
# For php-cli in the command line
user@computer:/# sudo ln -sfn /usr/bin/php5.6 /etc/alternatives/php
user@computer:/# php -v
# PHP 5.6.21-1+donate.sury.org~xenial+2 (cli) 
# Copyright (c) 1997-2016 The PHP Group
# Zend Engine v2.6.0, Copyright (c) 1998-2016 Zend Technologies
#    with Zend OPcache v7.0.6-dev, Copyright (c) 1999-2016, by Zend Technologies


From the commandline, I have both php5.6 and php7.0 available as commands. I also still have a php command - look in /etc/alternatives to see that it symlinks to a particular version of PHP cli*. You can also quickly check which yours is using by running php -v.

Remember that php.ini and other files with settings are not in /etc/php5 anymore but in /etc/php/version/

1.9. Setting up the ProfilesTester

Install git, and fetch https://github.com/xavidp/TikiProfilesTester

Setup branches 12.x, 14.x, 15.x, 16.x and trunk under:
/var/www/tikiprofiletests/

Setup one mysql db for each branch (phpmyadmin to the rescue)

And setup cron job to run the script on a weekly basis.

10 0 * * 0 cd /home/xavi/code/TikiProfilesTester/;R CMD BATCH TikiProfilesTester.R

1.10. Setup nextr.tiki.org - nextr.seeds4c.org

Setting up Tiki18 to test r.tiki.org with the new pluginR pre-installed witin Tiki itself.

mpdf/mpdf 7.0.3 installed through Tiki packages (web composer). I had to temporarily set /var/www/tiki18svn/ to 777 to allow web composer to work properly, before reverting back to 755.
Some system packages were missing:

sudo apt-get install php7.0-cgi php7.0-gd



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Servidor r.dimensis.com - 2016

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