Shiny on Webfaction: VPS installing without root

February 15, 2016
By

(This article was first published on Life in Code, and kindly contributed to R-bloggers)

I’ve been using Webfaction as an inexpensive managed VPN. Part of me wants VPS root access, but I’m mostly happy to leave the administrative details to others. Webfaction seems to be a good example of a common VPS plan: user-only access in a rich development environment. Compilers, zsh, and even tmux are available from the shell, making this a very comfortable dev environment overall.

Most times root doesn’t matter, but sometimes it complicates new software installs. I’ve been looking forwards to testing R’s webapp package Shiny, but all of the docs assume root access (and some even state that it’s required). I set off without knowing if this would work, attempting to see how far I could get. What follows is a (hopefully) reproducible account of a user-land install of R & Shiny via ssh on a Webfaction slice. To the best of my knowledge, this requires only standard development tools, and so should(??) work.

In the following I use [tab] to indicate hitting tab key for auto-completion. The VPS login username is [user]. [edit] means call your editor of choice (vim, emacs, or, god forbid, nano). This assumes you are using bash (which seems to be the default shell on most VPNs).

Prepare the build environment

## ssh to webhost
## make directories, set paths, etc
## source build dir
mkdir ~/src
## software install dir
mkdir ~/local
## personal content dir
CONTENTDIR=~/var
mkdir $CONTENTDIR
## some hosts have /tmp set noexec?
mkdir src/tmp
## Install software here
INSTPREFIX=$HOME/local

## set paths:  
##
echo 'export PATH=$PATH:~/local/bin:~/local/shiny-server/bin' >> ~/.bashrc
echo 'export TMPDIR=$HOME/src/tmp' >>~/.bashrc

## check that all is well
[edit] ~/.bashrc
## update env
. .bashrc

[Ref: temp dir and R packages]

Install R from source: fast and (mostly) easy

cd ~/src
wget http://cran.us.r-project.org/src/base/R-3/R-3.2.3.tar.gz
tar xzf R-3.2.3.tar.gz
cd R-[tab]
./configure --prefix=$INSTPREFIX
## missing library, search and add directory
CPPFLAGS=/usr/lib/jvm/java/include/ make
make install
cd ~

Prep R environment

## The following commands are in R
install.packages(c('shiny', 'rmarkdown'))
## From the shell:
## on a headless / no-X11 box, need cairo for png
echo "options(bitmapType='cairo')" >> ~/.Rprofile
## check that all is well
[edit] ~/.Rprofile

[Ref: R png without X11]

Install cmake (if needed)

## first install cmake - skip if's already available 
`which cmake`
## nothing?  continue
## NOTE - I'm using the source tarball here, not binaries
wget https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz 
tar xzf cmake-[tab]
cd cmake-[tab]
./configure --prefix=$INSTPREFIX
gmake
make install

Install Shiny Server

## From shell
cd ~/src
git clone https://github.com/rstudio/shiny-server.git
cd shiny-server
cmake -DCMAKE_INSTALL_PREFIX=$INSTPREFIX
make 
## "make install" Complains about no build dir
## I'm not sure what happens here, but this seems to work
PYTHON=`which python`
mkdir build
./bin/npm --python="$PYTHON" rebuild 
./bin/node ./ext/node/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js --python="$PYTHON" rebuild 
make install

[Ref: shiny build docs]

Configure Shiny Server

All of the Shiny Server docs assume the config file is located in /etc/, which I don’t have access to. There’s _zero_ documentation on running shiny, nor does running shiny-server -h or shiny-server --help provide any indication. Trial and error and reading source code on github finally leads to shiny-server path-to-config-file. So, let’s make a shiny site!

## Nest content in ~/var
mkdir $CONTENTDIR/shiny
cp -rp ~/src/shiny-server/samples $CONTENTDIR/shiny/apps
mkdir $CONTENTDIR/shiny/logs
## copy the packaged settings template to the content dir
cp ~/src/shiny-server/config/default.config $CONTENTDIR/shiny/server.conf
[edit] $CONTENTDIR/shiny/server.conf
##
## server.conf content follows:
run_as [user];
## leave location as-is
## substitute var with $CONTENTDIR if needed
    site_dir /home/[user]/var/shiny/apps;
    log_dir /home/[user]/var/shiny/logs;    
## save file
## back at shell, run shiny, put in background
shiny-server ~/var/shiny/server.conf &

[Ref: Shiny-server docs]

Testing

Shiny should give messages about Starting listener on 0.0.0.0:3838. First up, let’s use ssh to connect remote port 3838 to a local port. As an aside, if you’re not using ~/.ssh/config on a local machine to manage keys and hostname shortcuts, you should!

## on local machine:
ssh -nNT -L 9000:127.0.0.1:3838 [user]@webhost

Now, if all went well, you should be able to navigate to the welcome page via browser on local machine:
http://127.0.0.1:9000

Once shiny is working, don’t forget to take a look at your logs:

ls -alh $CONTENTDIR/shiny/logs

I had trouble with the packaged rmd example app (which renders a .Rmd file). Reading logs showed install issues with pandoc, and I had to manually fiddle with the links:

ln -s $INSTPREFIX/shiny-server/ext/pandoc/static/pandoc $INSTPREFIX/shiny-server/ext/pandoc/

[Ref: port forwarding]

Wrap-up

For a full production environment, you would want a process monitor to keep shiny-server running, as well a public-facing server. See your webhost’s documentation for process monitors. More details on shiny-server and apache are here (I haven’t tried these proxy methods).

Finally, a more conventional approach using root access on a VPS (such as DigitalOcean) is available here.

I should point out that I like Webfaction (referral link) well enough to pay them money. Their intro plan is $10/month for 1GB RAM + 100GB full SSD, with a 1-month free trial. I like that the webfaction user-base is big enough that lots of my questions are already answered, but small enough that staff actually answer new questions.

I’ve done my best to document exactly what I did, but I’m sure there are typos. Let me know if you encounter any issues!

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