I’ve been using Webfaction (plug) 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].  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  ~/.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=$INSTPREFIX ## missing library, search and add directory CPPFLAGS=/usr/lib/jvm/java/include/ make make install cd ~
Prep R environment
## The following commands are in R install.packages(c('shiny', 'rmarkdown'))
## From the shell: ## on a headless / no-X11 box, need cairo for png echo "options(bitmapType='cairo')" >> ~/.Rprofile ## check that all is well  ~/.Rprofile
[Ref: R png without X11]
Install cmake (if needed)
## first install cmake - skip if's already available `which cmake` ## nothing? continue ## NOTE - I'm using the source tarball here, not binaries wget https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz tar xzf cmake-[tab] cd cmake-[tab] ./configure --prefix=$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  $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]
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. This allows local testing without deployment. 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:
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]
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.
Update – 17 Feb 2016: Deployment Logistics
After a day of kicking the tires, I’m happy to report Shiny-server is working well on Webfaction in production mode. Two points:
Making a webapp. In the Webfaction control panel, I added a custom application. In the following, substitute [appname] for the value entered in the Name field. For
App category I selected “Websockets”, and then clicked “Save”. Copy the port number. Edit the
server.conf file from above, replacing the number in
listen 3838; with the port number copied from Webfaction. Finally, create a website, add a name (can be the same as [appname] from above), and a domain. It typically takes a few minutes for DNS changes to propagate.
The above steps creates a directory named
$HOME/webapps/[appname]. I placed the
server.conf file here, created app and log directories, and then updated server.conf to reflect the new locations:
## Create the following directories ## add these paths to server.conf, ## and don't forget the trailing ; mkdir $HOME/[appname]/logs ## shiny app files go here: mkdir $HOME/[appname]/app
Running the server. Shiny-server will use a PID file, which makes job-spawning a simple shell script + cron job. If shiny-server is already running, it will recognize the PID file and not start another process. I made the following script:
#!/bin/sh ## executable shell script names $HOME/bin/my.shiny.sh ## make sure to run: chmod +x $HOME/bin/my.shiny.sh APPROOT=$HOME/webapps/[appname] PIDFN=$APPROOT/shiny-server.pid ## using full path $HOME/local/shiny-server/bin/shiny-server $APPROOT/server.conf --pidfile=$PIDFN>> $APPROOT/logs/server.log 2>&1 &
crontab -e and add an entry for the script (above):
## try once an hour, on the 10th minute of the hour 10 * * * * /home/[user]/bin/my.shiny.sh
Finally, take a look at memory usage. If you exceed memory limits, Webfaction automatically kills everything. And R’s memory use grows with more connections (which themselves persist, because websockets). Webfaction distributes a nice python script that shows per-process and total memory usage.
I should point out that I like Webfaction (plug) 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!