shiny-server returning "Not Found" on apps

[bbest]

When visiting a Shiny app, eg http://mbon.marine.usf.edu:3838/test/, I'm now getting Not Found error:

Was working until 4am PST this morning, but had to change a bunch of permissions on rstudio-shiny server so may be related.

[bbest]

Hi @7yl4r,

Everything was working pretty well up until 4am PST, and then at 10:30am PST I see this error, which is a total show stopper. I'm pretty sure is related to https://github.com/marinebon/sdg14/issues/25. I'm having a hell of a time sorting through this and could use an extra set of eyes. Would you have time tomorrow to look at this with me?

Thanks, Ben

[bbest]

Confused b/c according to mbon host, shiny should be hosting shiny apps located in /srv/shiny-server, per /etc/shiny-server/shiny-server.conf on rstudio-shiny docker instance per ...

docker logs rstudio-shiny

[2017-08-01 20:21:32.908] [INFO] shiny-server - Shiny Server v1.5.4.847 (Node.js v6.10.3)
[2017-08-01 20:21:32.913] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
[2017-08-01 20:21:32.966] [WARN] shiny-server - Running as root unnecessarily is a security risk! You could be running more securely as non-root.
[2017-08-01 20:21:32.970] [INFO] shiny-server - Starting listener on 0.0.0.0:3838

Then to inspect /etc/shiny-server/shiny-server.conf on rstudio-shiny, login into terminal ...

docker exec -it rstudio-shiny bash

So in instance...

view /etc/shiny-server/shiny-server.conf

Here's the contents of /etc/shiny-server/shiny-server.conf:

# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;

# Define a server that listens on port 3838
server {
  listen 3838;

  # Define a location at the base URL
  location / {

    # Host the directory of Shiny Apps stored in this directory
    site_dir /srv/shiny-server;

    # Log all Shiny output to files in this directory
    log_dir /var/log/shiny-server;

    # When a user visits the base URL rather than a particular application,
    # an index of the applications available in this directory will be shown.
    directory_index on;
  }
}

But weirdly docker logs rstudio-shiny reported:

Running as root unnecessarily is a security risk! You could be running more securely as non-root.

This, despite the /etc/shiny-server/shiny-server.conf having the run_as shiny; argument.

[bbest]

Ah hah! Thanks so much Tylar for awesome help with this. Turns out the extra Rmd in the shiny root folder was giving it issues, so this fixed it:

cd /mbon/shiny
mv seascape_prep.Rmd ../.
mv mbon_postgis_db.R ../.

This was found by visiting http://mbon.marine.usf.edu:8787/ which gave a different error about checking your logs and then noticing on host mbon:

cd /mbon/shiny-log/
ls -latr /mbon/shiny-log
cat env-shiny-20170801-204237-41950.log

processing file: seascape_prep.Rmd
Quitting from lines 48-61 (seascape_prep.Rmd) 
Warning: Error in raster: could not find function "raster"
Stack trace (innermost first):
    115: eval
    114: eval
    113: withVisible
    112: withCallingHandlers
    111: handle
    110: timing_fn
    109: evaluate_call
    108: evaluate::evaluate
    107: evaluate
    106: in_dir
    105: block_exec
    104: call_block
    103: process_group.block
    102: process_group
    101: withCallingHandlers
    100: process_file
     99: knitr::knit
     98: <Anonymous>
     97: do.call
     96: contextFunc
     95: .getReactiveEnvironment()$runWith
     94: shiny::maskReactiveContext
     93: <reactive>
     82: doc
     81: shiny::renderUI
     80: func
     79: origRenderFunc
     78: output$__reactivedoc__
      3: <Anonymous>
      2: do.call
      1: rmarkdown::run