title: R shiny / shiny-server - issue with finding packages
body: <p>I have installed shiny and shiny-server on an ubuntu server. I did a similar install on a dev server which is working. R sessions when they open up load some packages. The app runs fine locally but I'm getting messages that it can't find the packages when running on shiny-server. </p>
  
  <p>The error on the app</p>
  
  <pre><code>During startup - Warning messages:
  
  1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called ‘shiny’
  2: package ‘shiny’ in options("defaultPackages") was not found 
  3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called ‘data.table’
  4: package ‘data.table’ in options("defaultPackages") was not found 
  5: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called ‘optiRum’
  6: package ‘optiRum’ in options("defaultPackages") was not found 
  Error in eval(expr, envir, enclos) : 
    The Shiny package was not found in the library. Ensure that 
  Shiny is installed and is available in the Library of the 
  user you're running this application as.
  Calls: local -&gt; eval.parent -&gt; eval -&gt; eval -&gt; eval -&gt; eval
  Execution halted
  </code></pre>
  
  <p>In Rprofile.site I have</p>
  
  <pre><code># ## Example of Rprofile.site
   local({
  #  # add MASS to the default packages, set a CRAN mirror
    old &lt;- getOption("defaultPackages"); r &lt;- getOption("repos")
  #  r["CRAN"] &lt;- "http://my.local.cran"
    options(defaultPackages = c(old, "shiny","data.table","optiRum"), repos = r)
  })
  
  .First &lt;- function() {
     cat("\n   Welcome to R!\n\n")
  #    setwd("/home/OPTIMUMCREDIT/R/Projects")
      Sys.umask(mode="0002")
  }
  .libPaths(c("/home/R/WorkingPackages","/home/R/ApprovedPackages"))
  </code></pre>
  
  <p>In shiny-server config I have just the default config  (so run as shiny and default port).</p>
  
  <p>My sessionInfo()</p>
  
  <pre><code>&gt; sessionInfo()
  R version 3.0.3 (2014-03-06)
  Platform: x86_64-pc-linux-gnu (64-bit)
  
  locale:
   [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C            LC_COLLATE=C         LC_MONETARY=C        LC_MESSAGES=C        LC_PAPER=C          
   [8] LC_NAME=C            LC_ADDRESS=C         LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C 
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  other attached packages:
  [1] ggplot2_0.9.3.1  scales_0.2.3     RCurl_1.95-4.1   bitops_1.0-6     rstudio_0.98.501 optiRum_0.30     data.table_1.9.2 shiny_0.8.0     
  
  loaded via a namespace (and not attached):
   [1] MASS_7.3-29        RColorBrewer_1.0-5 RJSONIO_1.0-3      Rcpp_0.11.0        caTools_1.16       colorspace_1.2-4   dichromat_2.0-0   
   [8] digest_0.6.4       grid_3.0.3         gtable_0.1.2       httpuv_1.2.3       labeling_0.2       munsell_0.4.2      plyr_1.8.1        
  [15] proto_0.3-10       reshape2_1.2.2     stringr_0.6.2      tools_3.0.3        xtable_1.7-3
  </code></pre>
  
  <p>I tried adding a message to output the libPaths above <code>library(shiny)</code> in my code but unfortunately the same error message happens. I did some uninstalling and reinstalling as I'd a bit unusually installed shiny-server first then remembered I needed shiny but no joy. I've confirmed that shiny is installed in ApprovedPackages.  The packages at load up, I added in the hopes of circumventing the problem or finding out more information.</p>
  
  <p><strong>UPDATE - running as shiny</strong>
  Ah - the plot thickens... logging in with the user shiny on console caused the same warnings the app was getting, and .libPaths() is not like everyone else's: </p>
  
  <pre><code>&gt; sessionInfo()
  R version 3.0.3 (2014-03-06)
  Platform: x86_64-pc-linux-gnu (64-bit)
  
  locale:
   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
   [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
   [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
   [9] LC_ADDRESS=C               LC_TELEPHONE=C
  [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base
  &gt; .libPaths()
  [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
  [3] "/usr/lib/R/library"
  </code></pre>
  
  <p><strong>I'm a bit stumped and was hoping someone could point me in the right direction to solve the problem.</strong></p>