ERROR: package or namespace load failed for 'shinyURL'

[dkulp2]

Any clue why shinyURL fails to load in a server environment?
The library loads and the functionality works nicely in my RStudio development environment.
When I deploy to a remote server running shiny, I get the "load failed" error. Log files literally disappear on error, suggesting a crash.
Interactive R on the remote server loads shinyURL just fine.

[aoles]

Thank you for reporting your problems! I'm not sure what could be the reason for shinyURL failing to load in an app deployed on a server, but otherwise working just fine. I've never experienced this before. If you provide me with the example app which fails for you, I could deploy it on some other system to see whether this is reproducible.

Cheers,
Andrzej

[dkulp2]

Thanks for the reply, Andrzej.
The example app that fails only in the server environment is the Add-URL-state branch of my repo called opex. It would be a great help if you could try it yourself, which would help me determine whether it is a problem specifically with my server environment.

[aoles]

Hi David,

I just tried your app and I didn't experience any problems. It runs just fine on my local linux machine, and I was also able to successfully deploy it on my shinyapps.io account. There must be something specific to your server configuration. Not sure what could help, but maybe it just needs a fresh restart or R package updates?

If the problem persists, I suggest that you try to boil it down to some minimal example to simplify debugging. For instance, you could try one of the sample apps distributed with shinyURL, see https://github.com/aoles/shinyURL/tree/master/inst/examples

I hope this helps. Once this is resolved, please let me know what the actual problem was.

Cheers,
Andrzej

[dkulp2]

Hi Andrzej,
I've updated to the most recent shiny-server, rebuilt and reinstalled. No luck.
When I tried to reinstall shinyURL, I get the following warning:

devtools::install_github("aoles/shinyURL", force=TRUE)
devtools::install_github("aoles/shinyURL", force=TRUE)
Downloading GitHub repo aoles/shinyURL@master
from URL https://api.github.com/repos/aoles/shinyURL/zipball/master
Installing shinyURL
'/usr/gsl/user4/dkulp/local/lib64/R/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore CMD INSTALL  \
  '/tmp/RtmpH4HEys/devtools4b6c4e742b39/aoles-shinyURL-1928454'  \
  --library='/usr/gsl/user4/dkulp/local/lib64/R/library' --install-tests

* installing *source* package 'shinyURL' ...
** R
**Warning: unable to re-encode 'shinyURL.R' line 11**
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (shinyURL)

Is that a clue? I don't see this warning in my development environment.
Thank you very much for your patience.

[aoles]

Hi,
the error message you get indicates that there might be a problem with the encoding of non-ASCII characters, in particular line 11 of 'shinyURL.R' contains 'ś' in my name. The package correctly specifies UTF-8 encoding in the DESCRIPTION file, but for some reason this doesn't seem to work on your system. What's the result of running Sys.getlocale('LC_CTYPE') in your R session?

[dkulp2]

Sys.getlocale('LC_CTYPE')
[1] "en_US"

On Wed, Jun 22, 2016 at 4:02 AM Andrzej Oleś [email protected]
wrote:

Hi,
the error message you get indicates that there might be a problem with the
encoding of special characters, in particular line 11 of 'shinyURL.R'
https://github.com/aoles/shinyURL/blob/master/R/shinyURL.R#L11 contains
'ś' in my name. The package correctly specifies UTF-8 encoding in the
description file, but for some reason this doesn't seem to work on your
system. What's the result of running Sys.getlocale('LC_CTYPE') in your R
session?

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[aoles]

As mentioned before, you're most probably experiencing some problems with UTF-8 encoding on the server. Maybe a good starting point in tracking this down is to compare the output of locale on the server and on your development environment. Below I include the output on my system for reference.

[oles@localhost ~]$ locale
LANG=en_US.UTF-8
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=

[dkulp2]

Thanks again for your patience. Problem mostly solved. First, the locale issue was a red herring. My locale was en_US and when I set it to en_US.UTF-8, then I did not get the build warning, but I still had the problem with the package load, as described above.
(Debugging the problem was confounded by a shiny-server bug in which the log file disappears on error. It was only after rapid fire "cat" that I displayed the error before the file disappeared!)
I discovered that the problem is that the RCurl package could not load the necessary shared libraries. Shiny-server sets a minimal LD_LIBRARY_PATH. My libcurl and libssh are located in non-standard locations on the server. No matter if I started shiny-server with an exported or prefaced LD_LIBRARY_PATH or if I tried to Sys.setenv(LD_LIBRARY_PATH=...), I can not get these .so files to be found unless I move them to one of the directories that shiny-server includes in its custom LD_LIBRARY_PATH. So that's what I did. shinyURL loads and the application works!

Sort of.

The remaining problem is that I'm using the DT package to use the DataTable JQuery plugin. There seems to be a conflict between the ajax URL and shinyURL as follows.

ShinyURL will mask fields that begin with ".". Although not explicitly shiny input values, I discovered that the DT package creates input fields corresponding to each datatable in order to maintain state via ajax. And these values are encoded by shinyURL. However, a large DT creates a very long list of name/value pairs encoded in the URL (1000s of chars). If I preface the table names with a dot, then they are excluded from the URL... and this works fine in RStudio's development environment. But on a remote server running the shiny-server node.js application, then the URLs with dots in them are blocked with a "403 forbidden". (I don't know why you were successful using shinyapps.io. There might be a difference between the open source DIY release of shiny-server and shinyapps.io that's hosted by RStudio.)

One solution might be to add a method in the ShinyURL package that lists the names of inputs to exclude as an alternative to the dot convention.

Any thoughts?

[aoles]

Hi,
Please excuse my delayed answer. I'm happy that you've eventually managed to overcome the server configuration issues.

Re the DT-related issue: I'm not sure I follow. When a DT table name starts with a dot, e.g. .mytable, all the DT-specific inputs associated with it are masked and they do not appear in the app's URL query string. Therefore, I don't quite understand the problem: the URLs with dots in them are blocked with a "403 forbidden". Can you clarify, please?

Cheers,
Andrzej

[yonicd]

I am getting the same error. I am running on the shiny-server code from here https://github.com/yonicd/shiny_apps/tree/master/ggtree and when i move to the table the ajax crashes. when i look at the error on the network log it shows a 403 error for the .table object.

this runs fine on shinyapps.io and localhost but not on shiny-server

on shinyapps.io it looks like this:

[ramindehghanpoor]

Hi,
I have the same problem. How did you move libssh to one of the directories that shiny-server includes in its custom LD_LIBRARY_PATH?
Thanks,