disconnected from server- local shiny server

[shunido]

Hello there

I having a sticky old question , I just took a project from someone left , there was an app running with shiny server , but now from days I see disconnected from server , I browsed the network trying to find a solution but was not able to find out, even by topics from here

I dont have updates on logs

the only thing I see , that rmarkdown package is installed but the default page [local-ip]:3838 is showing that box in the right still missing rmarkdown poackage , loading the app is giving disconnected from server ..

I dont know if something can help me find ouyt what ?

Thanks

[andresrcs]

You are not providing enough information for us to be able to help you. We need to see the app's logs to have an idea of what might be going on.

About shiny-server not being able to load rmarkdown files. This might be happening because rmarkdown is not installed system wide and the shiny user does not have access to it. You need to install R packages system wide in order for shiny apps to be able to use them.

[shunido]

Hello

I did installed it system wide with :
sudo su - -c "R -e "install.packages('rmarkdown', repos='http://cran.rstudio.com/')""

Also I am attaching photos for issue and setups...
Please tell me if there is any logs that I can share ?

[shunido]

[shunido]

[shunido]

[andresrcs]

Have you modified the run_as option in your shiny-server config file? Can you show the complete output of running sudo su - -c "R -e "install.packages('rmarkdown', repos='http://cran.rstudio.com/')"" in a system terminal?

BTW, please do not post screenshots of your terminal, they are considered a bad practice here, post the output as formatted code instead. Here is how to do it

FAQ: How to format your code

Formatting Code: the Basics All code or console output you include in your posts should be formatted properly. Luckily, this is very easy to do! Just use the code formatting button at the top of the post editing box: [image] Select some code Click the </> button! The code formatting button automatically adds special Markdown formatting symbols to whatever you selected. If you check the preview pane to the right of your post, you'll see that the forum software now outputs nicely formatted code . [04] The code formatting button is pretty smart! It can tell the difference between snippets of code that are part of a sentence and blocks of code that stand alone. …

[shunido]

Hi

The whole line command is giving a bash script error , so I install it with root user

*R version 3.6.3 (2020-02-29) -- "Holding the Windsock"*
*Copyright (C) 2020 The R Foundation for Statistical Computing*
*Platform: x86_64-pc-linux-gnu (64-bit)*

*R est un logiciel libre livré sans AUCUNE GARANTIE.*
*Vous pouvez le redistribuer sous certaines conditions.*
*Tapez 'license()' ou 'licence()' pour plus de détails.*

*R est un projet collaboratif avec de nombreux contributeurs.*
*Tapez 'contributors()' pour plus d'information et*
*'citation()' pour la façon de le citer dans les publications.*

*Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide*
*en ligne ou 'help.start()' pour obtenir l'aide au format HTML.*
*Tapez 'q()' pour quitter R.*

*[Sauvegarde de la session précédente restaurée]*

*> install.packages("rmarkdown")*
*Installation du package dans ‘/usr/local/lib/R/site-library’*
*(car ‘lib’ n'est pas spécifié)*
*essai de l'URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.19.tar.gz'*
*Content type 'application/x-gzip' length 3243575 bytes (3.1 MB)*
*==================================================*
*downloaded 3.1 MB*

** installing *source* package ‘rmarkdown’ ...*
*** package ‘rmarkdown’ correctement décompressé et sommes MD5 vérifiées*
*** using staged installation*
*** R*
*** inst*
*** byte-compile and prepare package for lazy loading*
*** help*
**** installing help indices*
**** copying figures*
*** building package indices*
*** installing vignettes*
*** testing if installed package can be loaded from temporary location*
*** testing if installed package can be loaded from final location*
*** testing if installed package keeps a record of temporary installation path*
** DONE (rmarkdown)*

*Les packages source téléchargés sont dans*
*        ‘/tmp/RtmpgIFHFK/downloaded_packages’*
*>*

for the user from file /etc/shiny-server/shiny-server.conf
run_as shiny;

[andresrcs]

It might be a permissions issue with the site-library folder, just to test my theory can you set the folder permissions to 777 just for a quick test?

sudo chmod 777 -r /usr/lib/R/site-library

Another possibility is that for some reason the .libPaths() of the shiny user are pointing to a different location but I can't think of an easy way to test that other than printing the .libPaths() in your app itself.

[shunido]

I just tried .... it is annoying as nothing came up ... getting same result

Also , using shiny user , I am able to find the library rmarkdown
and

.libPaths()
[1] "/home/shiny/R/x86_64-pc-linux-gnu-library/3.6"
[2] "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"
[4] "/usr/lib/R/library"

[andresrcs]

@shunido

Also , using shiny user , I am able to find the library rmarkdown
and

I thought it was not possible to log as the shiny user, my bad.

Sorry, I'm out of ideas. I can't think of a reason for shiny-server not recognizing rmarkdown.

[shunido]

If not , can you please think about how can I troubleshoot why an app is giving disconnected from server ?

[andresrcs]

@shunido

how can I troubleshoot why an app is giving disconnected from server ?

That is a generic message you get on the app client when the app crashes on the server, we would need to see the logs to have a clue of what is going on. Each app generates a log file in the /var/log/shiny-server/ folder when the app is running, if the app crashes, the file is kept.

[shunido]

Here are the last 2 logs from the APP by 5 January

==> /var/log/shiny-server/APP-shiny-20230105-104133-33049.log <==
closing unused RODBC handle 7
Warning in for (name in names(public_methods)) lockBinding(name, public_bind_env) :
closing unused RODBC handle 6
Warning in for (name in names(public_methods)) lockBinding(name, public_bind_env) :
closing unused RODBC handle 5
Warning in for (name in names(public_methods)) lockBinding(name, public_bind_env) :
closing unused RODBC handle 4

Exécution arrêtée

==> /var/log/shiny-server/APP-shiny-20230105-123237-43355.log <==
les noms de lignes sont trouvés dans une variable courte et ont été éliminés
Warning in for (i in seq_along(cenv$extra)) { :
closing unused RODBC handle 1

Exécution arrêtée
Warning messages:
1: closing unused RODBC handle 3
2: closing unused RODBC handle 2

[andresrcs]

Those logs are not very informative, I don't see an evident reason. I would explore the possibility that your RDBMS or some network security feature in your server might be closing the connection on its side.

I don't have experience debugging shiny apps on the client side but if you know your way around HTML and Javascript you could inspect the console on the client's browser to get more information.

If you can run the app interactively from RStudio you could also try to debug following this guideline

Shiny - Debugging Shiny applications

[shunido]

hello Andres

I have some few updates if you can assume something

I had upgraded R to latest 4.2 and shiny server too
I have them working with no issues and also on the sample default page everything is working even that part which require markdown package installed

but the app still not loading
trying to excute server.R giving
shiny@bims:/srv/shiny-server/APP$ ./server.R
./server.R: ligne 4: erreur de syntaxe près du symbole inattendu « XML »
./server.R: ligne 4: `require(XML)'

running R and checking XML and other required packages shiwing that they exist ... can you wonder if there is a mistake here ? do I change packages path to another shared location ? knowing that I tryed with chmod 777 at /usr/lib/R...

[andresrcs]

@shunido

shiny@bims:/srv/shiny-server/APP$ ./server.R
./server.R: ligne 4: erreur de syntaxe près du symbole inattendu « XML »
./server.R: ligne 4: `require(XML)'

This is not meant to be executed from the terminal but the syntax warning makes me think on a possible encoding issue, are you able to share a link to your app files so I can take a look?

[shunido]

Here is a folder with app files

https://drive.google.com/drive/folders/1GU5TdF11sHr-kZlNXoU0RouBcKXXYG5n?usp=share_link

[andresrcs]

Encoding seems to be OK but the library calls are a mess, there are a bunch of duplicated and commented library calls in both app files, and maybe that is causing the problem. I would start by tidying up the library calls and avoid using require(), use library() instead.