explore_endpoints not redirecting to website

[ccchatman]

It's difficult for me to determine if the error is due to something on my system or if the redirect option is experiencing issues. This is my first time trying to use the toxEval workflow.

library(toxEval)
explore_endpoints()

Listening on http://127.0.0.1:4353
The name provided ('fa-file-code-o') does not correspond to a known icon
Warning: Navigation containers expect a collection of bslib::nav()/shiny::tabPanel()s and/or bslib::nav_menu()/shiny::navbarMenu()s. Consider using header or footer if you wish to place content above (or below) every panel's contents.
Warning in file(con, "r") :
cannot open file 'www/footer.html': No such file or directory
Warning: Error in file: cannot open the connection
78: file
77: readLines
76: htmltools::includeHTML
2: shiny::runApp
1: explore_endpoints
The name provided ('fa-file-code-o') does not correspond to a known icon
Warning: Navigation containers expect a collection of bslib::nav()/shiny::tabPanel()s and/or bslib::nav_menu()/shiny::navbarMenu()s. Consider using header or footer if you wish to place content above (or below) every panel's contents.
Warning in file(con, "r") :
cannot open file 'www/footer.html': No such file or directory
Warning: Error in file: cannot open the connection
78: file
77: readLines
76: htmltools::includeHTML
2: shiny::runApp
1: explore_endpoints

[ldecicco-USGS]

Hmm....I think a file (the footer.html) didn't make it to the CRAN submission. The package as a whole comes super close to exceeding the CRAN requirement for size that I often need to figure out the best way to exclude non-essential files for the submission.

I think you can install via github and get the full set of files:

remotes::install_github("DOI-USGS/toxEval")

I'm having some internet issues at the moment so I wasn't able to test for sure. Let me know if that doesn't solve the problem. I'll also check later when I get to more stable internet. Another solution would be to use our hosted app:

https://rconnect.usgs.gov/toxEval

Side note...I see you are at UW-Madison? Our office is nearly on campus (Forest Products Lab near the UW hospital). I'd love to hear what you're working on and in which department! Feel free to email me directly ([email protected]) if you wanted to chat or had any toxEval questions.

[ccchatman]

Hello, Yes, I’m at UW-Madison over in the Microbial Sciences Building. I work in Dr. Erica Majumder’s lab on environmental exposure research. If you want to learn more about what I’m working on, I’d be happy to schedule a time to chat. Thank you so much for that tip! I will try that and let you know if it works. Best, CHAMIA CHATMAN Chamia Chatman (she/her) Majumder Lab, PhD candidate Molecular & Environmental Toxicology Graduate Program University of Wisconsin-Madison From: Laura DeCicco ***@***.***> Sent: Monday, August 7, 2023 12:47 PM To: DOI-USGS/toxEval ***@***.***> Cc: CHAMIA CHATMAN ***@***.***>; Author ***@***.***> Subject: Re: [DOI-USGS/toxEval] explore_endpoints not redirecting to website (Issue #405) Hmm....I think a file (the footer.html) didn't make it to the CRAN submission. The package as a whole comes super close to exceeding the CRAN requirement for size that I often need to figure out the best way to exclude non-essential files for the submission. I think you can install via github and get the full set of files: remotes::install_github("DOI-USGS/toxEval") I'm having some internet issues at the moment so I wasn't able to test for sure. Let me know if that doesn't solve the problem. I'll also check later when I get to more stable internet. Another solution would be to use our hosted app: https://rconnect.usgs.gov/toxEval Side note...I see you are at UW-Madison? Our office is nearly on campus (Forest Products Lab near the UW hospital). I'd love to hear what you're working on and in which department! Feel free to email me directly ***@***.******@***.***>) if you wanted to chat or had any toxEval questions. — Reply to this email directly, view it on GitHub<#405 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A6LTCXRKAJPRF5G6LBPUFQDXUESY5ANCNFSM6AAAAAA3FGUI6M>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[ccchatman]

The install worked but but still won't allow for me to connect to the website. I also tried using the link you provided and was able to upload data but then it shows that the server is disconnected. If you are willing and available this week, would it be possible to meet in person to explore options to resolve this?

[ldecicco-USGS]

I haven't played with the Shiny app lately, let me take a look this afternoon to see what is happening. From what I see just poking around, clicking "Load example data" seems to work just fine, but using some other files I'm getting errors.

Could you email me your formatted Excel data file? I'll try to make it work locally and then we could meet. My schedule is more free later in the week.

Not sure if you've seen this, but here are some slides on toxEval and ToxMixtures that we recently put together (use the arrow keys to navigate).
https://rconnect.usgs.gov/toxEval_NMC/toxEval.html#/title-slide
I tend to focus on script-based workflows instead of the Shiny app, so I apologize for not noticing something must have changed in the app. Again, I'll take a look this afternoon and see if it's an easy fix.

[maryclairebuell]

Hello I am having the same issue and have tried the above mentioned solutions with no luck.
Any tips on what to do next would be amazing, I have a lab set up for my students in toxEval tomorrow at noon EST. Unfortunately even the link to the app is having the same issues as the person above. Hoping I can figure this out before the students begin learning this! Thanks so much!

Below is what I am getting:

explore_endpoints()
Loading required package: shiny

Listening on http://127.0.0.1:6001

Attaching package: ‘shinydashboard’

The following object is masked from ‘package:graphics’:

box

The name provided ('fa-file-code-o') does not correspond to a known icon
Warning: Navigation containers expect a collection of bslib::nav_panel()/shiny::tabPanel()s and/or bslib::nav_menu()/shiny::navbarMenu()s. Consider using header or footer if you wish to place content above (or below) every panel's contents.
Warning in file(con, "r") :
cannot open file 'www/footer.html': No such file or directory
Warning: Error in file: cannot open the connection
69: file
68: readLines
67: htmltools::includeHTML
2: shiny::runApp
1: explore_endpoints
The name provided ('fa-file-code-o') does not correspond to a known icon
Warning: Navigation containers expect a collection of bslib::nav_panel()/shiny::tabPanel()s and/or bslib::nav_menu()/shiny::navbarMenu()s. Consider using header or footer if you wish to place content above (or below) every panel's contents.
Warning in file(con, "r") :
cannot open file 'www/footer.html': No such file or directory
Warning: Error in file: cannot open the connection
69: file
68: readLines
67: htmltools::includeHTML
2: shiny::runApp
1: explore_endpoints

[ldecicco-USGS]

@maryclairebuell re-install like this (I just pushed a fix):

remotes::install_github("DOI-USGS/toxEval", force = TRUE)

You might see this message:

Downloading GitHub repo DOI-USGS/toxEval@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

Choose 3 (which goes with "None"). After the package is installed, you might want to Update all packages if there was a large list.

[ldecicco-USGS]

Let me know if that doesn't fix it for you, and in the meantime I'll try to figure out what is going on with the rconnect app. It's working for me at the moment.

Assuming the fix above works, it would be best to have your students install with those directions and run the app locally. I've not tested the rconnect link with a bunch of simultaneous users.

[maryclairebuell]

Thank you so much! You are a hero :)
It worked! I'll have my students do this as well.
I think they will have a lot of fun learning this today. Thank you for your help!