Answers.Body: <p>Are you behind a firewall by chance? The default command requests the human genome files (hg19) from our website. In this case, you would have to provide your own genome to JBrowseR instead of using the simplified 'ViewHg19' command.</p>
  <p>You can also ask questions at our issue tracker here
  <a href="https://github.com/gmod/jbrowser" rel="nofollow noreferrer">https://github.com/gmod/jbrowser</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-17T13:09:47.997Z
Answers.Text: Thank you so much for replying! I edited my questions with more details as I try to debug the issue, still don't have a clue.
Answers.UserDisplayName: miri
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-23T20:42:08.240Z
Answers.Text: thanks for adding the details. that is odd that it is working in one environment for you (vscode) but not in RStudio. I tried using in "plain old R" (running R on the command line) and it appeared to work. I can't use rstudio at the moment (doesn't install on my machine) but it seems like it would be odd to see these differences that you are seeing
Answers.UserDisplayName: Colin D
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-05-05T05:43:03.990Z
Answers.Text: Hi @Colin
  Can you link the community to further consult with about me issues, please?
Answers.UserDisplayName: miri
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-05-07T01:54:33.593Z
Answers.Text: you can post in the issues at https://github.com/gmod/jbrowser or use any sort of contact we have listed here :) https://jbrowse.org/jb2/contact/
Answers.UserDisplayName: Colin D
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-15T20:57:04.650Z
Answers.LastActivityDate: 2024-04-15T20:57:04.650Z
Answers.UserDisplayName: Colin D
Body: <p>I took the simplest code from <a href="https://gmod.github.io/JBrowseR/" rel="nofollow noreferrer">https://gmod.github.io/JBrowseR/</a>:</p>
  <pre><code>JBrowseR(&quot;ViewHg19&quot;, location = &quot;10:29,838,737..29,838,819&quot;) 
  </code></pre>
  <p>I try to build a simple ShinyR app just with this code,
  but I get TypeError: Failed to fetch inside the Jbrowse web that opened.</p>
  <pre><code>TypeError: Failed to fetch
  TypeError: Failed to fetch
      at l.f [as fetchImplementation] (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:15:80910)
      at l.fetch (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:218:871828)
      at async l.readFile (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:218:872936)
      at async http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:2:179301
      at async l.getSequenceSizes (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:2:179921)
      at async i.getRegions (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:15:496733)
      at async Object.loadPre (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:2:284444)
      at async Proxy.waitForAssembly (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:2:287774)
      at async Object.navToLocString (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:15:464975)
      at async http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:218:1839814
  </code></pre>
  <p>I don't know who to proceed/ debug/ solve so any help would be blessed.</p>
  <p>I run the following code:</p>
  <pre><code>library(shiny)
  library(JBrowseR)
  library(bslib)
  
  ui &lt;- fluidPage(
    # Overriding the default bootstrap theme is needed to get proper font size
    theme = bs_theme(version = 5),
    titlePanel(&quot;JBrowseR Example&quot;),
    JBrowseROutput(&quot;widgetOutput&quot;)
  )
  server &lt;- function(input, output, session) {
    
    hg38 &lt;- assembly(
      &quot;https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz&quot;,
      bgzip = TRUE,
      aliases = c(&quot;GRCh38&quot;),
      refname_aliases = &quot;https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt&quot;
    )
  
    output$widgetOutput &lt;- renderJBrowseR(JBrowseR(
      &quot;View&quot;,
      location = &quot;10:29,838,737..29,838,819&quot;,
      assembly = hg38,
      text_index = text_index(
        &quot;https://jbrowse.org/genomes/GRCh38/trix/hg38.ix&quot;,
        &quot;https://jbrowse.org/genomes/GRCh38/trix/hg38.ixx&quot;,
        &quot;https://jbrowse.org/genomes/GRCh38/trix/meta.json&quot;,
        &quot;hg38&quot;
      )
    ))
  }
  shinyApp(ui, server)
  </code></pre>
  <p>On VSCode, as app.R, it works. It pops up a window with JBrowse on <a href="http://127.0.0.1:7688" rel="nofollow noreferrer">http://127.0.0.1:7688</a> But I need to choose track from the &quot;OPEN TRACK SELECTOR&quot;. In Rstudio, I get this error above and it is listening on a different port: <a href="http://127.0.0.1:4983" rel="nofollow noreferrer">http://127.0.0.1:4983</a>.
  Both run in the same server so I don't think it's a firewall.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-10T11:15:25.647Z
Comments.Text: Please [edit] your question and give us some context. What operating system are you using? What browser? How are you running this command? You have tagged with R, is this in an R script? Where's the script? What version of R? Did you even load the relevant library? Have you installed the package? Please give us more details so we can help you.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-10T17:46:10.400Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-15T05:08:53.700Z
Comments.Text: The JBrowseR package is for running Jbrowse in ShinyR. I tried to build a simple ShinyR app just with this code, given in the documentation of this library, but I get this error.
  I installed all relevant libraries, and copied all required code as in that example code.
Comments.UserDisplayName: miri
Tags: <r>
Title: JbrowseR usage - get error with the simplest example
ThreadText: # JbrowseR usage - get error with the simplest example
  
  (Asked by: username_0 on 2024-04-10)
  
  I took the simplest code from <https://gmod.github.io/JBrowseR/>:
  
  ```
  JBrowseR("ViewHg19", location = "10:29,838,737..29,838,819") 
  
  ```
  
  I try to build a simple ShinyR app just with this code,
  but I get TypeError: Failed to fetch inside the Jbrowse web that opened.
  
  ```
  TypeError: Failed to fetch
  TypeError: Failed to fetch
      at l.f [as fetchImplementation] (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:15:80910)
      at l.fetch (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:218:871828)
      at async l.readFile (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:218:872936)
      at async http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:2:179301
      at async l.getSequenceSizes (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:2:179921)
      at async i.getRegions (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:15:496733)
      at async Object.loadPre (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:2:284444)
      at async Proxy.waitForAssembly (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:2:287774)
      at async Object.navToLocString (http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:15:464975)
      at async http://127.0.0.1:6481/JBrowseR-binding-0.10.2/JBrowseR.js:218:1839814
  
  ```
  
  I don't know who to proceed/ debug/ solve so any help would be blessed.
  
  I run the following code:
  
  ```
  library(shiny)
  library(JBrowseR)
  library(bslib)
  
  ui <- fluidPage(
    # Overriding the default bootstrap theme is needed to get proper font size
    theme = bs_theme(version = 5),
    titlePanel("JBrowseR Example"),
    JBrowseROutput("widgetOutput")
  )
  server <- function(input, output, session) {
    
    hg38 <- assembly(
      "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz",
      bgzip = TRUE,
      aliases = c("GRCh38"),
      refname_aliases = "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
    )
  
    output$widgetOutput <- renderJBrowseR(JBrowseR(
      "View",
      location = "10:29,838,737..29,838,819",
      assembly = hg38,
      text_index = text_index(
        "https://jbrowse.org/genomes/GRCh38/trix/hg38.ix",
        "https://jbrowse.org/genomes/GRCh38/trix/hg38.ixx",
        "https://jbrowse.org/genomes/GRCh38/trix/meta.json",
        "hg38"
      )
    ))
  }
  shinyApp(ui, server)
  
  ```
  
  On VSCode, as app.R, it works. It pops up a window with JBrowse on <http://127.0.0.1:7688> But I need to choose track from the "OPEN TRACK SELECTOR". In Rstudio, I get this error above and it is listening on a different port: <http://127.0.0.1:4983>.
  Both run in the same server so I don't think it's a firewall.
  
  **Tags:** r
  
  > **Comments:**
  > **username_1**: Please [edit] your question and give us some context. What operating system are you using? What browser? How are you running this command? You have tagged with R, is this in an R script? Where's the script? What version of R? Did you even load the relevant library? Have you installed the package? Please give us more details so we can help you.  
  > **username_2**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_0**: The JBrowseR package is for running Jbrowse in ShinyR. I tried to build a simple ShinyR app just with this code, given in the documentation of this library, but I get this error. I installed all relevant libraries, and copied all required code as in that example code.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2024-04-15. Score: 0
  
  Are you behind a firewall by chance? The default command requests the human genome files (hg19) from our website. In this case, you would have to provide your own genome to JBrowseR instead of using the simplified 'ViewHg19' command.
  
  You can also ask questions at our issue tracker here
  <https://github.com/gmod/jbrowser>
  
  > **Comments:**
  > **username_0**: Thank you so much for replying! I edited my questions with more details as I try to debug the issue, still don't have a clue.  
  > **username_3**: thanks for adding the details. that is odd that it is working in one environment for you (vscode) but not in RStudio. I tried using in "plain old R" (running R on the command line) and it appeared to work. I can't use rstudio at the moment (doesn't install on my machine) but it seems like it would be odd to see these differences that you are seeing  
  > **username_0**: Hi @username_3 Can you link the community to further consult with about me issues, please?  
  > **username_3**: you can post in the issues at https://github.com/gmod/jbrowser or use any sort of contact we have listed here :) https://jbrowse.org/jb2/contact/  
  
  ---
  
  