From 178d35dfa45c4139d2e01ac7a45ad51375fbc604 Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Mon, 22 Apr 2024 11:37:25 +0530
Subject: [PATCH 01/39] update

---
 R/mod_code_explorer.R       | 51 +++++++++++++++++++++++++++++++++++++
 R/mod_code_explorer_utils.R | 11 ++++++++
 2 files changed, 62 insertions(+)

diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index 0a74d3337..ff2011fbd 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -31,6 +31,14 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
       } else {
         div(introJSUI(NS(id, "introJS")),
           br(),
+          fluidRow(column(2,offset = 8,
+                          conditionalPanel(
+                            condition = "typeof(window.$highlights_list) != 'undefined' && window.$highlights_list.length > 1",
+                          actionButton(ns("next_button"),label = "Next"))),
+                   column(2,
+                          conditionalPanel(
+                            condition = "typeof(window.$highlights_list) != 'undefined'  && window.$highlights_list.length > 1",
+                          actionButton(ns("prev_button"),label = "Prev")))),
           fluidRow(
             column(3,
                    wellPanel(
@@ -166,6 +174,49 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     
     introJSServer("introJS", text = reactive(fe_steps), user, credentials)
     
+    observeEvent(input$next_button,{
+      if (input$next_button > 0){
+      shinyjs::runjs('
+                      // debugger;
+                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
+              if( $index == window.$highlights_list.length -1) {
+              
+              var $gh = window.$highlights_list[0]
+              
+              }
+              else 
+              {
+              var $gh = window.$highlights_list[$index +1]
+              }  
+              var $target = document.querySelector("#code_explorer-file_viewer")
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+              ')
+      }
+      
+    })
+    
+    observeEvent(input$prev_button,{
+      if (input$next_button > 0){
+        shinyjs::runjs('
+                      // debugger;
+                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
+              if( $index ==0) {
+              var $gh = window.$highlights_list[window.$highlights_list.length -1]
+              
+              
+              }
+              else 
+              {
+              var $gh = window.$highlights_list[$index -1]
+              }  
+              var $target = document.querySelector("#code_explorer-file_viewer")
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+              ')
+      }
+      
+    })
     output$file_output <- renderUI({
       switch (input$file_type,
               test = test_code(),
diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
index f0cbcd6bf..f9bd5edea 100644
--- a/R/mod_code_explorer_utils.R
+++ b/R/mod_code_explorer_utils.R
@@ -169,9 +169,20 @@ renderCode <- function(lines, hlindex) {
                })
              ),
              tags$script(HTML("
+                             
         document.querySelectorAll('.code pre').forEach(bl => {
           hljs.highlightBlock(bl);
         }); 
+       
+        debugger;
+        var $highlights_list = document.querySelectorAll('.highlight')
+       if(typeof($highlights_list) != 'undefined'){
+        var $gh = document.querySelector('.highlight')
+        var $target = document.querySelector('#code_explorer-file_viewer')
+        // debugger;
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+       }
       "))
   )
 }

From 687dfd435e9af17c9ac10428a37c9227fbea990e Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Mon, 22 Apr 2024 11:37:25 +0530
Subject: [PATCH 02/39] update

---
 R/mod_code_explorer.R       | 51 +++++++++++++++++++++++++++++++++++++
 R/mod_code_explorer_utils.R | 11 ++++++++
 2 files changed, 62 insertions(+)

diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index 7d0ebffda..288dcf229 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -32,6 +32,14 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
       } else {
         div(introJSUI(NS(id, "introJS")),
           br(),
+          fluidRow(column(2,offset = 8,
+                          conditionalPanel(
+                            condition = "typeof(window.$highlights_list) != 'undefined' && window.$highlights_list.length > 1",
+                          actionButton(ns("next_button"),label = "Next"))),
+                   column(2,
+                          conditionalPanel(
+                            condition = "typeof(window.$highlights_list) != 'undefined'  && window.$highlights_list.length > 1",
+                          actionButton(ns("prev_button"),label = "Prev")))),
           fluidRow(
             column(3,
                    wellPanel(
@@ -167,6 +175,49 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     
     introJSServer("introJS", text = reactive(fe_steps), user, credentials)
     
+    observeEvent(input$next_button,{
+      if (input$next_button > 0){
+      shinyjs::runjs('
+                      // debugger;
+                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
+              if( $index == window.$highlights_list.length -1) {
+              
+              var $gh = window.$highlights_list[0]
+              
+              }
+              else 
+              {
+              var $gh = window.$highlights_list[$index +1]
+              }  
+              var $target = document.querySelector("#code_explorer-file_viewer")
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+              ')
+      }
+      
+    })
+    
+    observeEvent(input$prev_button,{
+      if (input$next_button > 0){
+        shinyjs::runjs('
+                      // debugger;
+                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
+              if( $index ==0) {
+              var $gh = window.$highlights_list[window.$highlights_list.length -1]
+              
+              
+              }
+              else 
+              {
+              var $gh = window.$highlights_list[$index -1]
+              }  
+              var $target = document.querySelector("#code_explorer-file_viewer")
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+              ')
+      }
+      
+    })
     output$file_output <- renderUI({
       switch (input$file_type,
               test = test_code(),
diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
index 9d73ceec6..621524b0d 100644
--- a/R/mod_code_explorer_utils.R
+++ b/R/mod_code_explorer_utils.R
@@ -172,9 +172,20 @@ renderCode <- function(lines, hlindex) {
                })
              ),
              tags$script(HTML("
+                             
         document.querySelectorAll('.code pre').forEach(bl => {
           hljs.highlightBlock(bl);
         }); 
+       
+        debugger;
+        var $highlights_list = document.querySelectorAll('.highlight')
+       if(typeof($highlights_list) != 'undefined'){
+        var $gh = document.querySelector('.highlight')
+        var $target = document.querySelector('#code_explorer-file_viewer')
+        // debugger;
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+       }
       "))
   )
 }

From 56df0cc77beb7eea70fab5cbb6e0f3b75dfd5fbc Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Tue, 14 May 2024 17:50:51 +0530
Subject: [PATCH 03/39] update

---
 R/mod_code_explorer.R       | 29 +++++++++++++++--------------
 R/mod_code_explorer_utils.R |  6 +++---
 2 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index 288dcf229..eaaeee44f 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -135,7 +135,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
       close(con)
       func_list <- c(input$exported_function, paste0("`", input$exported_function, "`"))
       highlight_index <- parse_data() %>% 
-        filter(stringr::str_ends(file, input$test_files) & func %in% func_list) %>% 
+        filter(basename(file) == input$test_files & func %in% func_list) %>% 
         pull(line)
       renderCode(lines, highlight_index)
     }) %>%
@@ -152,7 +152,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
       close(con)
       func_list <- c(input$exported_function, paste0("`", input$exported_function, "`"))
       highlight_index <- parse_data() %>% 
-        filter(stringr::str_ends(file, input$source_files) & func %in% func_list) %>% 
+        filter(basename(file) ==  input$source_files & func %in% func_list) %>% 
         pull(line)
       renderCode(lines, highlight_index)
     }) %>%
@@ -178,42 +178,43 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     observeEvent(input$next_button,{
       if (input$next_button > 0){
       shinyjs::runjs('
-                      // debugger;
-                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
-              if( $index == window.$highlights_list.length -1) {
+                     
+                     var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($gh));
+              if( $index == $highlights_list.length -1) {
               
-              var $gh = window.$highlights_list[0]
+              $gh = $highlights_list[0]
               
               }
               else 
               {
-              var $gh = window.$highlights_list[$index +1]
+              $gh = $highlights_list[$index +1]
               }  
+                
               var $target = document.querySelector("#code_explorer-file_viewer")
         $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+        $target.scrollTop =$gh.offsetTop -40; 
               ')
       }
       
     })
     
     observeEvent(input$prev_button,{
-      if (input$next_button > 0){
+      if (input$prev_button > 0){
         shinyjs::runjs('
-                      // debugger;
-                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
+                      
+                     var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($gh));
               if( $index ==0) {
-              var $gh = window.$highlights_list[window.$highlights_list.length -1]
+              $gh = $highlights_list[$highlights_list.length -1]
               
               
               }
               else 
               {
-              var $gh = window.$highlights_list[$index -1]
+             $gh = $highlights_list[$index -1]
               }  
               var $target = document.querySelector("#code_explorer-file_viewer")
         $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+        $target.scrollTop = $gh.offsetTop  - 40; 
               ')
       }
       
diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
index 621524b0d..299c39076 100644
--- a/R/mod_code_explorer_utils.R
+++ b/R/mod_code_explorer_utils.R
@@ -177,14 +177,14 @@ renderCode <- function(lines, hlindex) {
           hljs.highlightBlock(bl);
         }); 
        
-        debugger;
         var $highlights_list = document.querySelectorAll('.highlight')
        if(typeof($highlights_list) != 'undefined'){
+       
         var $gh = document.querySelector('.highlight')
+        
         var $target = document.querySelector('#code_explorer-file_viewer')
-        // debugger;
         $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+        $target.scrollTop = $gh.offsetTop  - 40; 
        }
       "))
   )

From 252f7ad29851ab5090e740cf90b46ae0d0aeb58a Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Tue, 14 May 2024 20:55:39 +0530
Subject: [PATCH 04/39] update

---
 R/mod_code_explorer.R       | 69 ++++++++++++++++++++-----------------
 R/mod_code_explorer_utils.R |  4 +--
 2 files changed, 40 insertions(+), 33 deletions(-)

diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index eaaeee44f..97d6ca78f 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -31,15 +31,24 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
         showHelperMessage(message = glue::glue("Source code not available for {{{selected_pkg$name()}}}"))
       } else {
         div(introJSUI(NS(id, "introJS")),
-          br(),
-          fluidRow(column(2,offset = 8,
+          fluidRow(style = "height:35px !important;",
+                   column(2,offset = 10,
                           conditionalPanel(
                             condition = "typeof(window.$highlights_list) != 'undefined' && window.$highlights_list.length > 1",
-                          actionButton(ns("next_button"),label = "Next"))),
-                   column(2,
+                          actionButton(ns("prev_button"),label = "",icon = icon("chevron-left"),
+                                       style ="width: 32px !important; 
+                            height: 32px !important;
+                            font-size: 16px !important;
+                            line-height: 5px !important;
+                            padding: 0px !important;") |>bslib::tooltip("Previous occurence"), style = "display: inline-block;"),
                           conditionalPanel(
                             condition = "typeof(window.$highlights_list) != 'undefined'  && window.$highlights_list.length > 1",
-                          actionButton(ns("prev_button"),label = "Prev")))),
+                          actionButton(ns("next_button"),label = "",icon = icon("chevron-right"),
+                                       style = "width: 32px !important; 
+                            height: 32px !important;
+                            font-size: 16px !important;
+                            line-height: 5px !important;
+                            padding: 0px !important;")|>bslib::tooltip("Next occurence",placement ="right"), style = "display: inline-block;"))),
           fluidRow(
             column(3,
                    wellPanel(
@@ -178,21 +187,21 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     observeEvent(input$next_button,{
       if (input$next_button > 0){
       shinyjs::runjs('
-                     
-                     var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($gh));
-              if( $index == $highlights_list.length -1) {
+                    var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel));
+                    if( $index == $highlights_list.length -1) 
+                    {
               
-              $gh = $highlights_list[0]
+                          $curr_sel = $highlights_list[0]
               
-              }
-              else 
-              {
-              $gh = $highlights_list[$index +1]
-              }  
+                    }
+                else 
+                    {
+                          $curr_sel = $highlights_list[$index +1]
+                    }  
                 
-              var $target = document.querySelector("#code_explorer-file_viewer")
-        $target.scrollTop = 0;
-        $target.scrollTop =$gh.offsetTop -40; 
+                    var $target = document.querySelector("#code_explorer-file_viewer")
+                    $target.scrollTop = 0;
+                    $target.scrollTop =$curr_sel.offsetTop -40; 
               ')
       }
       
@@ -201,20 +210,18 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     observeEvent(input$prev_button,{
       if (input$prev_button > 0){
         shinyjs::runjs('
-                      
-                     var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($gh));
-              if( $index ==0) {
-              $gh = $highlights_list[$highlights_list.length -1]
-              
-              
-              }
-              else 
-              {
-             $gh = $highlights_list[$index -1]
-              }  
-              var $target = document.querySelector("#code_explorer-file_viewer")
-        $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - 40; 
+                      var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel));
+                      if( $index ==0) 
+                      {
+                            $curr_sel = $highlights_list[$highlights_list.length -1]
+                      }
+                        else 
+                      {
+                            $curr_sel = $highlights_list[$index -1]
+                      }  
+                      var $target = document.querySelector("#code_explorer-file_viewer")
+                      $target.scrollTop = 0; # scroll to the top 
+                      $target.scrollTop = $curr_sel.offsetTop  - 40; 
               ')
       }
       
diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
index 299c39076..69300b70d 100644
--- a/R/mod_code_explorer_utils.R
+++ b/R/mod_code_explorer_utils.R
@@ -180,11 +180,11 @@ renderCode <- function(lines, hlindex) {
         var $highlights_list = document.querySelectorAll('.highlight')
        if(typeof($highlights_list) != 'undefined'){
        
-        var $gh = document.querySelector('.highlight')
+        var $curr_sel = document.querySelector('.highlight')
         
         var $target = document.querySelector('#code_explorer-file_viewer')
         $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - 40; 
+        $target.scrollTop = $curr_sel.offsetTop  - 40; 
        }
       "))
   )

From 397f5ad5dee942b1283c4fbdc0e6f305f5078f7a Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Tue, 14 May 2024 22:09:41 +0530
Subject: [PATCH 05/39] add navigation controls

Add navigation controls to function explorer tab
---
 DESCRIPTION | 2 +-
 NEWS.md     | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 09e7f6ba0..f0b818e91 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 3.0.0.9020
+Version: 3.0.0.9021
 Authors@R: c( 
     person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Robert", "Krajcik", role = "aut", email = "robert.krajcik@biogen.com"),
diff --git a/NEWS.md b/NEWS.md
index d9261afc7..2c2d89d0c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -23,6 +23,7 @@
 * Added more context to the metric score card visuals by inserting tool tips & creating a legend modal that describes & interprets all possible visuals (#652)
 * Added `{riskmetric}` assessment documentation URLs to About tab, on Risk Assessment Criteria page.
 * Updated the Dependency Cards to be slightly more informative
+* Added navigation controls in Function Explorer tab.
 
 
 # riskassessment 3.0.0

From bca68f948c515faab9d4b3f76a92467c6086a199 Mon Sep 17 00:00:00 2001
From: Github Actions <actions@github.com>
Date: Tue, 14 May 2024 19:37:26 +0000
Subject: [PATCH 06/39] Re-build manifest file

---
 manifest.json | 27 ++++++++++-----------------
 1 file changed, 10 insertions(+), 17 deletions(-)

diff --git a/manifest.json b/manifest.json
index f65595aed..878846f90 100644
--- a/manifest.json
+++ b/manifest.json
@@ -80,14 +80,7 @@
         "Maintainer": "Marcel Ramos <marcel.ramos@roswellpark.org>",
         "Repository": "RSPM",
         "Date/Publication": "2023-08-08 23:40:06 UTC",
-        "Built": "R 4.3.0; ; 2023-08-09 11:24:46 UTC; unix",
-        "RemoteType": "standard",
-        "RemotePkgRef": "BiocManager",
-        "RemoteRef": "BiocManager",
-        "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/latest",
-        "RemoteReposName": "CRAN",
-        "RemotePkgPlatform": "source",
-        "RemoteSha": "1.30.22"
+        "Built": "R 4.3.0; ; 2023-08-09 11:24:46 UTC; unix"
       }
     },
     "DBI": {
@@ -947,7 +940,7 @@
         "RoxygenNote": "7.3.0",
         "Author": "Sebastien Rochette [aut, cre] (<https://orcid.org/0000-0002-1565-9313>),\n  Vincent Guyader [aut] (<https://orcid.org/0000-0003-0671-9270>),\n  Arthur Bréant [aut] (<https://orcid.org/0000-0003-1668-0963>),\n  Murielle Delmotte [aut] (<https://orcid.org/0000-0002-1339-2424>),\n  ThinkR [cph]",
         "Maintainer": "Sebastien Rochette <sebastien@thinkr.fr>",
-        "Built": "R 4.3.3; ; 2024-04-30 19:03:05 UTC; unix",
+        "Built": "R 4.3.3; ; 2024-05-14 16:45:15 UTC; unix",
         "RemoteType": "github",
         "RemoteUsername": "thinkr-open",
         "RemoteRepo": "checkhelper",
@@ -1310,7 +1303,7 @@
         "Imports": "callr,\ncranlike (>= 1.0.2),\ncurl,\ndesc (>= 1.1.0),\ndigest,\nparsedate,\nrappdirs,\nrematch2,\ntools,\nutils,\nwithr",
         "Suggests": "covr,\npingr,\ntestthat,\nzip",
         "Encoding": "UTF-8",
-        "Built": "R 4.3.3; ; 2024-04-30 19:03:13 UTC; unix",
+        "Built": "R 4.3.3; ; 2024-05-14 16:45:23 UTC; unix",
         "RemoteType": "github",
         "RemoteHost": "api.github.com",
         "RemoteUsername": "r-lib",
@@ -4410,7 +4403,7 @@
         "RoxygenNote": "7.2.3",
         "Author": "Gábor Csárdi [cre, aut, cph],\n  Hadley Wickham [aut],\n  RConsortium [cph],\n  RStudio [cph, fnd]",
         "Maintainer": "Gábor Csárdi <csardi.gabor@gmail.com>",
-        "Built": "R 4.3.3; ; 2024-04-30 19:03:46 UTC; unix",
+        "Built": "R 4.3.3; ; 2024-05-14 16:45:55 UTC; unix",
         "RemoteType": "github",
         "RemoteUsername": "r-lib",
         "RemoteRepo": "revdepcheck",
@@ -4528,7 +4521,7 @@
         "Config/testthat/edition": "3",
         "Author": "R Validation Hub [aut],\n  Doug Kelkhoff [aut],\n  Marly Gotti [aut],\n  Eli Miller [cre, aut],\n  Kevin K [aut],\n  Yilong Zhang [aut],\n  Eric Milliman [aut],\n  Juliane Manitz [aut],\n  Mark Padgham [ctb],\n  PSI special interest group Application and Implementation of\n    Methodologies in Statistics [cph]",
         "Maintainer": "Eli Miller <eli.miller@atorusresearch.com>",
-        "Built": "R 4.3.3; ; 2024-04-30 19:03:52 UTC; unix",
+        "Built": "R 4.3.3; ; 2024-05-14 16:46:00 UTC; unix",
         "RemoteType": "github",
         "RemoteUsername": "pharmaR",
         "RemoteRepo": "riskmetric",
@@ -5101,7 +5094,7 @@
         "Maintainer": "Barret Schloerke <barret@posit.co>",
         "Repository": "RSPM",
         "Date/Publication": "2023-08-26 13:50:02 UTC",
-        "Built": "R 4.3.0; x86_64-pc-linux-gnu; 2023-12-04 11:55:11 UTC; unix"
+        "Built": "R 4.3.0; x86_64-pc-linux-gnu; 2023-08-28 11:40:29 UTC; unix"
       }
     },
     "sortable": {
@@ -6205,7 +6198,7 @@
       "checksum": "77a60b438dc99504d00b3f1b8bbc68c8"
     },
     "DESCRIPTION": {
-      "checksum": "ed68114e40c06e742a6cdb0d34f5ddf9"
+      "checksum": "0e46a273454297087402bede0202718b"
     },
     "inst/app/www/css/community_metrics.css": {
       "checksum": "f08eb25c2ee48ac22ed63b0d18994a04"
@@ -6409,7 +6402,7 @@
       "checksum": "60c2908e00b99b39cc28bdab6d6a5f3c"
     },
     "NEWS.md": {
-      "checksum": "3a683ee2adb456bdc7a58ab604c4c241"
+      "checksum": "e2459a4b82048dcb48db23f08b33f5b2"
     },
     "R/app_config.R": {
       "checksum": "c2b61f270b86b6833f0ee39c44a1a440"
@@ -6433,10 +6426,10 @@
       "checksum": "61459e71d1e62587597ac1dac2c7c650"
     },
     "R/mod_code_explorer_utils.R": {
-      "checksum": "fe3bd5c1243d0ba649d070a6ecf29560"
+      "checksum": "8c8d69c2431385b76971f6b413923c7e"
     },
     "R/mod_code_explorer.R": {
-      "checksum": "72a36a8c4d7f15e0da013104177328b1"
+      "checksum": "4be660d4a8b6f4b9835ec236d4f14dd5"
     },
     "R/mod_communityMetrics.R": {
       "checksum": "fdd39bd2a7e19b8dccc195aaec57a3d8"

From cea4988d12a7f3c1da662a9a0a07a6298e3f1504 Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Mon, 22 Apr 2024 11:37:25 +0530
Subject: [PATCH 07/39] update

---
 R/mod_code_explorer.R       | 51 +++++++++++++++++++++++++++++++++++++
 R/mod_code_explorer_utils.R | 11 ++++++++
 2 files changed, 62 insertions(+)

diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index 7d0ebffda..288dcf229 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -32,6 +32,14 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
       } else {
         div(introJSUI(NS(id, "introJS")),
           br(),
+          fluidRow(column(2,offset = 8,
+                          conditionalPanel(
+                            condition = "typeof(window.$highlights_list) != 'undefined' && window.$highlights_list.length > 1",
+                          actionButton(ns("next_button"),label = "Next"))),
+                   column(2,
+                          conditionalPanel(
+                            condition = "typeof(window.$highlights_list) != 'undefined'  && window.$highlights_list.length > 1",
+                          actionButton(ns("prev_button"),label = "Prev")))),
           fluidRow(
             column(3,
                    wellPanel(
@@ -167,6 +175,49 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     
     introJSServer("introJS", text = reactive(fe_steps), user, credentials)
     
+    observeEvent(input$next_button,{
+      if (input$next_button > 0){
+      shinyjs::runjs('
+                      // debugger;
+                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
+              if( $index == window.$highlights_list.length -1) {
+              
+              var $gh = window.$highlights_list[0]
+              
+              }
+              else 
+              {
+              var $gh = window.$highlights_list[$index +1]
+              }  
+              var $target = document.querySelector("#code_explorer-file_viewer")
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+              ')
+      }
+      
+    })
+    
+    observeEvent(input$prev_button,{
+      if (input$next_button > 0){
+        shinyjs::runjs('
+                      // debugger;
+                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
+              if( $index ==0) {
+              var $gh = window.$highlights_list[window.$highlights_list.length -1]
+              
+              
+              }
+              else 
+              {
+              var $gh = window.$highlights_list[$index -1]
+              }  
+              var $target = document.querySelector("#code_explorer-file_viewer")
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+              ')
+      }
+      
+    })
     output$file_output <- renderUI({
       switch (input$file_type,
               test = test_code(),
diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
index 9d73ceec6..621524b0d 100644
--- a/R/mod_code_explorer_utils.R
+++ b/R/mod_code_explorer_utils.R
@@ -172,9 +172,20 @@ renderCode <- function(lines, hlindex) {
                })
              ),
              tags$script(HTML("
+                             
         document.querySelectorAll('.code pre').forEach(bl => {
           hljs.highlightBlock(bl);
         }); 
+       
+        debugger;
+        var $highlights_list = document.querySelectorAll('.highlight')
+       if(typeof($highlights_list) != 'undefined'){
+        var $gh = document.querySelector('.highlight')
+        var $target = document.querySelector('#code_explorer-file_viewer')
+        // debugger;
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+       }
       "))
   )
 }

From 5bf11796335ac59bbcf4eb61b8e332ee7b79567f Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Tue, 14 May 2024 17:50:51 +0530
Subject: [PATCH 08/39] update

---
 R/mod_code_explorer.R       | 29 +++++++++++++++--------------
 R/mod_code_explorer_utils.R |  6 +++---
 2 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index 288dcf229..eaaeee44f 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -135,7 +135,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
       close(con)
       func_list <- c(input$exported_function, paste0("`", input$exported_function, "`"))
       highlight_index <- parse_data() %>% 
-        filter(stringr::str_ends(file, input$test_files) & func %in% func_list) %>% 
+        filter(basename(file) == input$test_files & func %in% func_list) %>% 
         pull(line)
       renderCode(lines, highlight_index)
     }) %>%
@@ -152,7 +152,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
       close(con)
       func_list <- c(input$exported_function, paste0("`", input$exported_function, "`"))
       highlight_index <- parse_data() %>% 
-        filter(stringr::str_ends(file, input$source_files) & func %in% func_list) %>% 
+        filter(basename(file) ==  input$source_files & func %in% func_list) %>% 
         pull(line)
       renderCode(lines, highlight_index)
     }) %>%
@@ -178,42 +178,43 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     observeEvent(input$next_button,{
       if (input$next_button > 0){
       shinyjs::runjs('
-                      // debugger;
-                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
-              if( $index == window.$highlights_list.length -1) {
+                     
+                     var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($gh));
+              if( $index == $highlights_list.length -1) {
               
-              var $gh = window.$highlights_list[0]
+              $gh = $highlights_list[0]
               
               }
               else 
               {
-              var $gh = window.$highlights_list[$index +1]
+              $gh = $highlights_list[$index +1]
               }  
+                
               var $target = document.querySelector("#code_explorer-file_viewer")
         $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+        $target.scrollTop =$gh.offsetTop -40; 
               ')
       }
       
     })
     
     observeEvent(input$prev_button,{
-      if (input$next_button > 0){
+      if (input$prev_button > 0){
         shinyjs::runjs('
-                      // debugger;
-                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
+                      
+                     var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($gh));
               if( $index ==0) {
-              var $gh = window.$highlights_list[window.$highlights_list.length -1]
+              $gh = $highlights_list[$highlights_list.length -1]
               
               
               }
               else 
               {
-              var $gh = window.$highlights_list[$index -1]
+             $gh = $highlights_list[$index -1]
               }  
               var $target = document.querySelector("#code_explorer-file_viewer")
         $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+        $target.scrollTop = $gh.offsetTop  - 40; 
               ')
       }
       
diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
index 621524b0d..299c39076 100644
--- a/R/mod_code_explorer_utils.R
+++ b/R/mod_code_explorer_utils.R
@@ -177,14 +177,14 @@ renderCode <- function(lines, hlindex) {
           hljs.highlightBlock(bl);
         }); 
        
-        debugger;
         var $highlights_list = document.querySelectorAll('.highlight')
        if(typeof($highlights_list) != 'undefined'){
+       
         var $gh = document.querySelector('.highlight')
+        
         var $target = document.querySelector('#code_explorer-file_viewer')
-        // debugger;
         $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+        $target.scrollTop = $gh.offsetTop  - 40; 
        }
       "))
   )

From 7a83009ca2aa8d97d5d0b28d9f3d10649c71de94 Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Tue, 14 May 2024 20:55:39 +0530
Subject: [PATCH 09/39] update

---
 R/mod_code_explorer.R       | 69 ++++++++++++++++++++-----------------
 R/mod_code_explorer_utils.R |  4 +--
 2 files changed, 40 insertions(+), 33 deletions(-)

diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index eaaeee44f..97d6ca78f 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -31,15 +31,24 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
         showHelperMessage(message = glue::glue("Source code not available for {{{selected_pkg$name()}}}"))
       } else {
         div(introJSUI(NS(id, "introJS")),
-          br(),
-          fluidRow(column(2,offset = 8,
+          fluidRow(style = "height:35px !important;",
+                   column(2,offset = 10,
                           conditionalPanel(
                             condition = "typeof(window.$highlights_list) != 'undefined' && window.$highlights_list.length > 1",
-                          actionButton(ns("next_button"),label = "Next"))),
-                   column(2,
+                          actionButton(ns("prev_button"),label = "",icon = icon("chevron-left"),
+                                       style ="width: 32px !important; 
+                            height: 32px !important;
+                            font-size: 16px !important;
+                            line-height: 5px !important;
+                            padding: 0px !important;") |>bslib::tooltip("Previous occurence"), style = "display: inline-block;"),
                           conditionalPanel(
                             condition = "typeof(window.$highlights_list) != 'undefined'  && window.$highlights_list.length > 1",
-                          actionButton(ns("prev_button"),label = "Prev")))),
+                          actionButton(ns("next_button"),label = "",icon = icon("chevron-right"),
+                                       style = "width: 32px !important; 
+                            height: 32px !important;
+                            font-size: 16px !important;
+                            line-height: 5px !important;
+                            padding: 0px !important;")|>bslib::tooltip("Next occurence",placement ="right"), style = "display: inline-block;"))),
           fluidRow(
             column(3,
                    wellPanel(
@@ -178,21 +187,21 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     observeEvent(input$next_button,{
       if (input$next_button > 0){
       shinyjs::runjs('
-                     
-                     var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($gh));
-              if( $index == $highlights_list.length -1) {
+                    var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel));
+                    if( $index == $highlights_list.length -1) 
+                    {
               
-              $gh = $highlights_list[0]
+                          $curr_sel = $highlights_list[0]
               
-              }
-              else 
-              {
-              $gh = $highlights_list[$index +1]
-              }  
+                    }
+                else 
+                    {
+                          $curr_sel = $highlights_list[$index +1]
+                    }  
                 
-              var $target = document.querySelector("#code_explorer-file_viewer")
-        $target.scrollTop = 0;
-        $target.scrollTop =$gh.offsetTop -40; 
+                    var $target = document.querySelector("#code_explorer-file_viewer")
+                    $target.scrollTop = 0;
+                    $target.scrollTop =$curr_sel.offsetTop -40; 
               ')
       }
       
@@ -201,20 +210,18 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     observeEvent(input$prev_button,{
       if (input$prev_button > 0){
         shinyjs::runjs('
-                      
-                     var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($gh));
-              if( $index ==0) {
-              $gh = $highlights_list[$highlights_list.length -1]
-              
-              
-              }
-              else 
-              {
-             $gh = $highlights_list[$index -1]
-              }  
-              var $target = document.querySelector("#code_explorer-file_viewer")
-        $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - 40; 
+                      var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel));
+                      if( $index ==0) 
+                      {
+                            $curr_sel = $highlights_list[$highlights_list.length -1]
+                      }
+                        else 
+                      {
+                            $curr_sel = $highlights_list[$index -1]
+                      }  
+                      var $target = document.querySelector("#code_explorer-file_viewer")
+                      $target.scrollTop = 0; # scroll to the top 
+                      $target.scrollTop = $curr_sel.offsetTop  - 40; 
               ')
       }
       
diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
index 299c39076..69300b70d 100644
--- a/R/mod_code_explorer_utils.R
+++ b/R/mod_code_explorer_utils.R
@@ -180,11 +180,11 @@ renderCode <- function(lines, hlindex) {
         var $highlights_list = document.querySelectorAll('.highlight')
        if(typeof($highlights_list) != 'undefined'){
        
-        var $gh = document.querySelector('.highlight')
+        var $curr_sel = document.querySelector('.highlight')
         
         var $target = document.querySelector('#code_explorer-file_viewer')
         $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - 40; 
+        $target.scrollTop = $curr_sel.offsetTop  - 40; 
        }
       "))
   )

From 866c0591cc215bd2b90d4c266aba00bfb5ef98f9 Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Mon, 22 Apr 2024 11:37:25 +0530
Subject: [PATCH 10/39] update

---
 R/mod_code_explorer.R       | 17 +++++++++++++++++
 R/mod_code_explorer_utils.R |  9 ++++++++-
 2 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index 97d6ca78f..03de377ea 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -49,6 +49,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
                             font-size: 16px !important;
                             line-height: 5px !important;
                             padding: 0px !important;")|>bslib::tooltip("Next occurence",placement ="right"), style = "display: inline-block;"))),
+
           fluidRow(
             column(3,
                    wellPanel(
@@ -202,12 +203,27 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
                     var $target = document.querySelector("#code_explorer-file_viewer")
                     $target.scrollTop = 0;
                     $target.scrollTop =$curr_sel.offsetTop -40; 
+                      
+                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
+              if( $index == window.$highlights_list.length -1) {
+              
+              var $gh = window.$highlights_list[0]
+              
+              }
+              else 
+              {
+              var $gh = window.$highlights_list[$index +1]
+              }  
+              var $target = document.querySelector("#code_explorer-file_viewer")
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
               ')
       }
       
     })
     
     observeEvent(input$prev_button,{
+ 
       if (input$prev_button > 0){
         shinyjs::runjs('
                       var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel));
@@ -222,6 +238,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
                       var $target = document.querySelector("#code_explorer-file_viewer")
                       $target.scrollTop = 0; # scroll to the top 
                       $target.scrollTop = $curr_sel.offsetTop  - 40; 
+
               ')
       }
       
diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
index 69300b70d..c86a8627b 100644
--- a/R/mod_code_explorer_utils.R
+++ b/R/mod_code_explorer_utils.R
@@ -176,7 +176,6 @@ renderCode <- function(lines, hlindex) {
         document.querySelectorAll('.code pre').forEach(bl => {
           hljs.highlightBlock(bl);
         }); 
-       
         var $highlights_list = document.querySelectorAll('.highlight')
        if(typeof($highlights_list) != 'undefined'){
        
@@ -185,6 +184,14 @@ renderCode <- function(lines, hlindex) {
         var $target = document.querySelector('#code_explorer-file_viewer')
         $target.scrollTop = 0;
         $target.scrollTop = $curr_sel.offsetTop  - 40; 
+        var $highlights_list = document.querySelectorAll('.highlight')
+       if(typeof($highlights_list) != 'undefined'){
+        var $gh = document.querySelector('.highlight')
+        var $target = document.querySelector('#code_explorer-file_viewer')
+         
+        $target.scrollTop = 0;
+        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+
        }
       "))
   )

From 6305885b7726ed5da4de0de03a6c6d830b80de62 Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Tue, 14 May 2024 22:09:41 +0530
Subject: [PATCH 11/39] add js to create and update search index

---
 DESCRIPTION                 |  2 ++
 NEWS.md                     |  2 +-
 R/mod_code_explorer.R       | 49 ++++++++++++++++++++++++++++++++++---
 R/mod_code_explorer_utils.R |  5 +++-
 4 files changed, 53 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fd83d1722..f1dcfbb73 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,8 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
+
 Version: 3.0.0.9023
+
 Authors@R: c( 
     person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Robert", "Krajcik", role = "aut", email = "robert.krajcik@biogen.com"),
diff --git a/NEWS.md b/NEWS.md
index bf828f38b..c771cb016 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -27,7 +27,7 @@
 * Allow users to specify decisions in the CSV upload file (#663)
 * Fix bug causing application to crash when trying to delete zero packages (#781)
 * Add `Decision` column to Package Dependencies tab so that users (#774)
-
+* Added navigation controls in Function Explorer tab.
 
 
 # riskassessment 3.0.0
diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index 03de377ea..1b4cca209 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -31,6 +31,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
         showHelperMessage(message = glue::glue("Source code not available for {{{selected_pkg$name()}}}"))
       } else {
         div(introJSUI(NS(id, "introJS")),
+ 
           fluidRow(style = "height:35px !important;",
                    column(2,offset = 10,
                           conditionalPanel(
@@ -50,6 +51,8 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
                             line-height: 5px !important;
                             padding: 0px !important;")|>bslib::tooltip("Next occurence",placement ="right"), style = "display: inline-block;"))),
 
+ 
+ 
           fluidRow(
             column(3,
                    wellPanel(
@@ -87,7 +90,28 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
                    div(id = ns("file_viewer"),
                      uiOutput(ns("file_output"), class = "file_browser"),
                      style = "height: 62vh; overflow: auto; border: 1px solid var(--bs-border-color-translucent);"
-                   )
+                   ),
+                   br(),
+                   fluidRow(style = "height:35px !important;",
+                            column(4,offset = 8,
+                                   conditionalPanel(
+                                     condition = "typeof(window.$highlights_list) != 'undefined' && window.$highlights_list.length > 1",
+                                     actionButton(ns("prev_button"),label = "",icon = icon("chevron-left"),
+                                                  style ="width: 32px !important; 
+                            height: 32px !important;
+                            font-size: 16px !important;
+                            line-height: 5px !important;
+                            padding: 0px !important;") |>bslib::tooltip("Previous occurence"), style = "display: inline-block;",
+                            
+                            div(id = "search_index","",style ="display:inline"),
+                            actionButton(ns("next_button"),label = "",icon = icon("chevron-right"),
+                                           style = "width: 32px !important; 
+                            height: 32px !important;
+                            font-size: 16px !important;
+                            line-height: 5px !important;
+                            padding: 0px !important;
+                            display:inline;
+                            ")|>bslib::tooltip("Next occurence",placement ="right"), style = "display: inline-block;")))
             )
           ),
           br(), br(),
@@ -184,24 +208,30 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
       bindEvent(input$man_files, input$exported_function, ignoreNULL = FALSE)
     
     introJSServer("introJS", text = reactive(fe_steps), user, credentials)
+    search_index_value <- reactiveVal(1)
+    highlight_list <- reactiveVal(1)
     
     observeEvent(input$next_button,{
       if (input$next_button > 0){
       shinyjs::runjs('
+       
                     var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel));
                     if( $index == $highlights_list.length -1) 
                     {
               
                           $curr_sel = $highlights_list[0]
+                          search_index.innerHTML = 1 + " of " + $highlights_list.length;
               
                     }
                 else 
                     {
                           $curr_sel = $highlights_list[$index +1]
+                          search_index.innerHTML =  ( $index+2) + " of " + $highlights_list.length;
                     }  
                 
                     var $target = document.querySelector("#code_explorer-file_viewer")
                     $target.scrollTop = 0;
+ 
                     $target.scrollTop =$curr_sel.offsetTop -40; 
                       
                      var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
@@ -217,6 +247,10 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
               var $target = document.querySelector("#code_explorer-file_viewer")
         $target.scrollTop = 0;
         $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
+ 
+                    $target.scrollTop =$curr_sel.offsetTop -40;
+                   
+ 
               ')
       }
       
@@ -225,21 +259,30 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     observeEvent(input$prev_button,{
  
       if (input$prev_button > 0){
-        shinyjs::runjs('
-                      var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel));
+        
+        shinyjs::runjs('var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel));
                       if( $index ==0) 
                       {
                             $curr_sel = $highlights_list[$highlights_list.length -1]
+                            search_index.innerHTML =   $highlights_list.length + " of " + $highlights_list.length;
                       }
                         else 
                       {
                             $curr_sel = $highlights_list[$index -1]
+                            search_index.innerHTML =   ($index) + " of " + $highlights_list.length;
                       }  
                       var $target = document.querySelector("#code_explorer-file_viewer")
+ 
                       $target.scrollTop = 0; # scroll to the top 
                       $target.scrollTop = $curr_sel.offsetTop  - 40; 
 
               ')
+ 
+                      $target.scrollTop = 0; // scroll to the top 
+                      $target.scrollTop = $curr_sel.offsetTop  - 40; 
+                     
+                      ')
+ 
       }
       
     })
diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
index c86a8627b..e0efe02da 100644
--- a/R/mod_code_explorer_utils.R
+++ b/R/mod_code_explorer_utils.R
@@ -183,7 +183,7 @@ renderCode <- function(lines, hlindex) {
         
         var $target = document.querySelector('#code_explorer-file_viewer')
         $target.scrollTop = 0;
-        $target.scrollTop = $curr_sel.offsetTop  - 40; 
+        $target.scrollTop = $curr_sel.offsetTop  - 40;
         var $highlights_list = document.querySelectorAll('.highlight')
        if(typeof($highlights_list) != 'undefined'){
         var $gh = document.querySelector('.highlight')
@@ -192,6 +192,9 @@ renderCode <- function(lines, hlindex) {
         $target.scrollTop = 0;
         $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
 
+        var $index1 =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel)) +1;
+                   
+        search_index.innerHTML =   $index1 + ' of ' + $highlights_list.length;
        }
       "))
   )

From d2d94608e803e81dd4e650218ff7d464b7602d5c Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Tue, 14 May 2024 22:09:41 +0530
Subject: [PATCH 12/39] add navigation controls

Add navigation controls to function explorer tab
---
 DESCRIPTION | 2 --
 1 file changed, 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f1dcfbb73..fd83d1722 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,6 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-
 Version: 3.0.0.9023
-
 Authors@R: c( 
     person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Robert", "Krajcik", role = "aut", email = "robert.krajcik@biogen.com"),

From d3703567e4ce92250427daedbe6d4372271a2f20 Mon Sep 17 00:00:00 2001
From: Github Actions <actions@github.com>
Date: Tue, 14 May 2024 19:37:26 +0000
Subject: [PATCH 13/39] Add navigation in function explorer

---
 R/mod_code_explorer.R       | 52 ++-----------------------------------
 R/mod_code_explorer_utils.R | 13 +---------
 manifest.json               |  4 +--
 3 files changed, 5 insertions(+), 64 deletions(-)

diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index 1b4cca209..d04d3d6e5 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -31,28 +31,6 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
         showHelperMessage(message = glue::glue("Source code not available for {{{selected_pkg$name()}}}"))
       } else {
         div(introJSUI(NS(id, "introJS")),
- 
-          fluidRow(style = "height:35px !important;",
-                   column(2,offset = 10,
-                          conditionalPanel(
-                            condition = "typeof(window.$highlights_list) != 'undefined' && window.$highlights_list.length > 1",
-                          actionButton(ns("prev_button"),label = "",icon = icon("chevron-left"),
-                                       style ="width: 32px !important; 
-                            height: 32px !important;
-                            font-size: 16px !important;
-                            line-height: 5px !important;
-                            padding: 0px !important;") |>bslib::tooltip("Previous occurence"), style = "display: inline-block;"),
-                          conditionalPanel(
-                            condition = "typeof(window.$highlights_list) != 'undefined'  && window.$highlights_list.length > 1",
-                          actionButton(ns("next_button"),label = "",icon = icon("chevron-right"),
-                                       style = "width: 32px !important; 
-                            height: 32px !important;
-                            font-size: 16px !important;
-                            line-height: 5px !important;
-                            padding: 0px !important;")|>bslib::tooltip("Next occurence",placement ="right"), style = "display: inline-block;"))),
-
- 
- 
           fluidRow(
             column(3,
                    wellPanel(
@@ -214,7 +192,6 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
     observeEvent(input$next_button,{
       if (input$next_button > 0){
       shinyjs::runjs('
-       
                     var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel));
                     if( $index == $highlights_list.length -1) 
                     {
@@ -232,32 +209,12 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
                     var $target = document.querySelector("#code_explorer-file_viewer")
                     $target.scrollTop = 0;
  
-                    $target.scrollTop =$curr_sel.offsetTop -40; 
-                      
-                     var $index =Array.from(window.$highlights_list).findIndex(node => node.isEqualNode(window.$gh));
-              if( $index == window.$highlights_list.length -1) {
-              
-              var $gh = window.$highlights_list[0]
-              
-              }
-              else 
-              {
-              var $gh = window.$highlights_list[$index +1]
-              }  
-              var $target = document.querySelector("#code_explorer-file_viewer")
-        $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
- 
-                    $target.scrollTop =$curr_sel.offsetTop -40;
-                   
- 
-              ')
+                    $target.scrollTop =$curr_sel.offsetTop -40; ')
       }
       
     })
     
     observeEvent(input$prev_button,{
- 
       if (input$prev_button > 0){
         
         shinyjs::runjs('var $index =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel));
@@ -273,16 +230,11 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
                       }  
                       var $target = document.querySelector("#code_explorer-file_viewer")
  
-                      $target.scrollTop = 0; # scroll to the top 
+                      $target.scrollTop = 0; 
                       $target.scrollTop = $curr_sel.offsetTop  - 40; 
 
               ')
  
-                      $target.scrollTop = 0; // scroll to the top 
-                      $target.scrollTop = $curr_sel.offsetTop  - 40; 
-                     
-                      ')
- 
       }
       
     })
diff --git a/R/mod_code_explorer_utils.R b/R/mod_code_explorer_utils.R
index e0efe02da..d2e1a2ab9 100644
--- a/R/mod_code_explorer_utils.R
+++ b/R/mod_code_explorer_utils.R
@@ -177,23 +177,12 @@ renderCode <- function(lines, hlindex) {
           hljs.highlightBlock(bl);
         }); 
         var $highlights_list = document.querySelectorAll('.highlight')
-       if(typeof($highlights_list) != 'undefined'){
-       
         var $curr_sel = document.querySelector('.highlight')
-        
+       if(typeof($highlights_list) != 'undefined' & $curr_sel != null){
         var $target = document.querySelector('#code_explorer-file_viewer')
         $target.scrollTop = 0;
         $target.scrollTop = $curr_sel.offsetTop  - 40;
-        var $highlights_list = document.querySelectorAll('.highlight')
-       if(typeof($highlights_list) != 'undefined'){
-        var $gh = document.querySelector('.highlight')
-        var $target = document.querySelector('#code_explorer-file_viewer')
-         
-        $target.scrollTop = 0;
-        $target.scrollTop = $gh.offsetTop  - $target.offsetTop + $target.scrollTop; 
-
         var $index1 =Array.from($highlights_list).findIndex(node => node.isEqualNode($curr_sel)) +1;
-                   
         search_index.innerHTML =   $index1 + ' of ' + $highlights_list.length;
        }
       "))
diff --git a/manifest.json b/manifest.json
index 83cfda632..b3286df63 100644
--- a/manifest.json
+++ b/manifest.json
@@ -6490,10 +6490,10 @@
       "checksum": "61459e71d1e62587597ac1dac2c7c650"
     },
     "R/mod_code_explorer_utils.R": {
-      "checksum": "fe3bd5c1243d0ba649d070a6ecf29560"
+      "checksum": "8c8d69c2431385b76971f6b413923c7e"
     },
     "R/mod_code_explorer.R": {
-      "checksum": "72a36a8c4d7f15e0da013104177328b1"
+      "checksum": "4be660d4a8b6f4b9835ec236d4f14dd5"
     },
     "R/mod_communityMetrics.R": {
       "checksum": "fdd39bd2a7e19b8dccc195aaec57a3d8"

From fd2cd34d1033ad8ce3e1b3bb1f80cc68a07db8d5 Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Tue, 11 Jun 2024 23:09:11 +0530
Subject: [PATCH 14/39] Add navigation to function explorer

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fd83d1722..20686c2b5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 3.0.0.9023
+Version: 3.0.0.9024
 Authors@R: c( 
     person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Robert", "Krajcik", role = "aut", email = "robert.krajcik@biogen.com"),
diff --git a/NEWS.md b/NEWS.md
index c771cb016..d047b7e8e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -27,7 +27,7 @@
 * Allow users to specify decisions in the CSV upload file (#663)
 * Fix bug causing application to crash when trying to delete zero packages (#781)
 * Add `Decision` column to Package Dependencies tab so that users (#774)
-* Added navigation controls in Function Explorer tab.
+* Added navigation controls in Function Explorer tab (#644)
 
 
 # riskassessment 3.0.0

From 4820531ec909af10e78638b1d4eddaa3d98c18d1 Mon Sep 17 00:00:00 2001
From: Github Actions <actions@github.com>
Date: Wed, 12 Jun 2024 12:31:20 +0000
Subject: [PATCH 15/39] Re-build manifest file

---
 manifest.json | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/manifest.json b/manifest.json
index b3286df63..b86583d36 100644
--- a/manifest.json
+++ b/manifest.json
@@ -4367,7 +4367,7 @@
         "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
         "Repository": "RSPM",
         "Date/Publication": "2024-02-29 01:10:07 UTC",
-        "Built": "R 4.3.3; ; 2024-06-06 17:15:02 UTC; unix"
+        "Built": "R 4.3.3; ; 2024-06-12 12:30:38 UTC; unix"
       }
     },
     "reprex": {
@@ -6220,7 +6220,7 @@
       "checksum": "99c5575cb81828e20a7fe1d205551316"
     },
     "DESCRIPTION": {
-      "checksum": "c4ce70d1592eea23d969d53b917c4a5b"
+      "checksum": "c7e19a728e7d1cb04961c5695ed151c2"
     },
     "inst/app/www/css/community_metrics.css": {
       "checksum": "f08eb25c2ee48ac22ed63b0d18994a04"
@@ -6463,7 +6463,7 @@
       "checksum": "97d1232340e04c53088bc8f814133dcd"
     },
     "NEWS.md": {
-      "checksum": "f9bc97131b3753ea173bff4248b97e1f"
+      "checksum": "876dad435c429e277f1f9b234ed8ec5c"
     },
     "R/app_config.R": {
       "checksum": "c2b61f270b86b6833f0ee39c44a1a440"
@@ -6490,10 +6490,10 @@
       "checksum": "61459e71d1e62587597ac1dac2c7c650"
     },
     "R/mod_code_explorer_utils.R": {
-      "checksum": "8c8d69c2431385b76971f6b413923c7e"
+      "checksum": "2588e180a69a79b7be4e3818eb3931dc"
     },
     "R/mod_code_explorer.R": {
-      "checksum": "4be660d4a8b6f4b9835ec236d4f14dd5"
+      "checksum": "13c706c439a980b617e960b93414ad5c"
     },
     "R/mod_communityMetrics.R": {
       "checksum": "fdd39bd2a7e19b8dccc195aaec57a3d8"

From 2c6c0b726ff717afa500216225fff4a60656fe35 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Wed, 26 Jun 2024 10:14:01 -0400
Subject: [PATCH 16/39] Initialize developmental version 3.1.0.9000

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cae55f247..2b0b0f030 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 3.1.0
+Version: 3.1.0.9000
 Authors@R: c( 
     person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Robert", "Krajcik", role = "aut", email = "robert.krajcik@biogen.com"),
diff --git a/NEWS.md b/NEWS.md
index 8882138a5..a492a3ca3 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,5 @@
+# riskassessment (development version)
+
 # riskassessment 3.1.0
 
 ### User Enhancements

From c0ddf6bc4e68c2f62961d1e8dd9f54887526ffa6 Mon Sep 17 00:00:00 2001
From: narayanan-iyer-pfizer
 <114721252+narayanan-iyer-pfizer@users.noreply.github.com>
Date: Mon, 8 Jul 2024 16:50:05 +0530
Subject: [PATCH 17/39] update code to handle help pages

---
 DESCRIPTION           | 2 +-
 R/mod_code_explorer.R | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4527f72f8..19b5e74ba 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 3.1.0.9001
+Version: 3.1.0.9002
 Authors@R: c( 
     person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Jeff", "Thompson", role = c("aut"),  email = "jeff.thompson51317@gmail.com", comment = "Co-Lead"),
diff --git a/R/mod_code_explorer.R b/R/mod_code_explorer.R
index 537fa7470..2259f2158 100644
--- a/R/mod_code_explorer.R
+++ b/R/mod_code_explorer.R
@@ -31,6 +31,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
         showHelperMessage(message = glue::glue("Source code not available for {{{selected_pkg$name()}}}"))
       } else {
         div(introJSUI(NS(id, "introJS")),
+            br(),
           fluidRow(
             column(3,
                    wellPanel(
@@ -177,8 +178,12 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
       con <- archive::archive_read(file.path("tarballs",
                                              glue::glue("{selected_pkg$name()}_{selected_pkg$version()}.tar.gz")),
                                    file = fp)
+      
       Rdfile <-tools::parse_Rd(con)
       close(con)
+      shinyjs::runjs('
+                    $highlights_list = undefined;')
+                    
       HTML(paste0(utils::capture.output(tools::Rd2HTML(Rdfile,
                                                package = c(selected_pkg$name(),
                                                            selected_pkg$version()), out = "")), collapse = "\n"))
@@ -222,6 +227,7 @@ mod_code_explorer_server <- function(id, selected_pkg, pkgarchive = reactiveVal(
                       {
                             $curr_sel = $highlights_list[$highlights_list.length -1]
                             search_index.innerHTML =   $highlights_list.length + " of " + $highlights_list.length;
+                      }
                         else 
                       {
                             $curr_sel = $highlights_list[$index -1]

From a360341490338f8b269ee91d59b6567c82e0d5e8 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Mon, 8 Jul 2024 08:26:21 -0400
Subject: [PATCH 18/39] Update DESCRIPTION

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 19b5e74ba..4527f72f8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 3.1.0.9002
+Version: 3.1.0.9001
 Authors@R: c( 
     person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Jeff", "Thompson", role = c("aut"),  email = "jeff.thompson51317@gmail.com", comment = "Co-Lead"),

From e6d8f8f1c05b8fd3536ec31622cd7d4b424a5976 Mon Sep 17 00:00:00 2001
From: Github Actions <actions@github.com>
Date: Mon, 8 Jul 2024 12:37:34 +0000
Subject: [PATCH 19/39] Re-build manifest file

---
 manifest.json | 126 +++++++++++++++++++++++++-------------------------
 1 file changed, 63 insertions(+), 63 deletions(-)

diff --git a/manifest.json b/manifest.json
index b86583d36..149014a82 100644
--- a/manifest.json
+++ b/manifest.json
@@ -495,7 +495,7 @@
         "Repository": "RSPM",
         "Date/Publication": "2019-03-21 14:53:46 UTC",
         "Encoding": "UTF-8",
-        "Built": "R 4.3.0; ; 2023-04-21 23:12:04 UTC; unix"
+        "Built": "R 4.3.0; ; 2024-06-25 22:08:11 UTC; unix"
       }
     },
     "attachment": {
@@ -884,7 +884,7 @@
         "Maintainer": "Gábor Csárdi <csardi.gabor@gmail.com>",
         "Repository": "RSPM",
         "Date/Publication": "2024-03-25 13:30:06 UTC",
-        "Built": "R 4.3.0; ; 2024-03-26 04:09:18 UTC; unix"
+        "Built": "R 4.3.0; ; 2024-06-25 22:13:07 UTC; unix"
       }
     },
     "cellranger": {
@@ -940,7 +940,7 @@
         "RoxygenNote": "7.3.0",
         "Author": "Sebastien Rochette [aut, cre] (<https://orcid.org/0000-0002-1565-9313>),\n  Vincent Guyader [aut] (<https://orcid.org/0000-0003-0671-9270>),\n  Arthur Bréant [aut] (<https://orcid.org/0000-0003-1668-0963>),\n  Murielle Delmotte [aut] (<https://orcid.org/0000-0002-1339-2424>),\n  ThinkR [cph]",
         "Maintainer": "Sebastien Rochette <sebastien@thinkr.fr>",
-        "Built": "R 4.3.3; ; 2024-05-31 13:18:53 UTC; unix",
+        "Built": "R 4.3.3; ; 2024-06-26 14:09:33 UTC; unix",
         "RemoteType": "github",
         "RemoteUsername": "thinkr-open",
         "RemoteRepo": "checkhelper",
@@ -1091,7 +1091,7 @@
         "Maintainer": "Gábor Csárdi <csardi.gabor@gmail.com>",
         "Repository": "RSPM",
         "Date/Publication": "2017-05-21 17:19:19 UTC",
-        "Built": "R 4.3.0; ; 2023-04-21 23:59:26 UTC; unix"
+        "Built": "R 4.3.0; ; 2024-06-25 22:08:30 UTC; unix"
       }
     },
     "codetools": {
@@ -1113,7 +1113,7 @@
         "Repository": "RSPM",
         "Date/Publication": "2024-03-31 20:10:06 UTC",
         "Encoding": "UTF-8",
-        "Built": "R 4.3.0; ; 2024-04-01 04:31:41 UTC; unix"
+        "Built": "R 4.3.0; ; 2024-06-25 22:09:39 UTC; unix"
       }
     },
     "colorspace": {
@@ -1168,7 +1168,7 @@
         "Maintainer": "Jeroen Ooms <jeroen@berkeley.edu>",
         "Repository": "RSPM",
         "Date/Publication": "2024-01-30 12:40:02 UTC",
-        "Built": "R 4.3.0; x86_64-pc-linux-gnu; 2024-01-31 11:23:09 UTC; unix"
+        "Built": "R 4.3.0; x86_64-pc-linux-gnu; 2024-06-25 22:11:40 UTC; unix"
       }
     },
     "config": {
@@ -1303,7 +1303,7 @@
         "Imports": "callr,\ncranlike (>= 1.0.2),\ncurl,\ndesc (>= 1.1.0),\ndigest,\nparsedate,\nrappdirs,\nrematch2,\ntools,\nutils,\nwithr",
         "Suggests": "covr,\npingr,\ntestthat,\nzip",
         "Encoding": "UTF-8",
-        "Built": "R 4.3.3; ; 2024-05-31 13:19:02 UTC; unix",
+        "Built": "R 4.3.3; ; 2024-06-26 14:09:41 UTC; unix",
         "RemoteType": "github",
         "RemoteHost": "api.github.com",
         "RemoteUsername": "r-lib",
@@ -1619,7 +1619,7 @@
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+      "checksum": "f79316fe637bb1f4038f085621d298f5"
     },
     "R/utils_config_db.R": {
       "checksum": "74cf2ee5e7283483a88f08d60e3728b0"
     },
     "R/utils_get_db.R": {
-      "checksum": "270a240f5882ec130989f252fe18011f"
+      "checksum": "6e87d4d43f93b4a4b556d72b848dc3f1"
     },
     "R/utils_insert_db.R": {
-      "checksum": "ee28bd9e4f053e7ee936d7d8ef5fe887"
+      "checksum": "2c02e4eab4d9262ef8c8e64eb0f1b4f5"
     },
     "R/utils_startup.R": {
       "checksum": "b689ee96f0761480ac65ca22cbbb4980"
     },
     "R/utils.R": {
-      "checksum": "dd8cda3fb9deb392b6f82798f26bd668"
+      "checksum": "995d947896038bdcec381ff4b4e94fd0"
     },
     "README.md": {
-      "checksum": "d7e84fce2c891619912b6cc552eecc94"
+      "checksum": "3050edd46ad46d37978030b0026d5d1f"
     },
     "README.Rmd": {
-      "checksum": "633aa5476aee5b230f43f1b935be34d7"
+      "checksum": "a2eefba927d32d8c78d4e385178a93b7"
     },
     "renv.lock": {
       "checksum": "d7b9816932ef58733e25081235f6fc78"

From ffb1dad13353baa6a75ec4cbcf8f6bd426782529 Mon Sep 17 00:00:00 2001
From: "Aaron Clark (Arcus)" <aclark02@arcusbio.com>
Date: Mon, 8 Jul 2024 09:51:06 -0400
Subject: [PATCH 20/39] fix bug crashing the app on pkg deps for pkgs with no
 dep information.

---
 R/mod_packageDependencies.R |  8 ++++-
 R/utils_build_cards.R       |  1 -
 R/utils_get_db.R            | 72 +++++++++++++++++++------------------
 3 files changed, 44 insertions(+), 37 deletions(-)

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index 78f6ed05a..72cadaac4 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -123,7 +123,13 @@ packageDependenciesServer <- function(id, selected_pkg, user, credentials, paren
         }
       )
       # this is so the dependencies is also a 0x2 tibble like suggests
-      if (rlang::is_empty(pkgref()$dependencies[[1]])) depends(dplyr::tibble(package = character(0), type = character(0), name = character(0)))
+      if (rlang::is_empty(pkgref()$dependencies[[1]])) {
+        depends(
+          dplyr::tibble(package = character(0), type = character(0), name = character(0),
+                        version = character(0), score = character(0), decision = character(0),
+                        decision_id = character(0))
+          )
+      }
         
       revdeps(pkgref()$reverse_dependencies[[1]] %>% as.vector())
       
diff --git a/R/utils_build_cards.R b/R/utils_build_cards.R
index 48ff9ae8e..f10d56f51 100644
--- a/R/utils_build_cards.R
+++ b/R/utils_build_cards.R
@@ -256,7 +256,6 @@ build_dep_cards <- function(data, loaded, toggled){
     is_url = numeric(),
     type = character()
   )
-
   
   deps <- data %>% 
     mutate(base = if_else(name %in% c(rownames(installed.packages(priority = "base"))), "Base", "Non-Base")) %>% 
diff --git a/R/utils_get_db.R b/R/utils_get_db.R
index 04f957d7a..3836be4ee 100644
--- a/R/utils_get_db.R
+++ b/R/utils_get_db.R
@@ -239,6 +239,42 @@ get_metric_data <- function(pkg_name, metric_class = 'maintenance', db_name = go
     )
 }
 
+#' Get Dependency Pkg Versions and Scores
+#'
+#' 
+#' @param pkg_name character name of the package
+#' @param verify_data a data.frame used to verify whether a pkg exists in the db
+#' @param cran_pkgs a data.frame containing all available cran package names/versions
+#'
+#' @returns a list
+#' @noRd
+get_versnScore <- function(pkg_name, verify_data, cran_pkgs) {
+  
+  if (rlang::is_empty(pkg_name)) 
+    return(list(name = character(), version = character(), score = character(),
+                decision_id = character(), decision = character()))
+  
+  if (pkg_name %in% verify_data$name) { #loaded2_db()$name
+    tmp_df <- verify_data %>% filter(name == pkg_name) %>% select(score, version, decision_id, decision)
+    pkg_score <- tmp_df %>% pull(score) %>% as.character
+    pkg_versn <- tmp_df %>% pull(version) %>% as.character
+    pkg_decision_id <- tmp_df %>% pull(decision_id) %>% as.character
+    pkg_decision <- tmp_df %>% pull(decision) %>% as.character
+  } else {
+    pkg_score <- ""
+    pkg_versn <- if_else(pkg_name %in% c(rownames(installed.packages(priority="base"))), "",
+                         subset(cran_pkgs, Package == pkg_name, c("Version")) %>% as.character())
+    pkg_decision_id <- ""
+    pkg_decision <- ""
+  } 
+  
+  return(list(name = pkg_name, version = pkg_versn, score = pkg_score,
+              decision_id = pkg_decision_id, decision = pkg_decision
+  ))   
+}
+
+
+
 #' The 'Get Dependencies Metrics Data' function
 #' 
 #' Pull the depenencies data for a specific package id, and create 
@@ -277,7 +313,7 @@ get_depends_data <- function(pkg_name,
     deps_decision_data <- purrr::map_df(deep_ends$name, ~get_versnScore(.x, loaded2_db, repo_pkgs))
     if(nrow(deps_decision_data) == 0) {
       deps_w_decision <- dplyr::tibble(name = character(0), version = character(0),
-                                       score = character(0), decision = character(0), decision_id = character(0))
+             score = character(0), decision = character(0), decision_id = character(0))
     } else {
       deps_w_decision <- deps_decision_data
     }
@@ -407,40 +443,6 @@ get_assess_blob <- function(pkg_lst, db_name = golem::get_golem_options('assessm
 }
 
 
-#' Get Dependency Pkg Versions and Scores
-#'
-#' 
-#' @param pkg_name character name of the package
-#' @param verify_data a data.frame used to verify whether a pkg exists in the db
-#' @param cran_pkgs a data.frame containing all available cran package names/versions
-#'
-#' @returns a list
-#' @noRd
-get_versnScore <- function(pkg_name, verify_data, cran_pkgs) {
-  
-  if (rlang::is_empty(pkg_name)) 
-    return(list(name = character(), version = character(), score = character(),
-                decision_id = character(), decision = character()))
-  
-  if (pkg_name %in% verify_data$name) { #loaded2_db()$name
-    tmp_df <- verify_data %>% filter(name == pkg_name) %>% select(score, version, decision_id, decision)
-    pkg_score <- tmp_df %>% pull(score) %>% as.character
-    pkg_versn <- tmp_df %>% pull(version) %>% as.character
-    pkg_decision_id <- tmp_df %>% pull(decision_id) %>% as.character
-    pkg_decision <- tmp_df %>% pull(decision) %>% as.character
-  } else {
-    pkg_score <- ""
-    pkg_versn <- if_else(pkg_name %in% c(rownames(installed.packages(priority="base"))), "",
-                 subset(cran_pkgs, Package == pkg_name, c("Version")) %>% as.character())
-    pkg_decision_id <- ""
-    pkg_decision <- ""
-  } 
-  
-  return(list(name = pkg_name, version = pkg_versn, score = pkg_score,
-              decision_id = pkg_decision_id, decision = pkg_decision
-              ))   
-}
-
 
 
 ##### End of get_* functions #####

From c92797c6566d34cb59711d1670dd2bdd137624e4 Mon Sep 17 00:00:00 2001
From: "Aaron Clark (Arcus)" <aclark02@arcusbio.com>
Date: Mon, 8 Jul 2024 10:04:12 -0400
Subject: [PATCH 21/39] fixed issue with 'package object not found'

---
 R/mod_packageDependencies.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index 72cadaac4..1b0a03650 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -64,7 +64,7 @@ packageDependenciesServer <- function(id, selected_pkg, user, credentials, paren
       req(pkgref())
       tryCatch(
         expr = {
-          deep_ends <- pkgref()$dependencies[[1]] %>% dplyr::as_tibble() %>% 
+          deep_ends <- {if(suppressWarnings(is.null(nrow(pkgref()$dependencies[[1]])) || nrow(pkgref()$dependencies[[1]]) == 0)) dplyr::tibble(package = character(0), type = character(0)) else pkgref()$dependencies[[1]] %>% dplyr::as_tibble()} %>% 
             mutate(package = stringr::str_replace(package, "\n", " ")) %>%
             mutate(name = stringr::str_extract(package, "^((([[A-z]]|[.][._[A-z]])[._[A-z0-9]]*)|[.])"))
           
@@ -94,7 +94,8 @@ packageDependenciesServer <- function(id, selected_pkg, user, credentials, paren
       )
       tryCatch(
         expr = {
-          shrug_jests <- pkgref()$suggests[[1]] %>% dplyr::as_tibble()%>% 
+          shrug_jests <- 
+            {if(suppressWarnings(is.null(nrow(pkgref()$suggests[[1]])) || nrow(pkgref()$suggests[[1]]) == 0)) dplyr::tibble(package = character(0), type = character(0)) else pkgref()$suggests[[1]] %>% dplyr::as_tibble()} %>% 
             mutate(package = stringr::str_replace(package, "\n", " ")) %>%
             mutate(name = stringr::str_extract(package, "^((([[A-z]]|[.][._[A-z]])[._[A-z0-9]]*)|[.])"))
           

From b03f3b8234e64f9279b4925fbb87a2ccff643187 Mon Sep 17 00:00:00 2001
From: "Aaron Clark (Arcus)" <aclark02@arcusbio.com>
Date: Mon, 8 Jul 2024 10:04:55 -0400
Subject: [PATCH 22/39] Increment version number to 3.1.0.9002

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4527f72f8..19b5e74ba 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 3.1.0.9001
+Version: 3.1.0.9002
 Authors@R: c( 
     person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Jeff", "Thompson", role = c("aut"),  email = "jeff.thompson51317@gmail.com", comment = "Co-Lead"),

From 3a32aec89652efdf5af09785e3081d2bdf54b5e5 Mon Sep 17 00:00:00 2001
From: "Aaron Clark (Arcus)" <aclark02@arcusbio.com>
Date: Mon, 8 Jul 2024 10:05:59 -0400
Subject: [PATCH 23/39] update news

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 5a9e345af..1f151aa96 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,7 @@
 # riskassessment (development version)
 
 * Added navigation controls in Function Explorer tab (#644)
+* Fixed bug that crashed the Package Dependencies tab for pkgs without any dependency info available (#802)
 
 # riskassessment 3.1.0
 

From 147bf34e50f66e804a5e9133abed3477b16790b0 Mon Sep 17 00:00:00 2001
From: Github Actions <actions@github.com>
Date: Mon, 8 Jul 2024 14:09:35 +0000
Subject: [PATCH 24/39] Re-build manifest file

---
 manifest.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/manifest.json b/manifest.json
index 149014a82..ae704ffb5 100644
--- a/manifest.json
+++ b/manifest.json
@@ -4367,7 +4367,7 @@
         "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
         "Repository": "RSPM",
         "Date/Publication": "2024-02-29 01:10:07 UTC",
-        "Built": "R 4.3.3; ; 2024-07-08 12:36:44 UTC; unix"
+        "Built": "R 4.3.3; ; 2024-07-08 14:08:48 UTC; unix"
       }
     },
     "reprex": {
@@ -6220,7 +6220,7 @@
       "checksum": "99c5575cb81828e20a7fe1d205551316"
     },
     "DESCRIPTION": {
-      "checksum": "ea81f750b1ae3fa6b3ebf79e5668a3ee"
+      "checksum": "b5ee23e93cf6e02fbaf74b0f44ec8a7c"
     },
     "inst/app/www/css/community_metrics.css": {
       "checksum": "f08eb25c2ee48ac22ed63b0d18994a04"
@@ -6463,7 +6463,7 @@
       "checksum": "97d1232340e04c53088bc8f814133dcd"
     },
     "NEWS.md": {
-      "checksum": "29db451dbb57771e940e1911eac5407f"
+      "checksum": "2a60a34e769071b45f30ee1f0bbacf47"
     },
     "R/app_config.R": {
       "checksum": "c2b61f270b86b6833f0ee39c44a1a440"
@@ -6532,7 +6532,7 @@
       "checksum": "a894eb9114e258feb99b76cdca557cd2"
     },
     "R/mod_packageDependencies.R": {
-      "checksum": "6fffb51829775826e242824f268062b6"
+      "checksum": "ff0b276e6d166a922415e68cc2267360"
     },
     "R/mod_pkg_explorer_utils.R": {
       "checksum": "b7792e08cc4a67296c9df0f452c0a72a"
@@ -6565,13 +6565,13 @@
       "checksum": "e5835b81f48d93ee0175507abbb3186f"
     },
     "R/utils_build_cards.R": {
-      "checksum": "f79316fe637bb1f4038f085621d298f5"
+      "checksum": "a7cfdc1f9a4ad1c2835cd22eb279d8dc"
     },
     "R/utils_config_db.R": {
       "checksum": "74cf2ee5e7283483a88f08d60e3728b0"
     },
     "R/utils_get_db.R": {
-      "checksum": "6e87d4d43f93b4a4b556d72b848dc3f1"
+      "checksum": "6c0e6fb4b3716cdd0c0d2953a1cf4393"
     },
     "R/utils_insert_db.R": {
       "checksum": "2c02e4eab4d9262ef8c8e64eb0f1b4f5"

From 13d3cb6f313eb941b4c0ce60ef66235aed45678e Mon Sep 17 00:00:00 2001
From: "Aaron Clark (Arcus)" <aclark02@arcusbio.com>
Date: Tue, 9 Jul 2024 09:23:00 -0400
Subject: [PATCH 25/39] Increment version number to 3.1.1

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 19b5e74ba..66601712e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 3.1.0.9002
+Version: 3.1.1
 Authors@R: c( 
     person("Aaron", "Clark", role = c("aut", "cre"), email = "clark.aaronchris@gmail.com"),
     person("Jeff", "Thompson", role = c("aut"),  email = "jeff.thompson51317@gmail.com", comment = "Co-Lead"),
diff --git a/NEWS.md b/NEWS.md
index 1f151aa96..49bb2eb2e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# riskassessment (development version)
+# riskassessment 3.1.1
 
 * Added navigation controls in Function Explorer tab (#644)
 * Fixed bug that crashed the Package Dependencies tab for pkgs without any dependency info available (#802)

From 7386c1552f63a5e3a46c7096541b318d648fbeaf Mon Sep 17 00:00:00 2001
From: "Aaron Clark (Arcus)" <aclark02@arcusbio.com>
Date: Tue, 9 Jul 2024 09:24:46 -0400
Subject: [PATCH 26/39] reword news file

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 49bb2eb2e..c24df3cfb 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,7 @@
 # riskassessment 3.1.1
 
 * Added navigation controls in Function Explorer tab (#644)
-* Fixed bug that crashed the Package Dependencies tab for pkgs without any dependency info available (#802)
+* Fixed bug that crashed the Package Dependencies page for pkgs without any dependency info available (#802)
 
 # riskassessment 3.1.0
 

From a1aafcc39f4f8b8a087656e255201c204a573ea7 Mon Sep 17 00:00:00 2001
From: Github Actions <actions@github.com>
Date: Tue, 9 Jul 2024 13:27:58 +0000
Subject: [PATCH 27/39] Re-build manifest file

---
 manifest.json | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/manifest.json b/manifest.json
index ae704ffb5..0eec13146 100644
--- a/manifest.json
+++ b/manifest.json
@@ -4367,7 +4367,7 @@
         "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
         "Repository": "RSPM",
         "Date/Publication": "2024-02-29 01:10:07 UTC",
-        "Built": "R 4.3.3; ; 2024-07-08 14:08:48 UTC; unix"
+        "Built": "R 4.3.3; ; 2024-07-09 13:27:11 UTC; unix"
       }
     },
     "reprex": {
@@ -6220,7 +6220,7 @@
       "checksum": "99c5575cb81828e20a7fe1d205551316"
     },
     "DESCRIPTION": {
-      "checksum": "b5ee23e93cf6e02fbaf74b0f44ec8a7c"
+      "checksum": "43f16dae5ba2122f4fd55e23f7229a40"
     },
     "inst/app/www/css/community_metrics.css": {
       "checksum": "f08eb25c2ee48ac22ed63b0d18994a04"
@@ -6463,7 +6463,7 @@
       "checksum": "97d1232340e04c53088bc8f814133dcd"
     },
     "NEWS.md": {
-      "checksum": "2a60a34e769071b45f30ee1f0bbacf47"
+      "checksum": "72bdae63c42eb2750d86e97fc0996a79"
     },
     "R/app_config.R": {
       "checksum": "c2b61f270b86b6833f0ee39c44a1a440"

From f2e3ff0c3f43c412312086a49da1a0263228ac7a Mon Sep 17 00:00:00 2001
From: "Aaron Clark (Arcus)" <aclark02@arcusbio.com>
Date: Tue, 9 Jul 2024 09:52:13 -0400
Subject: [PATCH 28/39] remove redunant code

---
 R/mod_packageDependencies.R | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/R/mod_packageDependencies.R b/R/mod_packageDependencies.R
index 1b0a03650..4145769ac 100644
--- a/R/mod_packageDependencies.R
+++ b/R/mod_packageDependencies.R
@@ -123,14 +123,7 @@ packageDependenciesServer <- function(id, selected_pkg, user, credentials, paren
                                  decision_id = character(0)))
         }
       )
-      # this is so the dependencies is also a 0x2 tibble like suggests
-      if (rlang::is_empty(pkgref()$dependencies[[1]])) {
-        depends(
-          dplyr::tibble(package = character(0), type = character(0), name = character(0),
-                        version = character(0), score = character(0), decision = character(0),
-                        decision_id = character(0))
-          )
-      }
+
         
       revdeps(pkgref()$reverse_dependencies[[1]] %>% as.vector())
       

From 32c31371fb8e3c61bf90350b1173e847dff718d4 Mon Sep 17 00:00:00 2001
From: Github Actions <actions@github.com>
Date: Tue, 9 Jul 2024 14:02:46 +0000
Subject: [PATCH 29/39] Re-build manifest file

---
 manifest.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/manifest.json b/manifest.json
index 0eec13146..ceee46fcb 100644
--- a/manifest.json
+++ b/manifest.json
@@ -4367,7 +4367,7 @@
         "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
         "Repository": "RSPM",
         "Date/Publication": "2024-02-29 01:10:07 UTC",
-        "Built": "R 4.3.3; ; 2024-07-09 13:27:11 UTC; unix"
+        "Built": "R 4.3.3; ; 2024-07-09 14:01:48 UTC; unix"
       }
     },
     "reprex": {
@@ -6532,7 +6532,7 @@
       "checksum": "a894eb9114e258feb99b76cdca557cd2"
     },
     "R/mod_packageDependencies.R": {
-      "checksum": "ff0b276e6d166a922415e68cc2267360"
+      "checksum": "f8cee3c4845b4d3c3c2f66796af28359"
     },
     "R/mod_pkg_explorer_utils.R": {
       "checksum": "b7792e08cc4a67296c9df0f452c0a72a"

From 4035e6e1265c06602622a7f6e44edaf0ebaecb24 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Tue, 9 Jul 2024 11:09:12 -0400
Subject: [PATCH 30/39] Correctly parse `riskmetric` dependency assessment

---
 R/utils_insert_db.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utils_insert_db.R b/R/utils_insert_db.R
index 3b9f9cb1e..0c95e09ae 100644
--- a/R/utils_insert_db.R
+++ b/R/utils_insert_db.R
@@ -202,7 +202,7 @@ insert_riskmetric_to_db <- function(pkg_name, pkg_version = "",
 
     metric_value <- case_when(
       "pkg_metric_error" %in% class(riskmetric_assess[[metric$name]][[1]]) ~ "pkg_metric_error",
-      metric$name == "dependencies" ~ as.character(length(unlist(as.vector(riskmetric_assess[[metric$name]][[1]][1])))),
+      metric$name == "dependencies" ~ as.character(NROW(riskmetric_assess[[metric$name]][[1]])),
       metric$name == "reverse_dependencies" ~ as.character(length(as.vector(riskmetric_assess[[metric$name]][[1]]))),
       metric$is_perc == 1L ~ as.character(round(riskmetric_score[[metric$name]]*100, 2)[[1]]),
       TRUE ~ as.character(riskmetric_assess[[metric$name]][[1]][1:length(riskmetric_assess[[metric$name]])])

From f46c7035c34820e346b596243143119f1fe80de9 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Tue, 9 Jul 2024 13:33:25 -0400
Subject: [PATCH 31/39] Update NEWS

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index c24df3cfb..72307ff70 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,7 @@
 
 * Added navigation controls in Function Explorer tab (#644)
 * Fixed bug that crashed the Package Dependencies page for pkgs without any dependency info available (#802)
+* Fixed bug that incorrectly displayed 0 dependencies as 1 (#805)
 
 # riskassessment 3.1.0
 

From d2c3900f4e31f71735f5beecb6a67ecf76eef693 Mon Sep 17 00:00:00 2001
From: Github Actions <actions@github.com>
Date: Tue, 9 Jul 2024 17:39:05 +0000
Subject: [PATCH 32/39] Re-build manifest file

---
 manifest.json | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/manifest.json b/manifest.json
index ceee46fcb..2e41d9790 100644
--- a/manifest.json
+++ b/manifest.json
@@ -4367,7 +4367,7 @@
         "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
         "Repository": "RSPM",
         "Date/Publication": "2024-02-29 01:10:07 UTC",
-        "Built": "R 4.3.3; ; 2024-07-09 14:01:48 UTC; unix"
+        "Built": "R 4.3.3; ; 2024-07-09 17:38:19 UTC; unix"
       }
     },
     "reprex": {
@@ -6463,7 +6463,7 @@
       "checksum": "97d1232340e04c53088bc8f814133dcd"
     },
     "NEWS.md": {
-      "checksum": "72bdae63c42eb2750d86e97fc0996a79"
+      "checksum": "2273640b8da14304bc919f4fc83a58d7"
     },
     "R/app_config.R": {
       "checksum": "c2b61f270b86b6833f0ee39c44a1a440"
@@ -6574,7 +6574,7 @@
       "checksum": "6c0e6fb4b3716cdd0c0d2953a1cf4393"
     },
     "R/utils_insert_db.R": {
-      "checksum": "2c02e4eab4d9262ef8c8e64eb0f1b4f5"
+      "checksum": "5eaa94311e33014f000eb3cc5aec8282"
     },
     "R/utils_startup.R": {
       "checksum": "b689ee96f0761480ac65ca22cbbb4980"

From 14f5e97abe779a3ca1c8848894518ee2c7431a0f Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Tue, 9 Jul 2024 15:20:07 -0400
Subject: [PATCH 33/39] Access new token

---
 .github/workflows/test-coverage.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index dffb85e7c..76e51cde3 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -15,6 +15,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       RENV_CONFIG_SANDBOX_ENABLED: false
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - name: Install TexLive

From d7bcdf3e7c5dbf8ce95de0068017931497b46d2c Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Wed, 10 Jul 2024 08:57:47 -0400
Subject: [PATCH 34/39] Try newer workflow

---
 .github/workflows/test-coverage.yaml | 43 ++++++++++++++++++++++------
 1 file changed, 34 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 76e51cde3..ff2b70458 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
@@ -9,13 +9,14 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       RENV_CONFIG_SANDBOX_ENABLED: false
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - name: Install TexLive
@@ -25,21 +26,45 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y texlive-xetex
       
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          use-public-rspm: true
+          use-public-rspm: false
           r-version: 'renv'
 
       - uses: r-lib/actions/setup-renv@v2
       
-      - name: Install riskassessment
-        shell: bash
-        run: R CMD INSTALL --preclean .
-        
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

From b226994952cb6aa4f841242b1e43b03b661d5291 Mon Sep 17 00:00:00 2001
From: Github Actions <actions@github.com>
Date: Wed, 10 Jul 2024 13:12:32 +0000
Subject: [PATCH 35/39] Re-build manifest file

---
 manifest.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/manifest.json b/manifest.json
index ceee46fcb..98a26535f 100644
--- a/manifest.json
+++ b/manifest.json
@@ -4367,7 +4367,7 @@
         "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
         "Repository": "RSPM",
         "Date/Publication": "2024-02-29 01:10:07 UTC",
-        "Built": "R 4.3.3; ; 2024-07-09 14:01:48 UTC; unix"
+        "Built": "R 4.3.3; ; 2024-07-10 13:11:46 UTC; unix"
       }
     },
     "reprex": {
@@ -6175,7 +6175,7 @@
       "checksum": "d74482ddef0a4941a51c077f5ea60e10"
     },
     ".github/workflows/test-coverage.yaml": {
-      "checksum": "c0baef024db9ec1299aae4098e904e9c"
+      "checksum": "a854cdb9e1cfbcbbf5ccffdf4755606b"
     },
     ".github/workflows/write-manifest.yaml": {
       "checksum": "cdfc1470af653982867daed2b99d5b97"

From 934df7deb25268b3e9c5b34a7cf8872873bd438b Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Wed, 10 Jul 2024 09:51:38 -0400
Subject: [PATCH 36/39] Add `available_packages_filters` to session options

---
 R/app_server.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/R/app_server.R b/R/app_server.R
index 98bc3e974..3c9de0f5b 100644
--- a/R/app_server.R
+++ b/R/app_server.R
@@ -13,7 +13,13 @@ app_server <- function(input, output, session) {
   onStop(function() {
     options(old)
     })
-  options(repos = get_db_config("package_repo"))
+  options(
+    # Set session repo to value specified in configuration file
+    repos = get_db_config("package_repo"),
+    # Removes filters based on R version, OS type, sub-architecture. Only
+    # duplicates will be removed from the available package list
+    available_packages_filters = "duplicates"
+  )
   
   # Collect user info.
   user <- reactiveValues()

From caa65e298de5fefe3816676a26a792b78bd9f246 Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Wed, 10 Jul 2024 10:07:35 -0400
Subject: [PATCH 37/39] Properly reset option on stopping application

---
 R/app_server.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/R/app_server.R b/R/app_server.R
index 3c9de0f5b..6a9c86bfd 100644
--- a/R/app_server.R
+++ b/R/app_server.R
@@ -11,8 +11,13 @@ app_server <- function(input, output, session) {
   
   old <- options()
   onStop(function() {
-    options(old)
-    })
+    options(c(
+      # Unsets available packages filter if unset previously. Will be overriden
+      # otherwise.
+      list(available_packages_filters = NULL),
+      old
+    ))
+  })
   options(
     # Set session repo to value specified in configuration file
     repos = get_db_config("package_repo"),

From 67b7852a00657c02c5f4c95f992d3802595134cb Mon Sep 17 00:00:00 2001
From: Jeff Thompson <160783290+jthompson-arcus@users.noreply.github.com>
Date: Wed, 10 Jul 2024 11:43:12 -0400
Subject: [PATCH 38/39] Update NEWS

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 72307ff70..678888e23 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,6 +3,7 @@
 * Added navigation controls in Function Explorer tab (#644)
 * Fixed bug that crashed the Package Dependencies page for pkgs without any dependency info available (#802)
 * Fixed bug that incorrectly displayed 0 dependencies as 1 (#805)
+* Fixed bug that kept full list of available packages from populating (#776)
 
 # riskassessment 3.1.0
 

From 80833c95e8c8efc25d810bd92432a60fdcee27b9 Mon Sep 17 00:00:00 2001
From: Github Actions <actions@github.com>
Date: Wed, 10 Jul 2024 16:08:51 +0000
Subject: [PATCH 39/39] Re-build manifest file

---
 manifest.json | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/manifest.json b/manifest.json
index a17b9c101..2546af102 100644
--- a/manifest.json
+++ b/manifest.json
@@ -4367,7 +4367,7 @@
         "Maintainer": "Kevin Ushey <kevin@rstudio.com>",
         "Repository": "RSPM",
         "Date/Publication": "2024-02-29 01:10:07 UTC",
-        "Built": "R 4.3.3; ; 2024-07-10 13:11:46 UTC; unix"
+        "Built": "R 4.3.3; ; 2024-07-10 16:07:53 UTC; unix"
       }
     },
     "reprex": {
@@ -6463,13 +6463,13 @@
       "checksum": "97d1232340e04c53088bc8f814133dcd"
     },
     "NEWS.md": {
-      "checksum": "2273640b8da14304bc919f4fc83a58d7"
+      "checksum": "8f1dc97771e1911ac13a12a45300a516"
     },
     "R/app_config.R": {
       "checksum": "c2b61f270b86b6833f0ee39c44a1a440"
     },
     "R/app_server.R": {
-      "checksum": "e2a53d90bd4289198e29bec4ff19eba7"
+      "checksum": "8408e324004d2991c855c03040cb2dca"
     },
     "R/app_ui.R": {
       "checksum": "50d68f46171151cd36457a7154e5a7a3"