Remove vendor and outbound links

.github/workflows/check-package.yml

@@ -10,13 +10,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: '4.2.2'
       - name: Install cURL Headers
         run: |
          sudo apt-get update
          sudo apt-get -y install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libgeos-dev
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          r-version: '4.3.0'
+      - name: Install required install packages and remote repos
+        run: |
+          install.packages(c("remotes", "BiocManager"))
+          BiocManager::install(version = "3.18")
+        shell: Rscript {0}
 # name: Install required packages not listed in the package description
 # run: |
 # install.packages(c("BiocManager", "caret", "Seurat", "tidyverse"))

.github/workflows/deploy.yml

@@ -28,7 +28,7 @@ jobs:
       - name: Install required install packages and remote repos
         run: |
           install.packages(c("remotes", "BiocManager"))
-          BiocManager::install(version = "3.17")
+          BiocManager::install(version = "3.18")
           BiocManager::install(c('BiocGenerics', 'GenomeInfoDbData', 'limma', 'zlibbioc'))
           BiocManager::install(ask = F)
           remotes::install_version("rsconnect", "0.8.29")
@@ -39,7 +39,7 @@ jobs:
           APPNAME: cytomarker
           SERVER: shinyapps.io
         run: |
-          options(repos=c(BiocManager::repositories(version = "3.17")), rsconnect.packrat = TRUE)
+          options(repos=c(BiocManager::repositories(version = "3.18")), rsconnect.packrat = TRUE)
           rsconnect::setAccountInfo("${{ secrets.SHINYAPPS_ACC }}", "${{ secrets.SHINYAPPS_TOKEN }}", "${{ secrets.SHINYAPPS_SEC }}")
           rsconnect::deployApp(appName = "${{ env.APPNAME }}", account = "${{ secrets.SHINYAPPS_ACC }}", server = "${{ env.SERVER }}")
         shell: Rscript {0}

DESCRIPTION

@@ -36,13 +36,11 @@ Imports:
     RColorBrewer,
     shinytest2,
     tidyr,
-    htmlwidgets,
     shinydashboard,
     shinyBS,
     stringr,
     rlang,
     rmarkdown,
-    rdrop2,
     lubridate,
     htmltools,
     fontawesome,
@@ -51,7 +49,8 @@ Imports:
     waiter,
     cicerone,
     shinyanimate,
-    feather
+    feather,
+    rdrop2
 Suggests:
   stringr,
   yardstick,
@@ -78,10 +77,12 @@ Remotes:
     github::MarioniLab/geneBasisR,
     github::camlab-bioml/inferorg,
     github::stephenturner/annotables,
-    github::rstudio/[email protected]
+    github::rstudio/[email protected],
+    github::karthik/rdrop2
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Depends:
-    R (>= 4.2.2)
+    R (>= 4.3.0),
+    htmlwidgets (== 1.6.2)

R/app.R

@@ -1107,8 +1107,7 @@ gtag('config', 'G-B26X9YQQGT');
                 #                 ),
                 # `External Link` = colDef(html = T),
                 `Human Protein Atlas` = colDef(html = T)
-                ,
-                `External Link` = colDef(html = T)
+                # `External Link` = colDef(html = T)
                 ),
                 sortable = TRUE,
                 elementId = "antibody-select")
@@ -1548,7 +1547,8 @@ gtag('config', 'G-B26X9YQQGT');
                                                         ifelse(Vendor == "Abcam", "Abcam.com",
                                                                "bdbiosciences.com"),
                                                         '</a>')) |>
-                        dplyr::select(-c(`Datasheet URL`, `Protein Expression`, `ensgene`)))
+                        dplyr::select(-c(`Datasheet URL`, `Protein Expression`, `ensgene`, `Vendor`,
+                                         `External Link`)))
 
           update_analysis()
 
@@ -2928,7 +2928,7 @@ gtag('config', 'G-B26X9YQQGT');
                                                                        type='scatter', hoverinfo="text", colors=cytomarker_palette()) %>% 
                                                          layout(title = "UMAP selected markers")),
                                 metric = plots_for_markdown()$metric))
-        
+
         download_data(fname, current_run_log()$map, plots_for_markdown(), heatmap_for_report(), df_antibody(), 
                       markdown_report_path, current_metrics()$summary, current_overall_score(),
                       markers_with_type())

deploy.R

@@ -2,6 +2,5 @@
 
 library(rsconnect)
 devtools::load_all()
-options(repos=c(BiocManager::repositories(version = "3.17")))
-rsconnect::deployApp(account = 'mwatson-ltri')
-
+options(repos=c(BiocManager::repositories(version = "3.18")))
+rsconnect::deployApp(account = 'camlab')

inst/report/rmarkdown-report.Rmd

@@ -90,7 +90,7 @@ reactable(params$df,
 #     return rows.filter(r => filterValues.includes(r.values[id]));
 # }")
 #                 ),
-                `External Link` = colDef(html = T),
+                # `External Link` = colDef(html = T),
                 `Human Protein Atlas` = colDef(html = T)
                 ),
                 sortable = TRUE,