update bioconductor in GA

downgrade htmlwidgets to 1.6.2 to be compatible with sortable 0.5.0
camlab-bioml · Nov 29, 2023 · 3412d97 · 3412d97
1 parent faa868e
commit 3412d97
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Showing 4 changed files with 8 additions and 4 deletions.
diff --git a/.github/workflows/check-package.yml b/.github/workflows/check-package.yml
@@ -17,6 +17,10 @@ jobs:
         run: |
          sudo apt-get update
          sudo apt-get -y install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libgeos-dev
+      - name: Install required install packages and remote repos
+        run: |
+          install.packages(c("remotes", "BiocManager"))
+          BiocManager::install(version = "3.18")
 # name: Install required packages not listed in the package description
 # run: |
 # install.packages(c("BiocManager", "caret", "Seurat", "tidyverse"))

diff --git a/.github/workflows/deploy.yml b/.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}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -36,7 +36,7 @@ Imports:
     RColorBrewer,
     shinytest2,
     tidyr,
-    htmlwidgets,
+    htmlwidgets (== 1.6.2),
     shinydashboard,
     shinyBS,
     stringr,

diff --git a/deploy.R b/deploy.R
@@ -2,6 +2,6 @@
 
 library(rsconnect)
 devtools::load_all()
-options(repos=c(BiocManager::repositories(version = "3.17")))
+options(repos=c(BiocManager::repositories(version = "3.18")))
 rsconnect::deployApp(account = 'camlab')