Propagate renv.lock from pharmaverse/admiralci (#2119)

renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <[email protected]> Co-authored-by: Ben Straub <[email protected]>
pharmaverse · Oct 8, 2023 · b575055 · b575055
1 parent ef44637
commit b575055
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Showing 10 changed files with 18 additions and 11 deletions.
diff --git a/.Rprofile b/.Rprofile
@@ -1,8 +1,7 @@
 # Set renv profile base on R version.
 .get_dependencies <- function(project_dir) {
-
   admdev_loc <- find.package("admiraldev", lib.loc = .libPaths(), quiet = TRUE)
-  adm_dev_suggests <- if(length(admdev_loc) != 0) {
+  adm_dev_suggests <- if (length(admdev_loc) != 0) {
     renv:::renv_dependencies_discover_description(admdev_loc, fields = c("Depends", "Imports", "LinkingTo", "Suggests"))
   } else {
     data.frame(Packages = character(0))
@@ -19,7 +18,7 @@
       ))
     )
   )
-  packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm", getwd()))]
+  packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "pharmaversesdtm", getwd()))]
 }
 
 options(renv.snapshot.filter = .get_dependencies)

diff --git a/.devcontainer/4.1/devcontainer.json b/.devcontainer/4.1/devcontainer.json
@@ -31,7 +31,7 @@
 
 	"postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
 
-	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"",
+	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'",
 
 	"customizations": {
 		"vscode": {

diff --git a/.devcontainer/4.2/devcontainer.json b/.devcontainer/4.2/devcontainer.json
@@ -31,7 +31,7 @@
 
 	"postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
 
-	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"",
+	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'",
 
 	"customizations": {
 		"vscode": {

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -31,7 +31,7 @@
 
 	"postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
 
-	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"",
+	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'",
 
 	"customizations": {
 		"vscode": {

diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh
@@ -1,5 +1,11 @@
 #!/bin/bash
 
+# move script rstudio into /usr/bin
+sudo cp "$(pwd)/.devcontainer/rstudio.sh" /usr/bin/rstudio
+sudo chmod +x /usr/bin/rstudio
+
+# Restore renv and install staged dependencies
 R -q -e 'renv::restore(lockfile = file.path("renv", "profiles", paste(R.version$major, substr(R.version$minor, 1, 1), sep = "."), "renv.lock")); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = ".", verbose = 1), verbose = 1);'
 
+# Define rstudio default working directory
 jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json
diff --git a/.devcontainer/rstudio.sh b/.devcontainer/rstudio.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+$BROWSER "https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}"
+
+exit 1
diff --git a/renv/profiles/4.1/renv/settings.json b/renv/profiles/4.1/renv/settings.json
@@ -4,7 +4,6 @@
   "ignored.packages": [
     "admiral",
     "admiraldev",
-    "admiral.test",
     "admiralci",
     "pharmaversesdtm"
   ],

diff --git a/renv/profiles/4.2/renv/settings.json b/renv/profiles/4.2/renv/settings.json
@@ -4,7 +4,6 @@
   "ignored.packages": [
     "admiral",
     "admiraldev",
-    "admiral.test",
     "admiralci",
     "pharmaversesdtm"
   ],

diff --git a/renv/profiles/4.3/renv/settings.json b/renv/profiles/4.3/renv/settings.json
@@ -4,7 +4,6 @@
   "ignored.packages": [
     "admiral",
     "admiraldev",
-    "admiral.test",
     "admiralci",
     "pharmaversesdtm"
   ],

diff --git a/renv/settings.json b/renv/settings.json
@@ -4,8 +4,8 @@
   "ignored.packages": [
     "admiral",
     "admiraldev",
-    "admiral.test",
-    "admiralci"
+    "admiralci",
+    "pharmaversesdtm"
   ],
   "package.dependency.fields": [
     "Imports",