Fix doc warnings and missing package in action

ESHackathon · Nov 9, 2024 · 963c54b · 963c54b
2 parents cbe03b2 + 8ee138d
commit 963c54b
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Showing 3 changed files with 4 additions and 12 deletions.
diff --git a/.github/workflows/document-and-deploy-manual.yml b/.github/workflows/document-and-deploy-manual.yml
@@ -32,15 +32,11 @@ jobs:
       - name: Set up R Dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: devtools
-
-      - name: set up devtools system 
-        run: sudo apt install libharfbuzz-dev libfribidi-dev libtiff5-dev
+          extra-packages: devtools, plogr, roxygen2, remotes, rsconnect, pkgdown
 
       - name: Create documentation
         run: |
           R -e "
-            install.packages(c('rcmdcheck', 'roxygen2', 'devtools'));
             file.remove('NAMESPACE');
             descr <- readLines('DESCRIPTION');
             descr <- stringr::str_replace(descr, '^Date.*$', paste('Date:', Sys.Date()));
@@ -63,7 +59,6 @@ jobs:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
           R -e "
-            install.packages(c('rsconnect', 'remotes'));
             remotes::install_github('ESHackathon/CiteSource', force = TRUE);
             rsconnect::setAccountInfo(name=${{secrets.SHINY_LUKAS_ACCOUNT}}, token=${{secrets.SHINY_LUKAS_TOKEN}}, secret=${{secrets.SHINY_LUKAS_SECRET}}); 
             rsconnect::deployApp(appName = 'CiteSource_latest', appDir = './inst/shiny-app/CiteSource', forceUpdate = TRUE)"   
@@ -74,7 +69,6 @@ jobs:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
           R -e "
-            install.packages(c('rsconnect', 'remotes'));
             remotes::install_github('ESHackathon/CiteSource', force = TRUE);
             rsconnect::setAccountInfo(name=${{secrets.SHINY_LUKAS_ACCOUNT}}, token=${{secrets.SHINY_LUKAS_TOKEN}}, secret=${{secrets.SHINY_LUKAS_SECRET}}); 
             rsconnect::deployApp(appName = 'CiteSource', appDir = './inst/shiny-app/CiteSource', forceUpdate = TRUE)"   
@@ -84,7 +78,6 @@ jobs:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
           R -e "
-            install.packages('pkgdown');
             if (!require(CiteSource)) remotes::install_github('ESHackathon/CiteSource', force = TRUE);
             pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
       

diff --git a/R/CiteSource.R b/R/CiteSource.R
@@ -4,10 +4,7 @@
 #' processing of results of various searches in different sources. It allows to
 #' deduplicate results while retaining meta-data on where those results were
 #' found and then enables users to compare the contribution of different sources
-#'
-#' @docType package
-#' @name CiteSource
-NULL
+"_PACKAGE"
 
 # Use magrittr rather than base R pipe to be compatible with older R versions
 # And data pronoun .data to avoid issues/warnings due to dplyr non-standard evaluation

diff --git a/R/import_export_helpers.R b/R/import_export_helpers.R
@@ -1144,6 +1144,8 @@ remove_factors <- function(z) {
   return(z)
 }
 
+#' @export
+
 as.data.frame.bibliography <- function(x, ...) {
   # Solves https://github.com/mjwestgate/synthesisr/issues/25 - but could likely be faster
   x <- purrr::map(x, \(x) {