Dear
The following pdf downloader for the GT table based on gtsave() i does not work in the shiny app deployed at posit connect cloud:
# Download handler for GO gene list table
output$download_go_gene_list <- downloadHandler(
filename = function() {
paste0("GO_Gene_List_Table_", format(Sys.time(), "%Y%m%d_%H%M"), ".pdf")
},
content = function(file) {
req(input$color_highlight, enrichment_results_list)
colors_to_use <- if(input$color_highlight) {
req(input$up_color, input$down_color)
c(input$down_color, input$up_color)
} else {
c("#000000", "#000000") # default black if highlighting is disabled
}
gt_table <- build_gt_gene_lists(
df = uploaded_df(),
annotation_col = input$annotation_col,
chosen_go = input$go_category,
go_data = GO,
alpha = input$alpha,
fold_col = input$fold_col,
color_highlight = colors_to_use,
log_messages_rv = log_messages,
log_event = log_event
)
gtsave(gt_table, file)
}
)
The log system at the server informs that it needs chrome like browser and that I should set the CHROMOTE_CHROME environment variable to the path of a Chromium/Chrome executable:
2025-01-10T15:35:28+01:00 `google-chrome`, `chromium-browser` and `chrome` were not found. Try setting the `CHROMOTE_CHROME` environment variable to the executable of a Chromium-based browser, such as Google Chrome, Chromium or Brave or adding one of these executables to your PATH.
2025-01-10T15:35:28+01:00 Warning: Error in initialize: Invalid path to Chrome
2025-01-10T15:35:28+01:00 15: <Anonymous>
2025-01-10T15:35:28+01:00 13: fn
2025-01-10T15:35:28+01:00 8: retry
2025-01-10T15:35:28+01:00 7: connect$retryingStartServer
2025-01-10T15:35:28+01:00 6: eval
2025-01-10T15:35:28+01:00 5: eval
2025-01-10T15:35:28+01:00 4: eval
2025-01-10T15:35:28+01:00 3: eval
2025-01-10T15:35:28+01:00 2: eval.parent
2025-01-10T15:35:28+01:00 1: local
How to locate this path - is chrome installed in the cloud system? How I can set this variable to the cloud enrironment? Everything else in a big app including other pdf file downloaders using ggsave() and not gtsave() are working correctly... all the help appreciated 