move org.Hs.eg.db to Suggests (#236)

Author: egeulgen

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pathfindR
 Type: Package
 Title: Enrichment Analysis Utilizing Active Subnetworks
-Version: 2.6.0.9000
+Version: 2.6.0.9001
 Authors@R: c(person("Ege", "Ulgen",
                     role = c("cre", "cph"), 
                     email = "[email protected]",
@@ -40,7 +40,6 @@ Imports:
     doParallel,
     foreach,
     rmarkdown,
-    org.Hs.eg.db,
     ggplot2,
     ggraph,
     ggupset,
@@ -55,8 +54,9 @@ Imports:
 Depends: R (>= 4.3.0),
     pathfindR.data (>= 2.0)
 Suggests: 
+    org.Hs.eg.db,
     testthat (>= 2.3.2),
     covr,
     mockery
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 VignetteBuilder: knitr

NEWS.md

@@ -1,4 +1,6 @@
 # pathfindR (development version)
+## Minor Changes and Bug Fixes
+- Moved org.Hs.eg.db from "Imports" to "Suggests" per new CRAN policy. Relevant functions revert to default behaviour if the required package is not installed.
 
 # pathfindR 2.6.0
 

R/utility.R

@@ -347,6 +347,18 @@ input_processing <- function(input, p_val_threshold = 0.05, pin_name_path = "Bio
     missing_symbols <- input$GENE[!base::toupper(input$GENE) %in% PIN_genes]
     non_missing_symbols <- input$GENE[base::toupper(input$GENE) %in% PIN_genes]
 
+    
+    if (convert2alias & !requireNamespace("org.Hs.eg.db", quietly = TRUE)) {
+      message(
+        "Package 'org.Hs.eg.db' is not installed; returning input genes unchanged.\n",
+        "Install it with:\n",
+        "  if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')\n",
+        "  BiocManager::install('TxDb.Hsapiens.UCSC.hg19.knownGene')",
+      )
+      convert2alias <- False
+    }
+    
+    
     if (convert2alias & length(missing_symbols) != 0) {
         ## use SQL to get alias table and gene_info table (contains the
         ## symbols) first open the database connection

R/visualization.R

@@ -258,6 +258,17 @@ visualize_KEGG_diagram <- function(
     legend.position = "top"
 ) {
     message("This function utilises one functionality of `ggkegg`. For more options, visit https://github.com/noriakis/ggkegg")
+     
+    if (!requireNamespace("org.Hs.eg.db", quietly = TRUE)) {
+      message(
+        "Package 'org.Hs.eg.db' is not installed; returning empty list.\n",
+        "Install it with:\n",
+        "  if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')\n",
+        "  BiocManager::install('TxDb.Hsapiens.UCSC.hg19.knownGene')",
+      )
+      return(list())
+    }
+    
     ############ Arg checks
 
     ### kegg_pw_ids