Add requireNamespace guards for Suggests deps (echolocatoR#151)

- MOTIFBREAKR.R: guard BSgenome, motifbreakR, MotifDb with stop + install instructions
- MOTIFBREAKR_plot.R: same guards for motifbreakR, MotifDb, BSgenome.Hsapiens.UCSC.hg19
- MOTIFBREAKR_calc_pvals.R: same guards for motifbreakR, MotifDb, BSgenome
- test_enrichment.R: guard regioneR with stop + install instructions

All bare requireNamespace() calls now stop with actionable BiocManager::install() messages.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: bschilder

R/MOTIFBREAKR.R

@@ -80,8 +80,16 @@ MOTIFBREAKR <- function(rsid_list,
                         granularity = NULL,
                         nThread = 1,
                         verbose = TRUE){
-  requireNamespace("BSgenome")
-  requireNamespace("motifbreakR")
+  if (!requireNamespace("BSgenome", quietly = TRUE)) {
+      stop("Package 'BSgenome' is required for motifbreakR.\n",
+           "Install it with: BiocManager::install('BSgenome')",
+           call. = FALSE)
+  }
+  if (!requireNamespace("motifbreakR", quietly = TRUE)) {
+      stop("Package 'motifbreakR' is required but not installed.\n",
+           "Install it with: BiocManager::install('motifbreakR')",
+           call. = FALSE)
+  }
   # echoverseTemplate:::args2vars(MOTIFBREAKR)
 
   #### Select genome build ####
@@ -102,7 +110,14 @@ MOTIFBREAKR <- function(rsid_list,
         dbSNP = gb_list$dbSNP,
         search.genome = gb_list$search.genome);
     #### Subset motif databases ####
-    if(is.null(pwmList)){pwmList <- MotifDb::MotifDb}
+    if(is.null(pwmList)){
+        if (!requireNamespace("MotifDb", quietly = TRUE)) {
+            stop("Package 'MotifDb' is required for motifbreakR.\n",
+                 "Install it with: BiocManager::install('MotifDb')",
+                 call. = FALSE)
+        }
+        pwmList <- MotifDb::MotifDb
+    }
     if(!is.null(organism)){
       messager("Filtering pwmList to only include organism:",organism)
       pwmList <- pwmList[grep(paste0("^",organism),names(pwmList),

R/MOTIFBREAKR_calc_pvals.R

@@ -26,9 +26,13 @@ MOTIFBREAKR_calc_pvals <- function(mb_res,
                                    nThread = 1,
                                    results_dir = file.path(tempdir(),"results"),
                                    verbose = TRUE){
-    requireNamespace("motifbreakR");
-    requireNamespace("MotifDb");
-    requireNamespace("BSgenome");
+    for (pkg in c("motifbreakR", "MotifDb", "BSgenome")) {
+        if (!requireNamespace(pkg, quietly = TRUE)) {
+            stop("Package '", pkg, "' is required but not installed.\n",
+                 "Install it with: BiocManager::install('", pkg, "')",
+                 call. = FALSE)
+        }
+    }
     #### Calculate p-values #### 
     messager("+ MOTIFBREAKR:: Calculating p-values for",
              length(mb_res),"RSID(s)...", v=verbose)

R/MOTIFBREAKR_plot.R

@@ -50,10 +50,13 @@ MOTIFBREAKR_plot <- function(mb_res,
                              width=7,
                              verbose=TRUE){
 
-    requireNamespace("motifbreakR")
-    requireNamespace("MotifDb")
-    requireNamespace("BSgenome.Hsapiens.UCSC.hg19")
-    requireNamespace("grDevices")
+    for (pkg in c("motifbreakR", "MotifDb", "BSgenome.Hsapiens.UCSC.hg19")) {
+        if (!requireNamespace(pkg, quietly = TRUE)) {
+            stop("Package '", pkg, "' is required but not installed.\n",
+                 "Install it with: BiocManager::install('", pkg, "')",
+                 call. = FALSE)
+        }
+    }
     id <- NULL;
 
     mb_res <- echodata::dt_to_granges(dat = mb_res, 

R/test_enrichment.R

@@ -54,7 +54,11 @@ test_enrichment <- function(grlist1,
                             verbose = TRUE,
                             ...){
 
-    requireNamespace("regioneR")
+    if (!requireNamespace("regioneR", quietly = TRUE)) {
+        stop("Package 'regioneR' is required but not installed.\n",
+             "Install it with: BiocManager::install('regioneR')",
+             call. = FALSE)
+    }
     #### Check inputs #### 
     grlist1 <- check_grlist(grlist=grlist1, 
                             prefix = "grlist1",