Fix doc and import issues

NAMESPACE

@@ -91,7 +91,6 @@ exportMethods(readRefRanges)
 exportMethods(readSamples)
 exportMethods(seqnames)
 exportMethods(serverInfo)
-exportMethods(show)
 importFrom(GenomeInfoDb,"seqnames<-")
 importFrom(GenomeInfoDb,seqnames)
 importFrom(curl,has_internet)

R/class_jvm_stats.R

@@ -12,6 +12,8 @@
 #' @slot phgVersion
 #' A character string representing the version of PHG (Practical Haplotype
 #' Graph).
+#' @slot classPath
+#' A character vector representing the JAR files found in the class path.
 #' @slot maxMem
 #' A numeric value representing the maximum amount of memory (in bytes) that
 #' the JVM can use.
@@ -133,7 +135,7 @@ jvmStats <- function() {
     freeMem  <- round(rJava::.jcall(runtime, "J", "freeMemory") / gbConv, 3)
     allocMem <- round(totMem - freeMem, 3)
 
-    new(
+    methods::new(
         Class       = "JvmStats",
         nJars       = nJars,
         javaVersion = javaVersion,
@@ -165,7 +167,9 @@ jvmStats <- function() {
 #' (maximum memory, total memory, free memory, and allocated memory) in a human-readable format.
 #' Memory values are shown in the respective units (e.g., bytes, MB, GB) defined in the object.
 #'
-#' @export
+#' @docType methods
+#' @rdname JvmStats-class
+#' @aliases show,JvmStats-method
 setMethod(
     f = "show",
     signature = "JvmStats",

R/utils_general.R

@@ -15,7 +15,7 @@ isValidColor <- function(color) {
         pattern = "^#([A-Fa-f0-9]{3}|[A-Fa-f0-9]{4}|[A-Fa-f0-9]{6}|[A-Fa-f0-9]{8})$",
         x = color
     )
-    isNamedColor <- color %in% colors()
+    isNamedColor <- color %in% grDevices::colors()
 
     return(isHex || isNamedColor)
 }

R/utils_jvm.R

@@ -18,8 +18,7 @@ getLatestPhgVersion <- function() {
     if (httr::http_status(response)$category != "Success") {
         rlang::abort(
             sprintf(
-                "Failed to fetch the latest release info for '%s'. HTTP status code: %s",
-                repo,
+                "Failed to fetch the latest release info for PHGv2. HTTP status code: %s",
                 httr::http_status(response)$reason
             )
         )