Merge pull request giotto-suite#327 from josschavezf/dev

fix recommendations from BiocCheck::BiocCheck()

Author: josschavezf

DESCRIPTION

@@ -26,7 +26,7 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
 Depends:
-    R (>= 4.4.0)
+    R (>= 4.5.0)
 Imports:
     checkmate,
     data.table (>= 1.12.2),

R/combine_metadata.R

@@ -695,10 +695,10 @@ calculateLabelProportions <- function(gobject, labels,
         ), call. = FALSE)
     }
 
-    spat_unit = set_default_spat_unit(
+    spat_unit <- set_default_spat_unit(
         gobject = gobject, spat_unit = spat_unit
     )
-    feat_type = set_default_feat_type(
+    feat_type <- set_default_feat_type(
         gobject = gobject, spat_unit = spat_unit, feat_type = feat_type
     )
 
@@ -881,7 +881,7 @@ calculateLabelProportions <- function(gobject, labels,
         sn <- sn[, c("source", "target")] # drop weights info if any
     } else if (!"weight" %in% colnames(sn) || isFALSE(weights)) {
         warning(wrap_txt("No 'weight' information present in spatial network.
-                         Using adjacency instead."), call. = FALSE)
+                        Using adjacency instead."), call. = FALSE)
         sn[, "weight" := 1] # fallback if no weight info exists
     }
     # ensure unique

R/data_evaluation.R

@@ -152,7 +152,7 @@ evaluate_input <- function(type, x, ...) {
         .gstop(
             "expression input needs to be a path to matrix-like data or an",
             "object of class 'Matrix', 'data.table', 'data.frame', 'matrix'",
-      "'DelayedMatrix' or 'dbSparseMatrix'."
+            "'DelayedMatrix' or 'dbSparseMatrix'."
         )
     }
 
@@ -321,7 +321,7 @@ evaluate_input <- function(type, x, ...) {
     rnames <- rownames(x)
     if (!is.null(rnames)) {
         vmsg(.v = verbose, "[spatlocs] matrix input has rownames.
-             Using these as IDs.")
+            Using these as IDs.")
         dt[, id := rnames]
     }
     .evaluate_spatial_locations(dt, verbose = verbose, ...)

R/images.R

@@ -2850,7 +2850,7 @@ to_simple_tif <- function(input_file,
             unlink(outpath, force = TRUE) # if overwrite, delete original
         } else {
             stop("File already exists: ", outpath,
-                 "\nSet overwrite = TRUE to replace.\n",
+                "\nSet overwrite = TRUE to replace.\n",
                 call. = FALSE
             )
         }

R/spatial_query.R

@@ -177,7 +177,7 @@ spatQuery <- function(gobject,
     if (!is.null(name)) checkmate::assert_character(name)
     checkmate::assert_list(filters,
         types = c("character", "giottoPolygon", "spatLocsObj", "numeric",
-                  "integer", "SpatVector")
+                "integer", "SpatVector")
     )
     checkmate::assert_character(use_centroids, null.ok = TRUE)
     checkmate::assert_numeric(buffer)
@@ -190,29 +190,29 @@ spatQuery <- function(gobject,
     # more specific checks on inputs  ----------------------------------- #
     if (length(filters) < 2L) {
         stop(wrap_txt("At least two elements in filters are needed."),
-             call. = FALSE)
+            call. = FALSE)
     }
     # `filters` input must be named.
     filter_names <- names(filters)
     if (any(vapply(filter_names, is_empty_char, FUN.VALUE = logical(1L)))) {
         stop(wrap_txt("All elements in filters list must be named"),
-             call. = FALSE)
+            call. = FALSE)
     }
     if (!is.null(use_centroids)) {
         if (!all(use_centroids %in% filter_names)) {
             stop("all entries in `use_centroids` must be names in `filters`\n",
-                 call. = FALSE)
+                call. = FALSE)
         }
     }
     if (length(buffer) > 1L) {
         buffer_names <- names(buffer)
         if (is.null(buffer_names)) {
             stop("if multiple `buffer` values given, they must be named\n",
-                 call. = FALSE)
+                call. = FALSE)
         }
         if (!all(buffer_names %in% filter_names)) {
             stop("all names for `buffer` values must be names in `filters`\n",
-                 call. = FALSE)
+                call. = FALSE)
         }
     }
 
@@ -334,7 +334,7 @@ spatQuery <- function(gobject,
         # not allowed.
         stop(wrap_txtf(
             "'%s' is not the last layer of query.
-                Assigned 'buffer' may not be 0", fname
+            Assigned 'buffer' may not be 0", fname
         ), call. = FALSE)
     }
 }
@@ -355,7 +355,7 @@ spatQueryGiottoPolygons <- spatQuery
 
 .squery_get_sv.default <- function(x, ...) {
     stop(wrap_txt("[spatQuery] unrecognized filter input type:", class(x)),
-         call. = FALSE)
+        call. = FALSE)
 }
 
 .squery_get_sv.character <- function(x, gobject, centroids, spat_unit, ...) {
@@ -429,7 +429,7 @@ spatQueryGiottoPolygons <- spatQuery
 
     if (is.null(sv)) {
         stop(sprintf("Requested filter '%s' not found in giotto object\n", x),
-             call. = FALSE)
+            call. = FALSE)
     }
 
     # filter by x if needed