fix recommendations from BiocCheck::BiocCheck() #327
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| } | ||
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| spat_unit = set_default_spat_unit( | ||
| spat_unit <- set_default_spat_unit( |
Check warning
Code scanning / lintr
no visible global function definition for 'set_default_spat_unit' Warning
| gobject = gobject, spat_unit = spat_unit | ||
| ) | ||
| feat_type = set_default_feat_type( | ||
| feat_type <- set_default_feat_type( |
Check warning
Code scanning / lintr
no visible global function definition for 'set_default_feat_type' Warning
| checkmate::assert_list(filters, | ||
| types = c("character", "giottoPolygon", "spatLocsObj", "numeric", | ||
| "integer", "SpatVector") | ||
| "integer", "SpatVector") |
Check notice
Code scanning / lintr
Hanging indent should be 18 spaces but is 16 spaces. Note
| if (length(filters) < 2L) { | ||
| stop(wrap_txt("At least two elements in filters are needed."), | ||
| call. = FALSE) | ||
| call. = FALSE) |
Check notice
Code scanning / lintr
Hanging indent should be 13 spaces but is 12 spaces. Note
| 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) |
Check notice
Code scanning / lintr
Hanging indent should be 13 spaces but is 12 spaces. Note
| if (!all(use_centroids %in% filter_names)) { | ||
| stop("all entries in `use_centroids` must be names in `filters`\n", | ||
| call. = FALSE) | ||
| call. = FALSE) |
Check notice
Code scanning / lintr
Hanging indent should be 17 spaces but is 16 spaces. Note
| if (is.null(buffer_names)) { | ||
| stop("if multiple `buffer` values given, they must be named\n", | ||
| call. = FALSE) | ||
| call. = FALSE) |
Check notice
Code scanning / lintr
Hanging indent should be 17 spaces but is 16 spaces. Note
| if (!all(buffer_names %in% filter_names)) { | ||
| stop("all names for `buffer` values must be names in `filters`\n", | ||
| call. = FALSE) | ||
| call. = FALSE) |
Check notice
Code scanning / lintr
Hanging indent should be 17 spaces but is 16 spaces. Note
| .squery_get_sv.default <- function(x, ...) { | ||
| stop(wrap_txt("[spatQuery] unrecognized filter input type:", class(x)), | ||
| call. = FALSE) | ||
| call. = FALSE) |
Check notice
Code scanning / lintr
Hanging indent should be 9 spaces but is 8 spaces. Note
| if (is.null(sv)) { | ||
| stop(sprintf("Requested filter '%s' not found in giotto object\n", x), | ||
| call. = FALSE) | ||
| call. = FALSE) |
Check notice
Code scanning / lintr
Hanging indent should be 13 spaces but is 12 spaces. Note
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