pushing new features and avoiding curl.

DESCRIPTION

@@ -89,8 +89,7 @@ Imports:
     signal,
     glmnet,
     jpeg,
-    shiny,
-    ggplot2
+    shiny
 Suggests:
     knitr,
     rmarkdown,
@@ -104,7 +103,7 @@ Suggests:
     dplyr, 
     DT,
     mongolite, 
-    loggit
+    ggplot2
 RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3

R/def_features.R

@@ -68,11 +68,13 @@ collapse_spec.OpenSpecy <- function(x, ...) {
   ts$id <- x$metadata$feature_id
   x$spectra <- ts[, lapply(.SD, median, na.rm = T), by = "id"] |>
     transpose(make.names = "id")
-
+
+  r <- g <- b <- NULL # workaround for data.table non-standard
+
   if(all(c("r", "g", "b") %in% names(x$metadata))){
-      x$metadata[, r := as.integer(sqrt(mean(r^2))), by = "feature_id"]
-      x$metadata[, g := as.integer(sqrt(mean(g^2))), by = "feature_id"]
-      x$metadata[, b := as.integer(sqrt(mean(b^2))), by = "feature_id"]
+      x$metadata[, "r" := as.integer(sqrt(mean(r^2))), by = "feature_id"]
+      x$metadata[, "g" := as.integer(sqrt(mean(g^2))), by = "feature_id"]
+      x$metadata[, "b" := as.integer(sqrt(mean(b^2))), by = "feature_id"]
       x$metadata <- x$metadata |>
           unique(by = c("feature_id", "area", "feret_max", "centroid_y",
                         "centroid_x", "first_x", "first_y", "rand_x", "rand_y",

tests/testthat/test-manage_lib.R

@@ -2,14 +2,14 @@
 tmp <- file.path(tempdir(), "OpenSpecy-testthat")
 dir.create(tmp, showWarnings = F)
 
-test_that("stop if OSF not reachable", {
-  skip_on_cran()
-  skip_if_not(is.null(curl::nslookup("api.osf.io", error = F)),
-              message = "OSF is online")
-
-  get_lib(type = "test", path = tmp) |>
-    expect_error()
-})
+#test_that("stop if OSF not reachable", {
+#  skip_on_cran()
+  #skip_if_not(is.null(curl::nslookup("api.osf.io", error = F)),
+  #            message = "OSF is online") #Curl doesn't work nicely with shinylive
+
+#  get_lib(type = "test", path = tmp) |>
+#    expect_error()
+#})
 
 test_that("get_lib() downloads test library", {
   skip_on_cran()