I am working with the R programming language.

I am trying to recreate this map here myself : https://crtc.gc.ca/cartovista/LTEOverTheYearsYE2019_EN/index.html (e.g. for 2019)

First, I downloaded the JSON for 2019:

library(jsonlite)
library(httr)


response <- GET("https://crtc.gc.ca/cartovista/LTEOverTheYearsYE2019_EN/map/LTE_YE2019.json")

content <- content(response, as = "text")

data <- fromJSON(content)

Next, I tried to extract the longitude/latitude for all the polygons in this file and convert them into the correct Coordinate Reference System:

library(sp)
library(rgdal)

polygons <- lapply(LTE_YE2019$f$g$c[[1]], function(x) {
  Polygon(matrix(x, ncol = 2, byrow = TRUE))
})

sp_polygons <- SpatialPolygons(list(Polygons(polygons, ID = 1)))


spdf <- SpatialPolygonsDataFrame(sp_polygons, data.frame(id = 1, row.names = 1))

proj4string(spdf) <- CRS(LTE_YE2019$proj)

The file now looks something like this:

> str(spdf)
Formal class 'SpatialPolygonsDataFrame' [package "sp"] with 5 slots
  ..@ data       :'data.frame': 1 obs. of  1 variable:
  .. ..$ id: num 1
  ..@ polygons   :List of 1
  .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
  .. .. .. ..@ Polygons :List of 606

....

  .. .. .. .. .. [list output truncated]
  .. .. .. ..@ plotOrder: int [1:606] 321 322 324 329 330 325 372 290 267 373 ...
  .. .. .. ..@ labpt    : num [1:2] 994419 305033
  .. .. .. ..@ ID       : chr "1"
  .. .. .. ..@ area     : num 1.17e+11
  ..@ plotOrder  : int 1
  ..@ bbox       : num [1:2, 1:2] -2319216 -307601 2981680 3014094
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "x" "y"
  .. .. ..$ : chr [1:2] "min" "max"
  ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot
  .. .. ..@ projargs: chr "+proj=lcc +lat_0=49 +lon_0=-95 +lat_1=49 +lat_2=77 +x_0=0 +y_0=0 +ellps=GRS80 +units=m +no_defs"
  .. .. ..$ comment: chr "PROJCRS[\"unknown\",\n    BASEGEOGCRS[\"unknown\",\n        DATUM[\"Unknown based on GRS80 ellipsoid\",\n      "| __truncated__
  ..$ comment: chr "FALSE"

My Question: When I try to plot this, I get the following error:

library(leaflet)

m <- leaflet() %>%
  addTiles() %>%
  addPolygons(data = spdf)

#Error in rgeos::createPolygonsComment(pgons) : 
  #rgeos_PolyCreateComment: orphaned hole, cannot find containing polygon for hole at index 2

I tried to read more about what might be causing this error (e.g. Fixing orphaned holes in R) and tried to follow the advice provided there:

report <- clgeo_CollectionReport(spdf)
summary <- clgeo_SummaryReport(report)
issues <- report[report$valid == FALSE,]

spdf.clean <- clgeo_Clean(spdf)

However I am not sure if this is working because it still says 0% after having run for some time:

 spdf.clean <- clgeo_Clean(spdf)

  |                                                  | 0 % ~calculating  

Can someone please tell me if I am doing this correctly?

Thanks!