Error setup_r5(): Invalid number of points in LineString

First of all, thank you so much for developing this very useful package!

I am working on calculating a travel time matrix (by car) between each "iris" (essentially neighborhoods) in France. Since the full .pbf file for France was too large for r5r to process (4.5 GB), I first filtered the file following guidelines from conveyal . Then, I implemented a solution where I select a 100 km buffer around each French department, calculate the bounding box, and crop the .pbf file accordingly.

For cropping the .pbf file, I used Osmosis as recommended in FAQ 4 of r5r. However, for several departments I encountered errors when setting up r5. Specifically, I was receiving this error: Error in setup_r5(...) : java.lang.NullPointerException.

According to these issues (1, 2), it seemed to me that this error may occur when ways and relations are excluded during cropping. Therefore, I modified the Osmosis cropping code by including clipIncompleteEntities=yes (as suggested here).

This approach has allowed me to compute the travel time matrix for most departments successfully. However, I am still encountering an issue with two departments (departments code==33 and 60). When setting up r5r using the pbf files related to these departments, I receive the following error:

r5r_core <- setup_r5("D:\\France\\network_60\\bo", verbose = FALSE)
No raster .tif files found. Using elevation = 'NONE'.
Using cached R5 version from C:/Users/Asus/AppData/Local/R/win-library/4.2/r5r/jar/r5-v6.9-all.jar
2024-11-11 17:10:06,587 [main] ERROR c.c.r.s.StreetLayer - Continuing to load but ignoring generalized costs due to exception: java.lang.RuntimeException: All ways are expected to have generalized cost tags. Missing: slope_1:forward
Error in setup_r5(sprintf("D:\\France\\network_%s\\bo", dep_code), verbose = FALSE) : 
  java.lang.IllegalArgumentException: Invalid number of points in LineString (found 1 - must be 0 or >= 2)

This is the result form running the r5r::r5r_sitrep() function:

 r5r::r5r_sitrep()
$r5r_package_version
[1] ‘1.0.1’

$r5_jar_version
[1] "6.9"

$java_version
[1] "11.0.20"

$set_memory
[1] "-Xmx12G"

$session_info
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 26100)

Matrix products: default

locale:
[1] LC_COLLATE=Italian_Italy.utf8  LC_CTYPE=Italian_Italy.utf8    LC_MONETARY=Italian_Italy.utf8
[4] LC_NUMERIC=C                   LC_TIME=Italian_Italy.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] mapview_2.11.0      accessibility_1.2.0 fs_1.5.2            arrow_13.0.0        forcats_0.5.2      
 [6] stringr_1.5.0       dplyr_1.1.4         purrr_1.0.1         readr_2.1.3         tidyr_1.3.1        
[11] tibble_3.2.1        ggplot2_3.4.0       tidyverse_1.3.2     sf_1.0-9            r5r_1.0.1          
[16] rJava_1.0-6        

loaded via a namespace (and not attached):
 [1] httr_1.4.4              bit64_4.0.5             jsonlite_1.8.4          modelr_0.1.10          
 [5] Rdpack_2.4              assertthat_0.2.1        stats4_4.2.2            sp_1.5-1               
 [9] googlesheets4_1.0.1     cellranger_1.1.0        yaml_2.3.6              pillar_1.9.0           
[13] backports_1.4.1         lattice_0.20-45         glue_1.6.2              digest_0.6.30          
[17] checkmate_2.1.0         rbibutils_2.2.11        rvest_1.0.3             leaflet.providers_1.9.0
[21] colorspace_2.0-3        htmltools_0.5.5         pkgconfig_2.0.3         broom_1.0.1            
[25] raster_3.6-11           haven_2.5.1             s2_1.1.1                webshot_0.5.4          
[29] scales_1.3.0            satellite_1.0.4         terra_1.6-47            tzdb_0.4.0             
[33] timechange_0.1.1        proxy_0.4-27            googledrive_2.0.0       generics_0.1.3         
[37] ellipsis_0.3.2          withr_2.5.2             cli_3.4.1               magrittr_2.0.3         
[41] crayon_1.5.2            readxl_1.4.1            fansi_1.0.3             xml2_1.3.3             
[45] class_7.3-20            tools_4.2.2             data.table_1.14.6       hms_1.1.2              
[49] gargle_1.2.1            lifecycle_1.0.3         munsell_0.5.0           reprex_2.0.2           
[53] compiler_4.2.2          e1071_1.7-12            rlang_1.1.2             classInt_0.4-8         
[57] units_0.8-0             grid_4.2.2              rstudioapi_0.14         htmlwidgets_1.5.4      
[61] crosstalk_1.2.0         leafem_0.2.0            base64enc_0.1-3         wk_0.7.0               
[65] codetools_0.2-18        gtable_0.3.1            DBI_1.1.3               R6_2.5.1               
[69] lubridate_1.9.0         fastmap_1.1.0           bit_4.0.5               utf8_1.2.2             
[73] KernSmooth_2.23-20      stringi_1.7.8           Rcpp_1.0.9              vctrs_0.6.5            
[77] png_0.1-8               leaflet_2.1.1           dbplyr_2.2.1            tidyselect_1.2.0

Do you have any idea on waht might be causing this issue? I am including my code, and the cropped .pbf file for one of the two departments causing the error.

Thank you in advance for your help!

Here is the full r code:


options(java.parameters = '-Xmx12G')
options(scipen=999)

library(sf)
library(r5r)
library(tidyverse)
library(arrow)
library(fs)
library(accessibility)
library(mapview)

departement_fr <- st_read(here::here("coordinates\\ADMIN-EXPRESS-COG_1-1__SHP__FRA_2018-04-03\\ADMIN-EXPRESS-COG\\1_DONNEES_LIVRAISON_2018-03-28\\ADE-COG_1-1_SHP_LAMB93_FR\\DEPARTEMENT.shp"))
load("data\\iris_adm.Rdata")
load("data\\school_france_ttm.Rdata")

fr_iris <- st_transform(fr_iris, 4326)

fr_iris_tmp <- fr_iris %>% 
  select(code_iris)

centroids_fr <- as.data.frame(st_coordinates(st_centroid(fr_iris$geometry))) %>% 
  rename(lon = 1, lat = 2)

centroids_fr <- cbind(centroids_fr, fr_iris_tmp)

# List all unique department codes
unique_departments <- unique(departement_fr$INSEE_DEP)

# Initialize timing for the full process
total_start_time <- Sys.time()

# Initialize a vector to store department codes with errors
error_departments <- c()

for (dep_code in unique_departments ) {

  cat(paste0("Processing department: ", dep_code, "\n"))

  # Select current department
  department_x <- departement_fr %>%
    st_transform(4326) %>%
    filter(INSEE_DEP == dep_code)

  # Create a 100 km buffer around the selected department
  buffer_100km <- st_buffer(department_x, dist = 100000)  # 100 km

  # Find all neighborhoods that intersect with this 100 km buffer
  neighborhoods_in_buffer <- fr_iris %>%
    st_filter(buffer_100km, .predicate = st_intersects)

  # Compute bounding box for area
  area_bbox <- st_bbox(neighborhoods_in_buffer)
  area_bbox_sf <- st_as_sfc(area_bbox)

  # Define paths for temporary files created by Osmosis
  folder_path <- sprintf("D:\\France\\network_%s\\", dep_code)
  dir.create(folder_path, recursive = TRUE)
  smaller_pbf <- sprintf("D:\\France\\network_%s\\smaller_%s.pbf", dep_code,dep_code)
  network_dat <- "D:\\France\\network\\network.dat"
  network_settings <- "D:\\France\\network\\network_settings.json"
  mapdb <- paste0(smaller_pbf, ".mapdb")
  mapdb_p <- paste0(smaller_pbf, ".mapdb.p")

  large_pbf_path <- "D:\\France\\ttm\\filtered.osm.pbf"

  # Run Osmosis command to create a smaller .pbf file
  osmosis_cmd <- sprintf("%s --read-pbf %s --bounding-box left=%s bottom=%s right=%s top=%s clipIncompleteEntities=yes --write-pbf %s",
                         "osmosis",
                         large_pbf_path,
                         as.numeric(area_bbox$xmin), as.numeric(area_bbox$ymin),
                         as.numeric(area_bbox$xmax), as.numeric(area_bbox$ymax),
                         smaller_pbf)

  # Execute the Osmosis command
  shell(osmosis_cmd, translate = TRUE)

  gc()

  # Try to set up r5r core with error handling
  r5r_core <- tryCatch({
    setup_r5(sprintf("D:\\France\\network_%s\\", dep_code), verbose = FALSE)
  }, error = function(e) {
    cat(paste0("Error in setting up r5r for department ", dep_code, ": ", e$message, "\n"))
    # Append the department code to error_departments vector
    error_departments <<- c(error_departments, dep_code)
    return(NULL)  # Return NULL if there's an error
  })

  # Skip to the next iteration if setup_r5 failed
  if (is.null(r5r_core)) {
    files_to_delete <- c(folder_path, smaller_pbf, network_dat, network_settings, mapdb, mapdb_p)
    for (file_path in files_to_delete) {
      if (file.exists(file_path)) {
        file.remove(file_path)
        cat(paste0("Deleted temporary file: ", file_path, "\n"))
      }
    }
    next
  }

  stop_r5(r5r_core)
  gc()

  files_to_delete <- c(folder_path, smaller_pbf, network_dat, network_settings, mapdb, mapdb_p)
  for (file_path in files_to_delete) {
    if (file.exists(file_path)) {
      file.remove(file_path)
      cat(paste0("Deleted temporary file: ", file_path, "\n"))
    }
  }

  gc()
}

total_end_time <- Sys.time()
cat(paste0("Total processing time: ", total_end_time - total_start_time, " seconds.\n"))

ipeaGIT / r5r

Error setup_r5(): Invalid number of points in LineString #410