clean_geometry error before and after node.js install

[spencer-tassone]

I am trying to use the hyRefactor::clean_geometry function to clean up polygon fragments but I keep getting an error message:

Error : The mapshaper node library must be installed and on your PATH. Install node.js (https://nodejs.org/en/) and then install mapshaper with: npm install -g mapshaper

I have installed node.js and run npm install -g mapshaper but still get the error after restarting R and rerunning the code.

# Clear the workspace and reset graphics ----
rm(list = ls())
dev.off()
#> null device 
#>           1

# Load necessary libraries ----
library(tidyverse)
library(nhdplusTools)
library(sf)
#> Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.3.1; sf_use_s2() is TRUE
library(ggspatial)
library(rmapshaper)
library(hyRefactor)

# 1. Define the starting point (pour point) ----
start_point <- st_sfc(st_point(c(-78.336, 38.976)), crs = 4269)

## 1a. Snap point to the nearest NHDPlus flowline ----
trace <- get_raindrop_trace(start_point)

## 1b. Use the intersection point as the pour point ----
snap_point <- st_sfc(st_point(trace$intersection_point[[1]]),
                         crs = 4269)

# 2. Retrieve NHDPlus COMID for the snapped point ----
start_comid <- discover_nhdplus_id(snap_point)

# 3. Navigate and extract upstream tributary flowlines ----
flowline <- navigate_nldi(list(featureSource = "comid", 
                               featureID = start_comid), 
                          mode = "upstreamTributaries", 
                          distance_km = 1000)

# 4. Download and subset NHDPlus data for the flowlines ----
subset_file <- tempfile(fileext = ".gpkg")
subset <- subset_nhdplus(comids = as.integer(flowline$UT$nhdplus_comid),
                         output_file = subset_file,
                         nhdplus_data = "download", 
                         flowline_only = FALSE,
                         return_data = TRUE, overwrite = TRUE)
#> All intersections performed in latitude/longitude.
#> Reading NHDFlowline_Network
#> Writing NHDFlowline_Network
#> Reading CatchmentSP
#> Writing CatchmentSP
flowline <- subset$NHDFlowline_Network

# Define the NLDI feature list for the starting COMID ----
nldi_nwis <- list(featureSource = "comid", featureID = start_comid)

# 5. Delineate the basin for the snap point ----
basin <- get_split_catchment(snap_point, upstream = TRUE)
basin$ID <- 'Strasburg'
basin <- clean_geometry(basin, ID = "ID")
#> Error : The mapshaper node library must be installed and on your PATH.
#> Install node.js (https://nodejs.org/en/) and then install mapshaper with:
#>     npm install -g mapshaper

sessionInfo()
#> R version 4.4.1 (2024-06-14 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 22631)
#> 
#> Matrix products: default
#> 
#> 
#> locale:
#> [1] LC_COLLATE=English_United States.utf8 
#> [2] LC_CTYPE=English_United States.utf8   
#> [3] LC_MONETARY=English_United States.utf8
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.utf8    
#> 
#> time zone: America/New_York
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] hyRefactor_0.4.11  rmapshaper_0.5.0   ggspatial_1.1.9    sf_1.0-16         
#>  [5] nhdplusTools_1.2.1 lubridate_1.9.3    forcats_1.0.0      stringr_1.5.1     
#>  [9] dplyr_1.1.4        purrr_1.0.2        readr_2.1.5        tidyr_1.3.1       
#> [13] tibble_3.2.1       ggplot2_3.5.1      tidyverse_2.0.0   
#> 
#> loaded via a namespace (and not attached):
#>  [1] gtable_0.3.5         xfun_0.45            lattice_0.22-6      
#>  [4] tzdb_0.4.0           vctrs_0.6.5          tools_4.4.1         
#>  [7] generics_0.1.3       curl_5.2.1           parallel_4.4.1      
#> [10] proxy_0.4-27         fansi_1.0.6          pkgconfig_2.0.3     
#> [13] KernSmooth_2.23-24   data.table_1.15.4    assertthat_0.2.1    
#> [16] lifecycle_1.0.4      compiler_4.4.1       munsell_0.5.1       
#> [19] terra_1.7-78         codetools_0.2-20     fst_0.9.8           
#> [22] htmltools_0.5.8.1    class_7.3-22         yaml_2.3.9          
#> [25] pillar_1.9.0         classInt_0.4-10      hydroloom_1.0.2     
#> [28] cachem_1.1.0         wk_0.9.2             rvest_1.0.4         
#> [31] zip_2.3.1            tidyselect_1.2.1     digest_0.6.36       
#> [34] stringi_1.8.4        arrow_16.1.0         fastmap_1.2.0       
#> [37] grid_4.4.1           colorspace_2.1-0     cli_3.6.3           
#> [40] magrittr_2.0.3       utf8_1.2.4           e1071_1.7-14        
#> [43] withr_3.0.0          scales_1.3.0         sp_2.1-4            
#> [46] bit64_4.0.5          timechange_0.3.0     rmarkdown_2.27      
#> [49] httr_1.4.7           dataRetrieval_2.7.15 bit_4.0.5           
#> [52] RANN_2.6.1           hms_1.1.3            fstcore_0.9.18      
#> [55] memoise_2.0.1        pbapply_1.7-2        evaluate_0.24.0     
#> [58] knitr_1.48           V8_4.4.2             s2_1.1.7            
#> [61] rlang_1.1.4          Rcpp_1.0.12          glue_1.7.0          
#> [64] DBI_1.2.3            geojsonsf_2.0.3      xml2_1.3.6          
#> [67] reprex_2.1.1         rstudioapi_0.16.0    jsonlite_1.8.8      
#> [70] R6_2.5.1             fs_1.6.4             units_0.8-5

^{Created on 2024-08-05 with reprex v2.1.1}