Remove raster, rgdal, sp packages from dependencies (#187)

* removes packages rgdal, raster, sp * replaced one line that was using raster * landscapemetrics changed to 2.0.0 * added macOS dependency, CI was failing * added to changelog
ncsu-landscape-dynamics · Nov 30, 2023 · ba7dd0b · ba7dd0b
1 parent 9aabb09
commit ba7dd0b
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -38,7 +38,7 @@ jobs:
 
       - name: Install macOS system dependencies
         if: runner.os == 'macOS'
-        run: brew install gdal proj
+        run: brew install gdal proj fribidi
 
       - uses: r-lib/actions/setup-renv@v2
       - uses: r-lib/actions/setup-r-dependencies@v2

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -32,6 +32,10 @@ this repository.
 
 - Fixed quarantine directions outputs in pops-multirun (@petrasovaa, #162).
 
+### Removed
+
+- Removed dependencies: packages rgdal, raster, sp
+
 ## [2.0.1] 2022-11-16
 
 ### Added

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -31,7 +31,6 @@ Imports:
     MASS,
     aws.s3,
     Metrics,
-    raster,
     methods
 License: GPL-3 | file LICENSE
 BugReports: https://github.com/ncsu-landscape-dynamics/rpops/issues
@@ -42,8 +41,6 @@ SystemRequirements:
     GNU make
 Suggests: 
     testthat,
-    rgdal,
-    sp,
     rlist,
     knitr,
     rmarkdown,

diff --git a/NAMESPACE b/NAMESPACE
@@ -31,9 +31,6 @@ importFrom(methods,is)
 importFrom(parallel,detectCores)
 importFrom(parallel,makeCluster)
 importFrom(parallel,stopCluster)
-importFrom(raster,calc)
-importFrom(raster,cellStats)
-importFrom(raster,extract)
 importFrom(stats,cov)
 importFrom(stats,median)
 importFrom(stats,rnorm)

diff --git a/R/configuration.R b/R/configuration.R
@@ -5,8 +5,6 @@
 #'
 #' @param config list of all data necessary used to set up c++ model
 #'
-#' @importFrom raster
-#' cellStats  calc extract
 #' @importFrom terra app rast xres yres classify extract ext as.points ncol nrow
 #' nlyr rowFromCell colFromCell values as.matrix rowFromCell colFromCell crs
 #' rowColFromCell global vect

diff --git a/R/pops_multirun.R b/R/pops_multirun.R
@@ -573,7 +573,7 @@ pops_multirun <- function(infected_file,
     west_distance_to_quarantine <- data.frame(t(rep(NA, length(probability_runs[[1]]))))
   }
 
-  which_median <- function(x) raster::which.min(abs(x - median(x)))
+  which_median <- function(x) which.min(abs(x - median(x)))
 
   median_run_index <- which_median(infected_number[[ncol(infected_number)]])
   min_run_index <- which.min(infected_number[[ncol(infected_number)]])

diff --git a/renv.lock b/renv.lock
@@ -569,26 +569,6 @@
       ],
       "Hash": "7e5e3cbd2a7bc07880c94e22348fb661"
     },
-    "igraph": {
-      "Package": "igraph",
-      "Version": "1.4.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "Matrix",
-        "R",
-        "cpp11",
-        "grDevices",
-        "graphics",
-        "magrittr",
-        "methods",
-        "pkgconfig",
-        "rlang",
-        "stats",
-        "utils"
-      ],
-      "Hash": "f7f74f5fbff27d52b1283ac512bc5430"
-    },
     "isoband": {
       "Package": "isoband",
       "Version": "0.2.7",
@@ -660,7 +640,7 @@
     },
     "landscapemetrics": {
       "Package": "landscapemetrics",
-      "Version": "1.5.6",
+      "Version": "2.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -670,12 +650,11 @@
         "cli",
         "ggplot2",
         "methods",
-        "raster",
-        "sp",
         "stats",
+        "terra",
         "tibble"
       ],
-      "Hash": "6c43fba1dd83b549ef471a36599898de"
+      "Hash": "101466a15b865990cd6e376df3f439de"
     },
     "lattice": {
       "Package": "lattice",
@@ -1005,20 +984,6 @@
       ],
       "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
     },
-    "raster": {
-      "Package": "raster",
-      "Version": "3.6-20",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "Rcpp",
-        "methods",
-        "sp",
-        "terra"
-      ],
-      "Hash": "ebebd9f0f203a129eb2da96470191b82"
-    },
     "rcmdcheck": {
       "Package": "rcmdcheck",
       "Version": "1.4.0",
@@ -1085,22 +1050,6 @@
       ],
       "Hash": "ae34cd56890607370665bee5bd17812f"
     },
-    "rgdal": {
-      "Package": "rgdal",
-      "Version": "1.6-7",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "methods",
-        "sp",
-        "stats",
-        "utils"
-      ],
-      "Hash": "10b777236c9e7855bc9dea8e347e30b7"
-    },
     "rlang": {
       "Package": "rlang",
       "Version": "1.1.1",
@@ -1205,23 +1154,6 @@
       ],
       "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f"
     },
-    "sp": {
-      "Package": "sp",
-      "Version": "1.6-1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "grid",
-        "lattice",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "ca27b2643e3593b7688244d035f2cd92"
-    },
     "stringi": {
       "Package": "stringi",
       "Version": "1.7.12",
@@ -1354,16 +1286,6 @@
       ],
       "Hash": "8548b44f79a35ba1791308b61e6012d7"
     },
-    "timechange": {
-      "Package": "timechange",
-      "Version": "0.2.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "8548b44f79a35ba1791308b61e6012d7",
-      "Requirements": [
-        "cpp11"
-      ]
-    },
     "tinytex": {
       "Package": "tinytex",
       "Version": "0.45",

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,5 +1,4 @@
 library(testthat)
-library(raster)
 library(PoPS)
 
 testthat::test_check("PoPS")