CRAN Package Check Results for Package slendr

Last updated on 2024-12-26 01:50:10 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 14.50 181.49 195.99 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.0 10.74 208.09 218.83 OK
r-devel-linux-x86_64-fedora-clang 1.0.0 507.88 OK
r-devel-linux-x86_64-fedora-gcc 1.0.0 493.69 OK
r-devel-windows-x86_64 1.0.0 35.00 708.00 743.00 OK
r-patched-linux-x86_64 1.0.0 14.91 283.12 298.03 OK
r-release-linux-x86_64 1.0.0 13.51 287.18 300.69 OK
r-release-macos-arm64 1.0.0 147.00 OK
r-release-macos-x86_64 1.0.0 197.00 OK
r-release-windows-x86_64 1.0.0 33.00 616.00 649.00 OK
r-oldrel-macos-arm64 1.0.0 163.00 OK
r-oldrel-macos-x86_64 1.0.0 217.00 OK
r-oldrel-windows-x86_64 1.0.0 39.00 487.00 526.00 OK

Check Details

Version: 1.0.0
Check: examples
Result: ERROR Running examples in ‘slendr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: area > ### Title: Calculate the area covered by the given slendr object > ### Aliases: area > > ### ** Examples > > region_a <- region("A", center = c(20, 50), radius = 20) Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ [9s/11s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(slendr) The 'slim' binary could not be found in your $PATH. Most of the functionality of slendr will work without any issues but you will not be able to simulate data with the `slim()` function. If you want to run SLiM simulations, make sure to modify the $PATH variable so that it points to the directory containing the slim command-line program. One easy way to do this is to add this: PATH="path/to/directory/with/slim/binary" to your ~/.Renviron file. Alternatively, use the `slim_path` argument of the `slim()` function. -------------------- In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. -------------------- A slendr Python (3.12) environment with the necessary versions of msprime (1.3.3), tskit (0.5.8), pyslim (1.0.4), and tspop (0.0.2) has not been found. You can setup a pre-configured environment with all of slendr's Python dependencies automatically by running the function `setup_env()`. > > test_check("slendr") [ FAIL 34 | WARN 0 | SKIP 30 | PASS 69 ] ══ Skipped tests (30) ══════════════════════════════════════════════════════════ • !is_slendr_env_present() is TRUE (29): 'test-compilation.R:69:1', 'test-engines.R:1:1', 'test-extensions.R:1:1', 'test-future.R:15:1', 'test-geneflow.R:50:3', 'test-ibd-squashing.R:1:1', 'test-ibd.R:1:1', 'test-interaction-changes.R:3:1', 'test-manual-ts.R:1:1', 'test-msprime-geneflow.R:5:1', 'test-msprime-metadata.R:1:1', 'test-msprime.R:23:1', 'test-nonserialized.R:1:1', 'test-population.R:43:3', 'test-population.R:60:3', 'test-population.R:142:3', 'test-pure-msprime-vs-slendr.R:4:1', 'test-pure-slim-vs-slendr.R:4:1', 'test-resizes-locked.R:1:1', 'test-resizes.R:1:1', 'test-runners.R:1:1', 'test-sampling.R:3:1', 'test-simulation-runs.R:1:1', 'test-time-direction.R:1:1', 'test-trees.R:1:1', 'test-ts-ancestors-descendants.R:1:1', 'test-ts-pure-nonspatial.R:1:1', 'test-ts.R:1:1', 'test-tspop.R:1:1' • !is_slendr_env_present() || !is_slim_present() is TRUE (1): 'test-ts-pure-spatial.R:1:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-abstract-vs-real-landscapes.R:3:3'): anything but the three allowed landsccape sources leads to error ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-abstract-vs-real-landscapes.R:3:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─slendr::world(xrange = c(-15, 60), yrange = c(20, 65), landscape = "blank123") 8. └─slendr:::check_spatial_pkgs() ── Error ('test-abstract-vs-real-landscapes.R:8:3'): blank abstract landscape is allowed ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-abstract-vs-real-landscapes.R:8:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─slendr::world(xrange = c(-15, 60), yrange = c(20, 65), landscape = "blank") 10. └─slendr:::check_spatial_pkgs() ── Error ('test-abstract-vs-real-landscapes.R:15:3'): user-defined abstract landscape is allowed ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-abstract-vs-real-landscapes.R:15:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─slendr::world(xrange = xrange, yrange = yrange, landscape = polygon) 10. └─slendr:::check_spatial_pkgs() ── Error ('test-compilation.R:9:3'): 'competition' must be specified in compile_model() if missing ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-compilation.R:9:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-compilation.R:18:3'): 'mating' must be specified in compile_model() if missing ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-compilation.R:18:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-compilation.R:27:3'): 'dispersal' must be specified in compile_model() if missing ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-compilation.R:27:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-compilation.R:36:3'): 'competition', 'mating', and 'dispersal' do not have to be specified in compile_model() if already present ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-compilation.R:36:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-compilation.R:49:3'): invalid blank maps are prevented ───────── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::world(xrange = c(0, 100), yrange = c(0, 100), landscape = "blank") at test-compilation.R:49:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-coordinate-conversions.R:2:1'): (code run outside of `test_that()`) ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-coordinate-conversions.R:2:1 2. └─slendr:::check_spatial_pkgs() ── Error ('test-dynamics.R:4:3'): move requires overlap between 0 and 1 ──────── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-dynamics.R:4:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-dynamics.R:13:3'): move requires a positive snapshot number ──── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-dynamics.R:13:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-dynamics.R:22:3'): move generates the correct number of snapshots ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-dynamics.R:22:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-dynamics.R:29:3'): only positive population sizes allowed ────── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-dynamics.R:29:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-dynamics.R:35:3'): only three values of population size changes allowed ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-dynamics.R:35:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geneflow.R:3:3'): non-overlapping geneflow leads to error ────── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-geneflow.R:3:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geneflow.R:13:3'): non-overlapping geneflow passes if the check is explicitly turned off ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-geneflow.R:13:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geneflow.R:25:3'): populations must be present within the given gene-flow time window (spatial) ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-geneflow.R:25:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:3:3'): circular ranges need two parameters ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-geometrical-operations.R:3:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─slendr::population("pop", time = 1, N = 1, map = map, center = 1) 8. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:16:3'): polygon boundary can be specified in two ways ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::region("Africa", map, polygon = coords) at test-geometrical-operations.R:16:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:25:3'): polygon ranges need at least three corners ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-geometrical-operations.R:25:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─slendr::region("Africa", map, polygon = coords) 8. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:34:3'): polygon ranges need at least three corners ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-geometrical-operations.R:34:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─slendr::population(...) 8. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:44:3'): union of a region with itself gives the same region ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::world(xrange = c(-15, 60), yrange = c(-20, 65), landscape = "blank") at test-geometrical-operations.R:44:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:51:3'): intersection of a region with itself gives the same region ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::world(xrange = c(-15, 60), yrange = c(-20, 65), landscape = "blank") at test-geometrical-operations.R:51:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:58:3'): subtraction of a region from itself gives an empty region ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::world(xrange = c(-15, 60), yrange = c(-20, 65), landscape = "blank") at test-geometrical-operations.R:58:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:65:3'): subtraction of a non-overlapping region does not change the result ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::world(xrange = c(-15, 60), yrange = c(-20, 65), landscape = "blank") at test-geometrical-operations.R:65:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:72:3'): nonoverlapping join gives empty intersection ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::world(xrange = c(-15, 60), yrange = c(-20, 65), landscape = "blank") at test-geometrical-operations.R:72:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:79:3'): custom landscapes can be specified ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::region(center = c(0, 0), radius = 10) at test-geometrical-operations.R:79:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:90:3'): boundaries are either circles or polygons ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. ├─testthat::expect_error(region(), "Either a circular range or a polygon range must be specified") at test-geometrical-operations.R:90:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─slendr::region() 8. └─slendr:::check_spatial_pkgs() ── Error ('test-geometrical-operations.R:97:1'): (code run outside of `test_that()`) ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::world(xrange = c(0, 100), yrange = c(0, 100), landscape = "blank") at test-geometrical-operations.R:97:1 2. └─slendr:::check_spatial_pkgs() ── Error ('test-naturalearth.R:2:3'): all three variants of the Natural Earth data can be downloaded ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. ├─utils::capture.output(...) at test-naturalearth.R:2:3 2. │ └─base::withVisible(...elt(i)) 3. └─slendr::world(xrange = c(-15, 40), yrange = c(30, 60), crs = "EPSG:3035") 4. └─slendr:::check_spatial_pkgs() ── Error ('test-naturalearth.R:15:3'): world dimensions are correctly specified ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. ├─testthat::expect_s3_class(...) at test-naturalearth.R:15:3 2. │ └─testthat::quasi_label(enquo(object), arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─slendr::world(c(1, 100), c(1, 100), landscape = "blank") 5. └─slendr:::check_spatial_pkgs() ── Error ('test-serialization.R:5:3'): read_model() restores a single-map model object ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-serialization.R:5:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-serialization.R:25:3'): read_model() restores a complex model object ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-serialization.R:25:3 2. └─slendr:::check_spatial_pkgs() ── Error ('test-serialization.R:60:3'): non-unique population names lead to error ── Error: In order to use spatial features of slendr, packages 'sf', 'stars', and 'rnaturalearth' are required but not all are present. You can install all of them with `install.packages(c("sf", "stars", "rnaturalearth"))`. Backtrace: ▆ 1. └─slendr::population(...) at test-serialization.R:60:3 2. └─slendr:::check_spatial_pkgs() [ FAIL 34 | WARN 0 | SKIP 30 | PASS 69 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang