CRAN Package Check Results for Maintainer ‘Martin Petr <contact at bodkan.net>’

Last updated on 2026-11-10 23:54:40 CET.

Package	OK	ERROR
admixr	13
slendr	11	2

Package admixr

Current CRAN status: OK: 13

Package slendr

Current CRAN status: OK: 11, ERROR: 2

Version: 1.6.0
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 Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.6.0
Check: tests
Result: ERROR Running ‘testthat.R’ [7s/8s] 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"))`. -------------------- > > test_check("slendr") Saving _problems/test-geometrical-operations-6.R Saving _problems/test-geometrical-operations-16.R Saving _problems/test-geometrical-operations-28.R Saving _problems/test-geometrical-operations-38.R Saving _problems/test-geometrical-operations-44.R Saving _problems/test-geometrical-operations-51.R Saving _problems/test-geometrical-operations-58.R Saving _problems/test-geometrical-operations-65.R Saving _problems/test-geometrical-operations-72.R Saving _problems/test-geometrical-operations-79.R Saving _problems/test-geometrical-operations-90.R Saving _problems/test-geometrical-operations-97.R [ FAIL 12 | WARN 0 | SKIP 38 | PASS 10 ] ══ Skipped tests (38) ══════════════════════════════════════════════════════════ • On CRAN (36): 'test-abstract-vs-real-landscapes.R:1:1', 'test-compilation.R:1:1', 'test-coordinate-conversions.R:1:1', 'test-deprecation.R:4:1', 'test-dynamics.R:1:1', 'test-engines.R:1:1', 'test-extensions.R:1:1', 'test-future.R:15:1', 'test-geneflow.R:1:1', 'test-interaction-changes.R:1:1', 'test-manual-ts.R:1:1', 'test-msprime-geneflow.R:1:1', 'test-msprime-metadata.R:1:1', 'test-msprime.R:1:1', 'test-named-sampling.R:1:1', 'test-naturalearth.R:1:1', 'test-nonserialized.R:1:1', 'test-population.R:26:1', '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-serialization.R:1:1', 'test-simulation-runs.R:1:1', 'test-time-direction.R:3:1', 'test-trees.R:1:1', 'test-ts-ancestors-descendants.R:1:1', 'test-ts-extend.R:1:1', 'test-ts-pure-nonspatial.R:1:1', 'test-ts-pure-spatial.R:1:1', 'test-ts.R:1:1', 'test-tspop.R:1:1', 'test-utililites.R:1:1', 'test-vcf.R:1:1' • TRUE is TRUE (2): 'test-ibd-squashing.R:6:1', 'test-ibd.R:5:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── 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() [ FAIL 12 | WARN 0 | SKIP 38 | PASS 10 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.6.0
Check: tests
Result: ERROR Running ‘testthat.R’ [5s/6s] 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"))`. -------------------- > > test_check("slendr") Saving _problems/test-geometrical-operations-6.R Saving _problems/test-geometrical-operations-16.R Saving _problems/test-geometrical-operations-28.R Saving _problems/test-geometrical-operations-38.R Saving _problems/test-geometrical-operations-44.R Saving _problems/test-geometrical-operations-51.R Saving _problems/test-geometrical-operations-58.R Saving _problems/test-geometrical-operations-65.R Saving _problems/test-geometrical-operations-72.R Saving _problems/test-geometrical-operations-79.R Saving _problems/test-geometrical-operations-90.R Saving _problems/test-geometrical-operations-97.R [ FAIL 12 | WARN 0 | SKIP 38 | PASS 10 ] ══ Skipped tests (38) ══════════════════════════════════════════════════════════ • On CRAN (36): 'test-abstract-vs-real-landscapes.R:1:1', 'test-compilation.R:1:1', 'test-coordinate-conversions.R:1:1', 'test-deprecation.R:4:1', 'test-dynamics.R:1:1', 'test-engines.R:1:1', 'test-extensions.R:1:1', 'test-future.R:15:1', 'test-geneflow.R:1:1', 'test-interaction-changes.R:1:1', 'test-manual-ts.R:1:1', 'test-msprime-geneflow.R:1:1', 'test-msprime-metadata.R:1:1', 'test-msprime.R:1:1', 'test-named-sampling.R:1:1', 'test-naturalearth.R:1:1', 'test-nonserialized.R:1:1', 'test-population.R:26:1', '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-serialization.R:1:1', 'test-simulation-runs.R:1:1', 'test-time-direction.R:3:1', 'test-trees.R:1:1', 'test-ts-ancestors-descendants.R:1:1', 'test-ts-extend.R:1:1', 'test-ts-pure-nonspatial.R:1:1', 'test-ts-pure-spatial.R:1:1', 'test-ts.R:1:1', 'test-tspop.R:1:1', 'test-utililites.R:1:1', 'test-vcf.R:1:1' • TRUE is TRUE (2): 'test-ibd-squashing.R:6:1', 'test-ibd.R:5:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── 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() [ FAIL 12 | WARN 0 | SKIP 38 | PASS 10 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc