R Under development (unstable) (2023-07-13 r84688 ucrt) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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/the/directory/with/slim/program" to your ~/.Renviron file. -------------------- The legacy packages maptools, rgdal, and rgeos, underpinning the sp package, which was just loaded, will retire in October 2023. Please refer to R-spatial evolution reports for details, especially https://r-spatial.org/r/2023/05/15/evolution4.html. It may be desirable to make the sf package available; package maintainers should consider adding sf to Suggests:. The sp package is now running under evolution status 2 (status 2 uses the sf package in place of rgdal) A slendr Python (3.11) environment with the necessary versions of msprime (1.2.0), tskit (0.5.5), and pyslim (1.0.3) 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 0 | WARN 0 | SKIP 31 | PASS 173 ] ══ Skipped tests (31) ══════════════════════════════════════════════════════════ • !is_slendr_env_present() is TRUE (31): 'test-compilation.R:65:1', 'test-engines.R:1:1', 'test-geneflow.R:50:3', 'test-ibd-squashing.R:1:1', 'test-ibd.R:1:1', 'test-interaction-changes.R:49:3', '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:70:3', 'test-sampling.R:127:3', 'test-sampling.R:228:3', 'test-sampling.R:254:3', 'test-sampling.R:287:3', '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-pure-spatial.R:1:1', 'test-ts.R:1:1' [ FAIL 0 | WARN 0 | SKIP 31 | PASS 173 ] > > proc.time() user system elapsed 36.06 2.56 128.34