- using R version 4.4.3 (2025-02-28 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'slendr/DESCRIPTION' ... OK
- this is package 'slendr' version '1.1.0'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'slendr' can be installed ... OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking 'build' directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [4s] OK
- checking whether the package can be loaded with stated dependencies ... [5s] OK
- checking whether the package can be unloaded cleanly ... [4s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s] OK
- checking whether the namespace can be unloaded cleanly ... [4s] OK
- checking loading without being on the library search path ... [4s] OK
- checking whether startup messages can be suppressed ... [5s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [23s] OK
- checking Rd files ... [2s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [6s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [101s] ERROR
Running 'testthat.R' [101s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(slendr)
The 'slim.exe' 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="C:\path\to\directory\with\slim.exe"
to your C:\Users\<your username>\Documents\.Renviron file.
Alternatively, use the `slim_path` argument of the `slim()` function.
--------------------
A slendr Python (3.12) environment with the necessary versions of
msprime (1.3.4), tskit (0.6.4), 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 1 | WARN 146 | SKIP 36 | PASS 152 ]
══ Skipped tests (36) ══════════════════════════════════════════════════════════
• !check_dependencies(python = TRUE) is TRUE (29): 'test-compilation.R:69:1',
'test-engines.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:3:1', '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', 'test-vcf.R:1:1'
• !check_dependencies(python = TRUE) || !is_slim_present() is TRUE (1):
'test-ts-pure-spatial.R:1:1'
• !check_dependencies(python = TRUE, slim = TRUE) is TRUE (1):
'test-extensions.R:1:1'
• Sys.info()[["sysname"]] == "Windows" is TRUE (5): 'test-compilation.R:12:3',
'test-compilation.R:19:3', 'test-compilation.R:28:3',
'test-compilation.R:37:3', 'test-serialization.R:73:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-naturalearth.R:2:3'): all three variants of the Natural Earth data can be downloaded ──
Error in `rnaturalearth::ne_load(scale = scale, type = "land", category = "physical",
destdir = ne_dir)`: The file 'D:\temp\2025_07_30_01_50_00_24069\RtmpIHbOlQ/naturalearth/ne_110m_land.gpkg' seems not to exist in your local folder 'D:\temp\2025_07_30_01_50_00_24069\RtmpIHbOlQ/naturalearth'. Did you download it using `rnaturalearth::ne_download()`?
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. └─rnaturalearth::ne_load(scale = scale, type = "land", category = "physical", destdir = ne_dir)
5. └─cli::cli_abort(error_msg)
6. └─rlang::abort(...)
[ FAIL 1 | WARN 146 | SKIP 36 | PASS 152 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [65s] OK
- checking PDF version of manual ... [21s] OK
- checking HTML version of manual ... [13s] OK
- DONE
Status: 1 ERROR