Last updated on 2025-07-29 08:51:43 CEST.
| Package | ERROR | OK |
|---|---|---|
| admixr | 13 | |
| slendr | 2 | 11 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 2, OK: 11
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [90s/192s]
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.
--------------------
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 0 | SKIP 31 | PASS 159 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• !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'
══ 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 '/tmp/RtmpusZYFd/working_dir/RtmpCgBBQ1/naturalearth/ne_110m_land.gpkg' seems not to exist in your local folder '/tmp/RtmpusZYFd/working_dir/RtmpCgBBQ1/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 0 | SKIP 31 | PASS 159 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [92s/229s]
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.
--------------------
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 0 | SKIP 31 | PASS 159 ]
══ Skipped tests (31) ══════════════════════════════════════════════════════════
• !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'
══ 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 '/tmp/RtmpIwjcXH/working_dir/Rtmp341OKA/naturalearth/ne_110m_land.gpkg' seems not to exist in your local folder '/tmp/RtmpIwjcXH/working_dir/Rtmp341OKA/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 0 | SKIP 31 | PASS 159 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc