- using R version 4.2.2 (2022-10-31 ucrt)
- using platform: x86_64-w64-mingw32 (64-bit)
- using session charset: UTF-8
- checking for file 'slendr/DESCRIPTION' ... OK
- this is package 'slendr' version '0.4.0'
- 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
- 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 R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... 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 ... [28s] 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 ... [17s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [225s] ERROR
Running 'testthat.R' [225s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(slendr)
The slim binary was not found in your $PATH variable. Most of
the functionality in this package 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.
--------------------
A slendr Python environment with the necessary versions of msprime (1.2.0),
tskit (0.5.2), and pyslim (1.0) has not been found. If this is not the
first time you're running slendr, the most likely explanation for this
message is that some of slendr's Python dependencies need an update.
You can setup a pre-configured environment with all of slendr's Python
dependencies by running the function setup_env().
>
> test_check("slendr")
proj_create_from_database: datum not found
proj_create_from_database: ellipsoid not found
proj_create_from_database: prime meridian not found
proj_create_from_database: datum not found
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proj_create_from_database: ellipsoid not found
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[ FAIL 5 | WARN 150 | SKIP 22 | PASS 168 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• !check_env_present() is TRUE (1)
• !slendr:::check_env_present() is TRUE (19)
• Sys.which("slim") == "" is TRUE (2)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compilation.R:6'): 'competition' must be specified in compile_model() if missing ──
`compile_model(...)` produced warnings.
── Failure ('test-compilation.R:14'): 'mating' must be specified in compile_model() if missing ──
`compile_model(...)` produced warnings.
── Failure ('test-compilation.R:22'): 'dispersal' must be specified in compile_model() if missing ──
`compile_model(...)` produced warnings.
── Failure ('test-compilation.R:28'): 'competition', 'mating', and 'dispersal' do not have to be specified in compile_model() if already present ──
`compile_model(...)` produced warnings.
── Failure ('test-serialization.R:72'): non-unique population names lead to error ──
`compile_model(...)` produced warnings.
[ FAIL 5 | WARN 150 | SKIP 22 | PASS 168 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in 'inst/doc' ... OK
- checking re-building of vignette outputs ... [103s] OK
- checking PDF version of manual ... OK
- DONE
Status: 1 ERROR