- using R version 4.5.2 Patched (2026-01-31 r89382)
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Apple clang version 14.0.0 (clang-1400.0.29.202)
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- this is package ‘dartR.base’ version ‘1.2.3’
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See the install log for details.
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- checking for unstated dependencies in examples ... OK
- checking examples ... [20s/26s] ERROR
Running examples in ‘dartR.base-Ex.R’ failed
The error most likely occurred in:
> ### Name: gl.filter.ld
> ### Title: Filters loci based on linkage disequilibrium (LD)
> ### Aliases: gl.filter.ld
>
> ### ** Examples
>
> if ((requireNamespace("snpStats", quietly = TRUE)) & (requireNamespace("fields", quietly = TRUE))) {
+ test <- gl.filter.callrate(platypus.gl, threshold = 1)
+ test <- gl.filter.monomorphs(test)
+ report <- gl.report.ld.map(test)
+ res <- gl.filter.ld(x=test,ld.report = report)
+ }
Starting gl.filter.callrate
Processing genlight object with SNP data
Warning: data include loci that are scored NA across all individuals.
Consider filtering using gl <- gl.filter.allna(gl)
Warning: Data may include monomorphic loci in call rate
calculations for filtering
Recalculating Call Rate
Removing loci based on Call Rate, threshold = 1
Completed: gl.filter.callrate
Starting gl.filter.monomorphs
Processing genlight object with SNP data
Identifying monomorphic loci
Removing monomorphic loci and loci with all missing
data
Completed: gl.filter.monomorphs
Starting gl.report.ld.map
Processing genlight object with SNP data
There is no information in the chromosome/position slot of the genlight object.
Assigning the same chromosome ('1') to all the SNPs in the dataset.
Assigning a sequence from 1 to n loci as the position of each SNP.
Calculating LD for all possible SNP pair combinations Calculating pairwise LD in population SEVERN_ABOVE
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: snpStats::ld(genotype_loci, genotype_loci, stats = ld.stat)
2: gl.report.ld.map(test)
An irrecoverable exception occurred. R is aborting now ...
- checking PDF version of manual ... [16s/25s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '