Last updated on 2024-12-27 03:49:32 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 23.07 | 157.80 | 180.87 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 16.24 | 120.67 | 136.91 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 342.76 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 301.59 | OK | |||
| r-devel-windows-x86_64 | 1.0.0 | 23.00 | 178.00 | 201.00 | OK | |
| r-patched-linux-x86_64 | 1.0.0 | 20.78 | 167.20 | 187.98 | OK | |
| r-release-linux-x86_64 | 1.0.0 | 18.81 | 167.79 | 186.60 | OK | |
| r-release-macos-arm64 | 1.0.0 | 80.00 | OK | |||
| r-release-macos-x86_64 | 1.0.0 | 228.00 | OK | |||
| r-release-windows-x86_64 | 1.0.0 | 23.00 | 171.00 | 194.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.0 | 86.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.0.0 | 154.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.0 | 30.00 | 215.00 | 245.00 | OK |
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘dartR.popgen-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gl.ld.haplotype
> ### Title: Visualize patterns of linkage disequilibrium and identification
> ### of haplotypes
> ### Aliases: gl.ld.haplotype
>
> ### ** Examples
>
> require("dartR.data")
> x <- platypus.gl
> x <- gl.filter.callrate(x, threshold = 1)
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
> # only the first 15 individuals because of speed during tests
> x <- gl.keep.pop(x, pop.list = "TENTERFIELD")[1:15, ]
Starting gl.keep.pop
Processing genlight object with SNP data
Checking for presence of nominated populations
Retaining only populations TENTERFIELD
Warning: Resultant dataset may contain monomorphic loci
Locus metrics not recalculated
Completed: gl.keep.pop
> x$chromosome <- as.factor(x$other$loc.metrics$Chrom_Platypus_Chrom_NCBIv1)
> x$position <- x$other$loc.metrics$ChromPos_Platypus_Chrom_NCBIv1
> ld_res <- gl.ld.haplotype(x,
+ chrom_name = "NC_041728.1_chromosome_1",
+ ld_max_pairwise = 10000000
+ )
Starting gl.ld.haplotype
Processing genlight object with SNP data
Calculating pairwise LD in population TENTERFIELD
Analysing chromosome NC_041728.1_chromosome_1
The maximum distance at which LD should be calculated
(ld_max_pairwise) is too short for chromosome NC_041728.1_chromosome_1 . Setting this distance to 40201976 bp
Error in loadNamespace(x) : there is no package called ‘raster’
Calls: gl.ld.haplotype ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
gl.ld.distance 5.299 0.11 6.747
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘snpStats’
Flavor: r-oldrel-macos-arm64
Version: 1.0.0
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘snpStats’
Flavor: r-oldrel-macos-arm64