Last updated on 2025-05-07 03:51:09 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.5 | 8.30 | 67.78 | 76.08 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 6.27 | 51.19 | 57.46 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 120.37 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 115.17 | OK | |||
| r-devel-windows-x86_64 | 1.0.0 | 11.00 | 75.00 | 86.00 | OK | |
| r-patched-linux-x86_64 | 0.9.5 | 8.74 | 63.03 | 71.77 | OK | |
| r-release-linux-x86_64 | 0.9.5 | 8.27 | 63.09 | 71.36 | OK | |
| r-release-macos-arm64 | 1.0.0 | 36.00 | ERROR | |||
| r-release-macos-x86_64 | 1.0.0 | 61.00 | OK | |||
| r-release-windows-x86_64 | 1.0.0 | 9.00 | 79.00 | 88.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.0 | 38.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.0.0 | 83.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.9.5 | 11.00 | 96.00 | 107.00 | OK |
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘pedprobr-Ex.R’ failed
The error most likely occurred in:
> ### Name: lumpAlleles
> ### Title: Allele lumping
> ### Aliases: lumpAlleles
>
> ### ** Examples
>
> x = nuclearPed() |> addMarker(geno = c(NA, NA, "1/1"), alleles = 1:5)
>
> # Before lumping
> afreq(x, 1)
1 2 3 4 5
0.2 0.2 0.2 0.2 0.2
>
> # Lump
> y = lumpAlleles(x, verbose = TRUE)
Marker NA: 1 of 5 alleles, no model. Regular lumping: 5 -> 2
> afreq(y, 1)
1 lump
0.2 0.8
>
> # With lumpable mutation model
> x2 = setMutmod(x, model = "equal", rate = 0.1)
> mutmod(x2, 1)
Unisex mutation matrix:
1 2 3 4 5
1 0.900 0.025 0.025 0.025 0.025
2 0.025 0.900 0.025 0.025 0.025
3 0.025 0.025 0.900 0.025 0.025
4 0.025 0.025 0.025 0.900 0.025
5 0.025 0.025 0.025 0.025 0.900
Model: Equal
Rate: 0.1
Frequencies: 0.2, 0.2, 0.2, 0.2, 0.2
Bounded: Yes
Stationary: Yes
Reversible: Yes
Lumpable: Always
Overall rate: 0.1
>
> y2 = lumpAlleles(x2, verbose = TRUE)
Marker NA: 1 of 5 alleles, equal model. Regular lumping: 5 -> 2
> mutmod(y2, 1)
Unisex mutation matrix:
1 lump
1 0.900 0.100
lump 0.025 0.975
Model: Equal
Rate: 0.1
Frequencies: 0.2, 0.8
Bounded: Yes
Stationary: Yes
Reversible: Yes
Lumpable: Always
Overall rate: 0.04
>
> # Mutation model requiring special lumping
> x3 = setMutmod(x, model = "random", rate = 0.1, seed = 1)
> mutmod(x3, 1)
Unisex mutation matrix:
1 2 3 4 5
1 0.867523435 0.054497816 0.038121075 0.036293256 0.003564417
2 0.016300348 0.884960904 0.013972290 0.054369386 0.030397073
3 0.021258422 0.013743480 0.917791239 0.019816337 0.027390522
4 0.004512246 0.009230788 0.011097972 0.972640177 0.002518817
5 0.065103325 0.012543169 0.026695802 0.038573459 0.857084245
Model: Random
Rate: 0.1
Frequencies: 0.2, 0.2, 0.2, 0.2, 0.2
Bounded: Yes
Stationary: No
Reversible: No
Lumpable: Not always
Overall rate: 0.1
>
> # Lump
> y3 = lumpAlleles(x3, verbose = TRUE)
Marker NA: 1 of 5 alleles, random model. Special lumping: 5 -> 2
> mutmod(y3, 1)
Unisex mutation matrix:
1 lump
1 0.86752343 0.13247657
lump 0.02679359 0.97320641
Model: Random, lumped
Rate: NA
Frequencies: 0.2, 0.8
Bounded: Yes
Stationary: No
Reversible: No
Lumpable: Always
Overall rate: 0.04793
>
> stopifnot(likelihood(x) == likelihood(y),
+ likelihood(x2) == likelihood(y2),
+ likelihood(x3) == likelihood(y3))
Error: likelihood(x3) == likelihood(y3) is not TRUE
Execution halted
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64