Last updated on 2023-12-06 10:03:26 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.17.2 | 33.07 | 92.82 | 125.89 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.17.2 | 21.78 | 71.45 | 93.23 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.17.2 | 174.01 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.17.2 | 152.05 | ERROR | |||
| r-devel-windows-x86_64 | 2.17.2 | 31.00 | 106.00 | 137.00 | ERROR | |
| r-patched-linux-x86_64 | 2.17.2 | 26.75 | 89.96 | 116.71 | ERROR | |
| r-release-linux-x86_64 | 2.17.2 | 23.07 | 90.50 | 113.57 | ERROR | |
| r-release-macos-arm64 | 2.17.2 | 49.00 | NOTE | |||
| r-release-macos-x86_64 | 2.17.2 | 77.00 | NOTE | |||
| r-release-windows-x86_64 | 2.17.2 | 39.00 | 127.00 | 166.00 | ERROR | |
| r-oldrel-macos-arm64 | 2.17.2 | 48.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2.17.2 | 62.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 2.17.2 | 39.00 | 117.00 | 156.00 | ERROR |
Version: 2.17.2
Check: package dependencies
Result: NOTE
Package which this enhances but not available for checking: ‘asreml’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 2.17.2
Check: Rd files
Result: NOTE
checkRd: (-1) aiFun.Rd:25: Lost braces
25 | A /code{matrix} of k x k dimensions is returned, if k is the number
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.17.2
Check: examples
Result: ERROR
Running examples in ‘nadiv-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeAinv
> ### Title: Creates the inverse additive genetic relationship matrix
> ### Aliases: makeAinv makeAinv.default makeAinv.fuzzy makeGGAinv
>
> ### ** Examples
>
>
> ## Without genetic groups ##
> makeAinv(Mrode2)
$Ainv
6 x 6 sparse Matrix of class "dgCMatrix"
1 1.8333333 0.5000000 -1.0 -0.6666667 . .
2 0.5000000 2.0333333 -1.0 . 0.5333333 -1.066667
3 -1.0000000 -1.0000000 2.5 0.5000000 -1.0000000 .
4 -0.6666667 . 0.5 1.8333333 -1.0000000 .
5 . 0.5333333 -1.0 -1.0000000 2.5333333 -1.066667
6 . -1.0666667 . . -1.0666667 2.133333
$listAinv
row column Ainv
1 1 1 1.8333333
5 2 1 0.5000000
6 2 2 2.0333333
10 3 1 -1.0000000
11 3 2 -1.0000000
12 3 3 2.5000000
15 4 1 -0.6666667
16 4 3 0.5000000
17 4 4 1.8333333
19 5 2 0.5333333
20 5 3 -1.0000000
21 5 4 -1.0000000
22 5 5 2.5333333
24 6 2 -1.0666667
25 6 5 -1.0666667
26 6 6 2.1333333
$f
[1] 0.000 0.000 0.000 0.000 0.125 0.125
$logDet
[1] -2.431662
$dii
[1] 1.00000 1.00000 0.50000 0.75000 0.50000 0.46875
>
> ## With genetic groups ##
> ## Type A
> typeAped <- Q1988[-c(3:7), c("id", "damGG", "sireGG")]
> AstarA <- makeAinv(typeAped, ggroups = 2, gOnTop = FALSE)$Ainv
> ## Type D
> typeDped <- Q1988[-c(1:7), c("id", "damGG", "sireGG")]
> AstarD <- makeAinv(typeDped, ggroups = c("g1", "g2"), gOnTop = FALSE)$Ainv
> stopifnot(identical(AstarA, AstarD))
>
> # Show that the augmented A-inverse with genetic groups
> # contains the normal A-inverse (i.e., without genetic groups)
> ## Augmented A-inverse with genetic groups
> ggAinv <- makeAinv(Mrode3[-c(1,2), c("calf", "damGG", "sireGG")],
+ ggroups = c("g1", "g2"), gOnTop = FALSE)$Ainv
> noggAinv <- makeAinv(Mrode3[-c(1,2), c("calf", "dam", "sire")],
+ ggroups = NULL)$Ainv
> # First 8 rows & columns of ggAinv are same as A-inverse without
> ## genetic groups
> ggAinv[1:8, 1:8]
8 x 8 sparse Matrix of class "dgCMatrix"
1 1.8333333 0.5 . -0.6666667 . -1.0 . .
2 0.5000000 2.0 0.5 . -1.0 -1.0 . .
3 . 0.5 2.0 . -1.0 0.5 . -1
4 -0.6666667 . . 1.8333333 0.5 . -1 .
5 . -1.0 -1.0 0.5000000 2.5 . -1 .
6 -1.0000000 -1.0 0.5 . . 2.5 . -1
7 . . . -1.0000000 -1.0 . 2 .
8 . . -1.0 . . -1.0 . 2
> noggAinv
8 x 8 sparse Matrix of class "dgCMatrix"
1 1.8333333 0.5 . -0.6666667 . -1.0 . .
2 0.5000000 2.0 0.5 . -1.0 -1.0 . .
3 . 0.5 2.0 . -1.0 0.5 . -1
4 -0.6666667 . . 1.8333333 0.5 . -1 .
5 . -1.0 -1.0 0.5000000 2.5 . -1 .
6 -1.0000000 -1.0 0.5 . . 2.5 . -1
7 . . . -1.0000000 -1.0 . 2 .
8 . . -1.0 . . -1.0 . 2
> stopifnot(all.equal(ggAinv[1:8, 1:8], noggAinv))
Error: ggAinv[1:8, 1:8] and noggAinv are not equal:
Attributes: < Modes: NULL, list >
Attributes: < Lengths: 0, 1 >
Attributes: < names for current but not for target >
....
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 2.17.2
Check: examples
Result: ERROR
Running examples in ‘nadiv-Ex.R’ failed
The error most likely occurred in:
> ### Name: makeAinv
> ### Title: Creates the inverse additive genetic relationship matrix
> ### Aliases: makeAinv makeAinv.default makeAinv.fuzzy makeGGAinv
>
> ### ** Examples
>
>
> ## Without genetic groups ##
> makeAinv(Mrode2)
$Ainv
6 x 6 sparse Matrix of class "dgCMatrix"
1 1.8333333 0.5000000 -1.0 -0.6666667 . .
2 0.5000000 2.0333333 -1.0 . 0.5333333 -1.066667
3 -1.0000000 -1.0000000 2.5 0.5000000 -1.0000000 .
4 -0.6666667 . 0.5 1.8333333 -1.0000000 .
5 . 0.5333333 -1.0 -1.0000000 2.5333333 -1.066667
6 . -1.0666667 . . -1.0666667 2.133333
$listAinv
row column Ainv
1 1 1 1.8333333
5 2 1 0.5000000
6 2 2 2.0333333
10 3 1 -1.0000000
11 3 2 -1.0000000
12 3 3 2.5000000
15 4 1 -0.6666667
16 4 3 0.5000000
17 4 4 1.8333333
19 5 2 0.5333333
20 5 3 -1.0000000
21 5 4 -1.0000000
22 5 5 2.5333333
24 6 2 -1.0666667
25 6 5 -1.0666667
26 6 6 2.1333333
$f
[1] 0.000 0.000 0.000 0.000 0.125 0.125
$logDet
[1] -2.431662
$dii
[1] 1.00000 1.00000 0.50000 0.75000 0.50000 0.46875
>
> ## With genetic groups ##
> ## Type A
> typeAped <- Q1988[-c(3:7), c("id", "damGG", "sireGG")]
> AstarA <- makeAinv(typeAped, ggroups = 2, gOnTop = FALSE)$Ainv
> ## Type D
> typeDped <- Q1988[-c(1:7), c("id", "damGG", "sireGG")]
> AstarD <- makeAinv(typeDped, ggroups = c("g1", "g2"), gOnTop = FALSE)$Ainv
> stopifnot(identical(AstarA, AstarD))
>
> # Show that the augmented A-inverse with genetic groups
> # contains the normal A-inverse (i.e., without genetic groups)
> ## Augmented A-inverse with genetic groups
> ggAinv <- makeAinv(Mrode3[-c(1,2), c("calf", "damGG", "sireGG")],
+ ggroups = c("g1", "g2"), gOnTop = FALSE)$Ainv
> noggAinv <- makeAinv(Mrode3[-c(1,2), c("calf", "dam", "sire")],
+ ggroups = NULL)$Ainv
> # First 8 rows & columns of ggAinv are same as A-inverse without
> ## genetic groups
> ggAinv[1:8, 1:8]
8 x 8 sparse Matrix of class "dgCMatrix"
1 1.8333333 0.5 . -0.6666667 . -1.0 . .
2 0.5000000 2.0 0.5 . -1.0 -1.0 . .
3 . 0.5 2.0 . -1.0 0.5 . -1
4 -0.6666667 . . 1.8333333 0.5 . -1 .
5 . -1.0 -1.0 0.5000000 2.5 . -1 .
6 -1.0000000 -1.0 0.5 . . 2.5 . -1
7 . . . -1.0000000 -1.0 . 2 .
8 . . -1.0 . . -1.0 . 2
> noggAinv
8 x 8 sparse Matrix of class "dgCMatrix"
1 1.8333333 0.5 . -0.6666667 . -1.0 . .
2 0.5000000 2.0 0.5 . -1.0 -1.0 . .
3 . 0.5 2.0 . -1.0 0.5 . -1
4 -0.6666667 . . 1.8333333 0.5 . -1 .
5 . -1.0 -1.0 0.5000000 2.5 . -1 .
6 -1.0000000 -1.0 0.5 . . 2.5 . -1
7 . . . -1.0000000 -1.0 . 2 .
8 . . -1.0 . . -1.0 . 2
> stopifnot(all.equal(ggAinv[1:8, 1:8], noggAinv))
Error: ggAinv[1:8, 1:8] and noggAinv are not equal:
Attributes: < Modes: NULL, list >
Attributes: < Lengths: 0, 1 >
Attributes: < names for current but not for target >
....
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64