Last updated on 2024-12-23 12:49:42 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| AlphaSimR | 1 | 4 | 8 |
Current CRAN status: ERROR: 1, NOTE: 4, OK: 8
Version: 1.6.1
Check: examples
Result: ERROR
Running examples in ‘AlphaSimR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SimParam
> ### Title: Simulation parameters
> ### Aliases: SimParam
>
> ### ** Examples
>
>
> ## ------------------------------------------------
> ## Method `SimParam$new`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
>
> ## ------------------------------------------------
> ## Method `SimParam$setTrackPed`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$setTrackPed(TRUE)
>
> ## ------------------------------------------------
> ## Method `SimParam$setTrackRec`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$setTrackRec(TRUE)
>
> ## ------------------------------------------------
> ## Method `SimParam$resetPed`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
>
> #Create population
> pop = newPop(founderPop, simParam=SP)
> pop@id # 1:10
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10"
>
> #Create another population after reseting pedigree
> SP$resetPed()
> pop2 = newPop(founderPop, simParam=SP)
> pop2@id # 1:10
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10"
>
> ## ------------------------------------------------
> ## Method `SimParam$restrSegSites`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$restrSegSites(minQtlPerChr=5, minSnpPerChr=5)
>
> ## ------------------------------------------------
> ## Method `SimParam$setSexes`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$setSexes("yes_sys")
>
> ## ------------------------------------------------
> ## Method `SimParam$addSnpChip`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addSnpChip(10)
>
> ## ------------------------------------------------
> ## Method `SimParam$addSnpChipByName`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> SP$addSnpChipByName(c("1_1","1_3"))
>
> ## ------------------------------------------------
> ## Method `SimParam$addTraitA`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addTraitA(10)
>
> ## ------------------------------------------------
> ## Method `SimParam$addTraitAD`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addTraitAD(10, meanDD=0.5)
>
> ## ------------------------------------------------
> ## Method `SimParam$altAddTraitAD`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$altAddTraitAD(nQtlPerChr=10, mean=0, varA=1, varD=0.05, inbrDepr=0.2)
A new trait called Trait1 was added.
varD = 0.01630348
inbrDepr = 0.2491569
meanDD = 0
varDD = 0.09211727
>
> ## ------------------------------------------------
> ## Method `SimParam$addTraitAG`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addTraitAG(10, varGxE=2)
>
> ## ------------------------------------------------
> ## Method `SimParam$addTraitADG`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addTraitADG(10, meanDD=0.5, varGxE=2)
>
> ## ------------------------------------------------
> ## Method `SimParam$addTraitAE`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addTraitAE(10, relAA=0.1)
>
> ## ------------------------------------------------
> ## Method `SimParam$addTraitADE`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addTraitADE(10)
>
> ## ------------------------------------------------
> ## Method `SimParam$addTraitAEG`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addTraitAEG(10, varGxE=2)
>
> ## ------------------------------------------------
> ## Method `SimParam$addTraitADEG`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addTraitADEG(10, meanDD=0.5, varGxE=2)
>
> ## ------------------------------------------------
> ## Method `SimParam$setVarE`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addTraitA(10)
> SP$setVarE(h2=0.5)
>
> ## ------------------------------------------------
> ## Method `SimParam$setCorE`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> ## Don't show:
> SP$nThreads = 1L
> ## End(Don't show)
> SP$addTraitA(10, mean=c(0,0), var=c(1,1), corA=diag(2))
> SP$setVarE(varE=c(1,1))
> E = 0.5*diag(2)+0.5 #Positively correlated error
> SP$setCorE(E)
Warning in SP$setCorE(E) :
This function has been deprecated. Use simParam$setVarE instead.
>
> ## ------------------------------------------------
> ## Method `SimParam$rescaleTraits`
> ## ------------------------------------------------
>
> #Create founder haplotypes
> founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)
>
> #Set simulation parameters
> SP = SimParam$new(founderPop)
> SP$addTraitA(10)
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Error: C stack usage 585056955860 is too close to the limit
Execution halted
Fatal error: error during cleanup
*** caught segfault ***
address (nil), cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
terminate called after throwing an instance of 'std::out_of_range'
what(): Mat::operator(): index out of bounds
Aborted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(AlphaSimR)
Loading required package: R6
>
> test_check("AlphaSimR")
*** caught segfault ***
address (nil), cause 'unknown'
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.6.1
Check: installed package size
Result: NOTE
installed size is 19.5Mb
sub-directories of 1Mb or more:
libs 18.2Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64