- using R Under development (unstable) (2024-12-18 r87448)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.5 (1)
Debian flang-new version 19.1.5 (1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘relMix/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘relMix’ version ‘1.4’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘relMix’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [4s/4s] OK
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- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
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- checking foreign function calls ... OK
- checking R code for possible problems ... [22s/27s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
createDatamatrix.Rd: FamiliasLocus
relMix.Rd: FamiliasPedigree, FamiliasLocus, Familias,
FamiliasPosterior
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
- checking for missing documentation entries ... OK
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- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [4s/5s] ERROR
Running examples in ‘relMix-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: relMix
> ### Title: Relationship inference based on mixtures
> ### Aliases: relMix
>
> ### ** Examples
>
> #Example 1: paternity trio with mixture of mother and child
> #Define alleles and frequencies
> alleles <- 1:2
> afreq <- c(0.4,0.6)
> #Define pedigrees
> persons <- c("CH","MO","AF")
> ped1 <- Familias::FamiliasPedigree(id=persons, dadid=c("AF",NA, NA), momid=c("MO", NA,NA),
+ sex=c("male", "female", "male"))
> ped2 <- Familias::FamiliasPedigree(id=c(persons, "TF"), dadid=c("TF", NA, NA,NA),
+ momid=c("MO", NA, NA,NA), sex=c("male", "female", "male", "male"))
> pedigrees <- list(isFather = ped1, unrelated=ped2)
> #Create locus object
> locus <- Familias::FamiliasLocus(frequencies=afreq,name="M1",
+ allelenames= alleles)
> #Known genotypes of alleged father and mother
> gAF <- c(1,1)
> gMO <- c(1,1)
> #Mixture alleles
> R <- c(1,2)
> datamatrix <- createDatamatrix(locus,knownGenos=list(AF=gAF,MO=gMO),idsU=c("CH"))
> #Define dropout and drop-in values
> d <- 0.1
> di <- 0.05
> res <- relMix(pedigrees, locus, R, datamatrix, ids=c("MO","CH"),
+ D=list(c(0,0),c(d,d^2)),di=di, kinship=0)
*** buffer overflow detected ***: terminated
Aborted
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- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE