- 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 ‘Familias/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘Familias’ version ‘2.6.1’
- 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 serialization versions ... OK
- checking whether package ‘Familias’ can be installed ... OK
See the install log for details.
- used C compiler: ‘Debian clang version 19.1.5 (1)’
- used C++ compiler: ‘Debian clang version 19.1.5 (1)’
- checking package directory ... OK
- checking for future file timestamps ... 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 ... [2s/2s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the package can be unloaded cleanly ... [2s/2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
- checking loading without being on the library search path ... [2s/2s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [14s/17s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
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- checking line endings in C/C++/Fortran sources/headers ... OK
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- checking compiled code ... OK
- checking examples ... [2s/3s] ERROR
Running examples in ‘Familias-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Familias-package
> ### Title: Familias: Inferring paternity and identification based on DNA
> ### data
> ### Aliases: Familias-package Familias
> ### Keywords: package
>
> ### ** Examples
>
> persons <- c("mother", "daughter", "AF")
>
> # Pedigrees
> ped1 <- FamiliasPedigree(id = persons,
+ dadid = c(NA, "AF", NA),
+ momid = c(NA, "mother", NA),
+ sex = c("female", "female", "male"))
>
> ped2 <- FamiliasPedigree(id = c(persons, "TF"),
+ dadid = c(NA, "TF", NA, NA),
+ momid = c(NA, "mother", NA, NA),
+ sex = c("female", "female", "male", "male"))
>
> ped3 <- FamiliasPedigree(id = c(persons, "TF", "gf", "gm"),
+ dadid = c(NA, "TF", "gf", "gf", NA, NA),
+ momid = c(NA, "mother", "gm", "gm", NA, NA),
+ sex = c("female", "female", "male", "male", "male", "female"))
> op <- par(mfrow = c(1,3))
> plot(ped1); title("ped1: AF is father")
> plot(ped2); title("ped2: AF is unrelated")
Did not plot the following people: AF
> plot(ped3); title("ped3: AF is uncle")
> par(op)
>
> mypedigrees <- list(isFather = ped1, unrelated=ped2, isUncle = ped3)
>
> # Loci
> locus1 <- FamiliasLocus(frequencies = c(0.1, 0.2, 0.3, 0.4),
+ allelenames = c("A", "B", "C", "D"),
+ name = "locus1")
> locus2 <- FamiliasLocus(c(0.2, 0.3, 0.5),
+ c(17, 18, 19),
+ "loc2",
+ femaleMutationRate = 0.05)
> myloci <- list(locus1, locus2)
>
> # Genotype data
> datamatrix <- data.frame(locus1.1 = c("A", "A", "A"),
+ locus1.2 = c("B", "B", "C"),
+ locus2.1 = c(17, 19, 19),
+ locus2.2 = c(18, 18, 18),
+ row.names = persons)
>
> # Calculate LR
> FamiliasPosterior(mypedigrees, myloci, datamatrix)
*** buffer overflow detected ***: terminated
Aborted
- checking PDF version of manual ... [4s/7s] OK
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- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR