* using log directory ‘/srv/hornik/tmp/CRAN/sequoia.Rcheck’ * using R Under development (unstable) (2023-12-08 r85664) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.5 (1) Debian flang-new version 17.0.5 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘sequoia/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sequoia’ version ‘2.7.5’ * checking CRAN incoming feasibility ... [4s/5s] Note_to_CRAN_maintainers Maintainer: ‘Jisca Huisman ’ * 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 ‘sequoia’ can be installed ... [48s/37s] OK * used C compiler: ‘Debian clang version 17.0.5 (1)’ * used Fortran compiler: ‘Debian flang-new version 17.0.5 (1)’ * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [10s/10s] 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 * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking usage of KIND in Fortran files ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/1s] ERROR Running examples in ‘sequoia-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CalcOHLLR > ### Title: Calculate OH and LLR for a pedigree > ### Aliases: CalcOHLLR > > ### ** Examples > > # count Mendelian errors in an existing pedigree > Ped.OH <- CalcOHLLR(Pedigree = Ped_HSg5, GenoM = SimGeno_example, + CalcLLR = FALSE) Counting Mendelian errors ... > Ped.OH[50:55,] id dam sire OHdam OHsire MEpair SNPd.id SNPd.id.dam SNPd.id.sire 50 a01010 a00008 b00016 0 0 1 200 199 198 51 b01011 a00008 b00016 0 0 1 200 199 198 52 b01012 a00008 b00016 0 0 1 198 197 196 53 b01013 a00011 b00001 0 0 0 199 199 199 54 b01014 a00011 b00001 0 0 0 198 198 198 55 b01015 a00011 b00001 0 0 1 198 198 198 > # view histograms > SummarySeq(Ped.OH, Panels="OH") > > # Parent likelihood ratios in an existing pedigree, including for > # non-genotyped parents > Ped.LLR <- CalcOHLLR(Pedigree = Ped_HSg5, GenoM = SimGeno_example, + CalcLLR = TRUE, LifeHistData=LH_HSg5, AgePrior=TRUE) Error: segfault from C stack overflow Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [41s/39s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘PedComp.Rmd’ using rmarkdown --- finished re-building ‘PedComp.Rmd’ --- re-building ‘quick_start_example1.rmd’ using rmarkdown Error: segfault from C stack overflow Execution halted --- re-building ‘vignette-age.Rmd’ using rmarkdown --- finished re-building ‘vignette-age.Rmd’ --- re-building ‘vignette-main.Rmd’ using rmarkdown Warning: LaTeX Warning: Hyper reference `sec:Herm' on page 21 undefined on input line 10 Warning: 16. Warning: LaTeX Warning: `!h' float specifier changed to `!ht'. Warning: LaTeX Warning: Hyper reference `sec:maybepar' on page 24 undefined on input lin Warning: e 1183. Warning: LaTeX Warning: There were undefined references. --- finished re-building ‘vignette-main.Rmd’ --- re-building ‘flowchart.pdf.asis’ using asis --- finished re-building ‘flowchart.pdf.asis’ --- re-building ‘vignette_mtDNA.pdf.asis’ using asis --- finished re-building ‘vignette_mtDNA.pdf.asis’ SUMMARY: processing the following file failed: ‘quick_start_example1.rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs