• 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 ‘dartR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘dartR’ version ‘2.9.7’
• 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 ‘dartR’ 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 ... [15s/22s] OK
• checking whether the package can be loaded with stated dependencies ... [15s/21s] OK
• checking whether the package can be unloaded cleanly ... [15s/23s] OK
• checking whether the namespace can be loaded with stated dependencies ... [14s/17s] OK
• checking whether the namespace can be unloaded cleanly ... [15s/18s] OK
• checking loading without being on the library search path ... [15s/19s] OK
• checking whether startup messages can be suppressed ... [15s/16s] 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 ... [140s/166s] OK
• checking Rd files ... [2s/3s] NOTE checkRd: (-1) gl.filter.maf.Rd:7: Lost braces; missing escapes or markup?      7 | {adegenet} object}        | ^ checkRd: (-1) gl.pcoa.Rd:68: Lost braces; missing escapes or markup?     68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}        | ^ checkRd: (-1) gl.play.history.Rd:17: Lost braces     17 | code{x2@other$history[c(1,4,5)]}). [optional].}        | ^ checkRd: (-1) utils.jackknife.Rd:49: Lost braces     49 | bold{Note} that when n is very small, jackknife resampling is not recommended.        | ^ checkRd: (-1) utils.jackknife.Rd:51: Lost braces     51 | Parallel computation is implemented. The argument code{n.cores} indicates the        | ^
• 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:   gl.genleastcost.Rd: landgenreport, popgenreport, wassermann, lgrMMRR   utils.dart2genlight.Rd: adegenet Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• 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 ... [4s/6s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [33s/42s] ERROR Running examples in ‘dartR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: gl.filter.ld > ### Title: Filters loci based on linkage disequilibrium (LD) > ### Aliases: gl.filter.ld > > ### ** Examples > > ## Not run: > ##D test <- bandicoot.gl > ##D test <- gl.filter.callrate(test,threshold = 1) > ##D res <- gl.report.ld.map(test) > ##D res_2 <- gl.filter.ld(x=test,ld_report = res) > ##D res_3 <- gl.report.ld.map(res_2) > ## End(Not run) > if ((requireNamespace("snpStats", quietly = TRUE)) & (requireNamespace("fields", quietly = TRUE))) { + test <- gl.filter.callrate(platypus.gl, threshold = 1) + test <- gl.filter.monomorphs(test) + test <- test[,1:20] + report <- gl.report.ld.map(test) + res <- gl.filter.ld(x=test,ld_report = report) + } Starting gl.filter.callrate   Processing genlight object with SNP data   Warning: data include loci that are scored NA across all individuals.   Consider filtering using gl <- gl.filter.allna(gl)   Warning: Data may include monomorphic loci in call rate                     calculations for filtering   Recalculating Call Rate   Removing loci based on Call Rate, threshold = 1 Completed: gl.filter.callrate Starting gl.filter.monomorphs   Processing genlight object with SNP data   Identifying monomorphic loci   Removing monomorphic loci and loci with all missing                        data Completed: gl.filter.monomorphs Starting gl.report.ld.map   Processing genlight object with SNP data   Calculating pairwise LD in population SEVERN_ABOVE  *** caught segfault *** address 0x1, cause 'memory not mapped' Traceback:  1: snpStats::ld(genotype_loci, genotype_loci, stats = ld_stat)  2: gl.report.ld.map(test) An irrecoverable exception occurred. R is aborting now ... Segmentation fault
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [16s/18s] OK   Running ‘testthat.R’ [16s/17s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [3s/4s] OK
• checking PDF version of manual ... [15s/19s] OK
• checking HTML version of manual ... [8s/15s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 2 NOTEs