* using log directory ‘/srv/hornik/tmp/CRAN_pretest/dartR.Rcheck’ * using R Under development (unstable) (2025-03-23 r88038) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * 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 ‘2.9.9.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] NOTE Maintainer: ‘Bernd Gruber ’ New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: heterozygosity (27:53) polymorphism (20:30) CRAN repository db overrides: X-CRAN-Comment: Archived on 2025-01-10 as issues were not corrected in time. Found the following (possibly) invalid URLs: URL: https://www.r-bloggers.com/2019/09/understanding-bootstrap-confidence-interval-output-from-the-r-boot-package (moved to https://www.r-bloggers.com/2019/09/understanding-bootstrap-confidence-interval-output-from-the-r-boot-package/) From: man/gl.report.fstat.Rd man/gl.report.heterozygosity.Rd Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. * 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 ... [36s/36s] OK * 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 ... [6s/6s] OK * checking whether the package can be loaded with stated dependencies ... [7s/7s] OK * checking whether the package can be unloaded cleanly ... [6s/6s] OK * checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK * checking whether the namespace can be unloaded cleanly ... [6s/6s] OK * checking loading without being on the library search path ... [6s/6s] OK * checking whether startup messages can be suppressed ... [7s/7s] 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 ... [59s/59s] OK * checking Rd files ... [1s/1s] 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: 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 ... [2s/2s] 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 ... [26s/26s] 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 vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [7s/7s] OK * checking HTML version of manual ... [4s/5s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs