• using R Under development (unstable) (2023-06-01 r84481 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by
      gcc.exe (GCC) 12.2.0
      GNU Fortran (GCC) 12.2.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8
• checking for file 'dartR/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'dartR' version '2.7.2'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: 'pca3d'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'dartR' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... 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 ... [11s] OK
• checking whether the package can be loaded with stated dependencies ... [13s] OK
• checking whether the package can be unloaded cleanly ... [12s] OK
• checking whether the namespace can be loaded with stated dependencies ... [12s] OK
• checking whether the namespace can be unloaded cleanly ... [12s] OK
• checking loading without being on the library search path ... [12s] OK
• checking startup messages can be suppressed ... [12s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... WARNING
  Missing or unexported object: 'maptools::elide'
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [67s] OK
• checking Rd files ... [4s] OK
• checking Rd metadata ... 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 ... [4s] 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 ... [67s] ERROR
  Running examples in 'dartR-Ex.R' failed
  The error most likely occurred in:
  
  > ### Name: gl.ld.haplotype
  > ### Title: Visualize patterns of linkage disequilibrium and identification
  > ### of haplotypes
  > ### Aliases: gl.ld.haplotype
  >
  > ### ** Examples
  >
  > require("dartR.data")
  > x <- platypus.gl
  > x <- gl.filter.callrate(x,threshold = 1)
  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
  > x <- gl.keep.pop(x, pop.list = "TENTERFIELD")
  Starting gl.keep.pop
    Processing genlight object with SNP data
    Checking for presence of nominated populations
    Retaining only populations TENTERFIELD
    Warning: Resultant dataset may contain monomorphic loci
    Locus metrics not recalculated
  Completed: gl.keep.pop
  > x$chromosome <- as.factor(x$other$loc.metrics$Chrom_Platypus_Chrom_NCBIv1)
  > x$position <- x$other$loc.metrics$ChromPos_Platypus_Chrom_NCBIv1
  > ld_res <- gl.ld.haplotype(x,chrom_name = "NC_041728.1_chromosome_1",
  + ld_max_pairwise = 10000000 )
  Starting gl.ld.haplotype
    Processing genlight object with SNP data
    Calculating pairwise LD in population TENTERFIELD
    Analysing chromosome NC_041728.1_chromosome_1
    The maximum distance at which LD should be calculated
                   (ld_max_pairwise) is too short for chromosome NC_041728.1_chromosome_1 . Setting this distance to 33814744 bp
  Please note that 'maptools' will be retired during October 2023,
  plan transition at your earliest convenience (see
  https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs
  for guidance);some functionality will be moved to 'sp'.
   Checking rgeos availability: FALSE
  Error: 'elide' is not an exported object from 'namespace:maptools'
  Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking re-building of vignette outputs ... [8s] OK
• checking PDF version of manual ... [32s] OK
• checking HTML version of manual ... [38s] OK
• DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE