* using log directory 'd:/RCompile/CRANincoming/R-devel/dartR.Rcheck'
* using R version 4.5.0 alpha (2025-03-23 r88038 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 '2.9.9.3'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [14s] NOTE
Maintainer: 'Bernd Gruber <bernd.gruber@canberra.edu.au>'

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 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 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 ... [13s] OK
* checking whether the package can be loaded with stated dependencies ... [13s] OK
* checking whether the package can be unloaded cleanly ... [13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s] OK
* checking loading without being on the library search path ... [13s] OK
* checking whether startup messages can be suppressed ... [13s] 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 ... [123s] OK
* checking Rd files ... 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 ... 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 ... [51s] 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 
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [37s] OK
* checking HTML version of manual ... [46s] OK
* DONE
Status: 1 ERROR, 2 NOTEs