* using log directory ‘/data/gannet/ripley/R/packages/tests-devel3/dartR.Rcheck’
* using R Under development (unstable) (2024-11-30 r87408)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* 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 ... [136s/334s] 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [22s/27s] OK
* checking whether the package can be loaded with stated dependencies ... [22s/24s] OK
* checking whether the package can be unloaded cleanly ... [24s/28s] OK
* checking whether the namespace can be loaded with stated dependencies ... [23s/25s] OK
* checking whether the namespace can be unloaded cleanly ... [23s/23s] OK
* checking loading without being on the library search path ... [23s/24s] OK
* checking whether startup messages can be suppressed ... [23s/24s] 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 ... [212s/216s] OK
* checking Rd files ... [3s/12s] 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 ... 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 ... 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 ... [50s/51s] ERROR
Running examples in ‘dartR-Ex.R’ failed
The error most likely occurred in:

> ### 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 
Error in as.integer(depth) : 
  cannot coerce type 'NULL' to vector of type 'integer'
Calls: gl.report.ld.map -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [25s/26s]
 [26s/26s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [18s/18s] OK
* checking PDF version of manual ... [22s/22s] OK
* checking HTML version of manual ... [14s/14s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-devel3/dartR.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 20:10.56, 901.70 + 57.04