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 
       |                                                       ^
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.
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
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 
       |                                                       ^
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.
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
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 
       |                                                       ^
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 

 *** 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 ...
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 
       |                                                       ^
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 

 *** 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 ...
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 
       |                                                       ^
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.
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
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$history[c(1,4,5)]}). [optional].}
       |     ^
checkRd: (-1) utils.jackknife.Rd:49: Lost braces
    49 | bold{Note} that when n is very small, jackknife resampling is not recommended.
       |     ^
checkRd: (-1) utils.jackknife.Rd:51: Lost braces
    51 | Parallel computation is implemented. The argument code{n.cores} indicates the 
       |                                                       ^
checkRd: (-1) gl.filter.maf.Rd:7: Lost braces; missing escapes or markup?
     7 |  {adegenet} object}
       |  ^
checkRd: (-1) gl.pcoa.Rd:68: Lost braces; missing escapes or markup?
    68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}
       |                                                 ^
checkRd: (-1) gl.play.history.Rd:17: Lost braces
    17 | code{x2@other$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 
       |                                                       ^
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$history[c(1,4,5)]}). [optional].}
       |     ^
checkRd: (-1) utils.jackknife.Rd:49: Lost braces
    49 | bold{Note} that when n is very small, jackknife resampling is not recommended.
       |     ^
checkRd: (-1) utils.jackknife.Rd:51: Lost braces
    51 | Parallel computation is implemented. The argument code{n.cores} indicates the 
       |                                                       ^
checkRd: (-1) gl.filter.maf.Rd:7: Lost braces; missing escapes or markup?
     7 |  {adegenet} object}
       |  ^
checkRd: (-1) gl.pcoa.Rd:68: Lost braces; missing escapes or markup?
    68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}
       |                                                 ^
checkRd: (-1) gl.play.history.Rd:17: Lost braces
    17 | code{x2@other$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 
       |                                                       ^
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 
       |                                                       ^
Package suggested but not available for checking: ‘snpStats’
Package unavailable to check Rd xrefs: ‘snpStats’