Last updated on 2026-05-05 20:51:32 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.3 | 48.90 | 363.04 | 411.94 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2.3 | 32.30 | 275.67 | 307.97 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.3 | 88.00 | 643.82 | 731.82 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.3 | 84.00 | 632.84 | 716.84 | OK | |
| r-devel-windows-x86_64 | 1.2.3 | 50.00 | 355.00 | 405.00 | ERROR | |
| r-patched-linux-x86_64 | 1.2.3 | 48.03 | 384.03 | 432.06 | OK | |
| r-release-linux-x86_64 | 1.2.3 | 48.00 | 391.54 | 439.54 | OK | |
| r-release-macos-arm64 | 1.2.3 | 11.00 | 82.00 | 93.00 | OK | |
| r-release-macos-x86_64 | 1.2.3 | 33.00 | 361.00 | 394.00 | OK | |
| r-release-windows-x86_64 | 1.2.3 | 57.00 | 434.00 | 491.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.3 | 4.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.2.3 | 33.00 | 281.00 | 314.00 | ERROR | |
| r-oldrel-windows-x86_64 | 1.2.3 | 81.00 | 575.00 | 656.00 | OK |
Version: 1.2.3
Check: examples
Result: ERROR
Running examples in ‘dartR.base-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gl.report.basics
> ### Title: Basic statistics for a genlight object
> ### Aliases: gl.report.basics
>
> ### ** Examples
>
> if (isTRUE(getOption("dartR_fbm"))) platypus.gl <- gl.gen2fbm(platypus.gl)
> gl.report.basics(platypus.gl)
Starting gl.report.basics
SUMMARY STATISTICS
Datatype: SNP
Loci: 1000
Individuals: 81
Populations: 3
Average Read Depth: 31.3504
Values: 81000
Error in as.data.frame.numeric(x[[i]], optional = TRUE) :
row names contain missing values
Calls: gl.report.basics ... data.frame -> as.data.frame -> as.data.frame.numeric
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
gl.filter.ld 5.884 0.153 6.394
gl.pcoa 4.859 0.001 5.232
gl.filter.factorloadings 3.993 0.050 5.427
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2.3
Check: examples
Result: ERROR
Running examples in 'dartR.base-Ex.R' failed
The error most likely occurred in:
> ### Name: gl.report.basics
> ### Title: Basic statistics for a genlight object
> ### Aliases: gl.report.basics
>
> ### ** Examples
>
> if (isTRUE(getOption("dartR_fbm"))) platypus.gl <- gl.gen2fbm(platypus.gl)
> gl.report.basics(platypus.gl)
Starting gl.report.basics
SUMMARY STATISTICS
Datatype: SNP
Loci: 1000
Individuals: 81
Populations: 3
Average Read Depth: 31.3504
Values: 81000
Error in as.data.frame.numeric(x[[i]], optional = TRUE) :
row names contain missing values
Calls: gl.report.basics ... data.frame -> as.data.frame -> as.data.frame.numeric
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.2.3
Check: package dependencies
Result: ERROR
Packages required but not available: 'SNPRelate', 'snpStats'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-arm64
Version: 1.2.3
Check: examples
Result: ERROR
Running examples in ‘dartR.base-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
>
> if ((requireNamespace("snpStats", quietly = TRUE)) & (requireNamespace("fields", quietly = TRUE))) {
+ test <- gl.filter.callrate(platypus.gl, threshold = 1)
+ test <- gl.filter.monomorphs(test)
+ 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
There is no information in the chromosome/position slot of the genlight object.
Assigning the same chromosome ('1') to all the SNPs in the dataset.
Assigning a sequence from 1 to n loci as the position of each SNP.
Calculating LD for all possible SNP pair combinations 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 ...
Flavor: r-oldrel-macos-x86_64