Last updated on 2024-09-27 17:51:16 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.9.7 | 78.49 | 598.45 | 676.94 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.9.7 | 51.30 | 380.95 | 432.25 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 2.9.7 | 1097.08 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 2.9.7 | 920.58 | ERROR | |||
| r-devel-windows-x86_64 | 2.9.7 | 71.00 | 579.00 | 650.00 | NOTE | |
| r-patched-linux-x86_64 | 2.9.7 | 83.44 | 556.37 | 639.81 | NOTE | |
| r-release-linux-x86_64 | 2.9.7 | 77.69 | 556.23 | 633.92 | NOTE | |
| r-release-macos-arm64 | 2.9.7 | 237.00 | NOTE | |||
| r-release-macos-x86_64 | 2.9.7 | 368.00 | NOTE | |||
| r-release-windows-x86_64 | 2.9.7 | 71.00 | 587.00 | 658.00 | NOTE | |
| r-oldrel-macos-arm64 | 2.9.7 | 250.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2.9.7 | 569.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.9.7 | 103.00 | 793.00 | 896.00 | OK |
Version: 2.9.7
Check: Rd files
Result: 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
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 2.9.7
Check: Rd cross-references
Result: NOTE
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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 2.9.7
Check: examples
Result: 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
*** 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-devel-linux-x86_64-fedora-gcc
Version: 2.9.7
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘snpStats’
Flavor: r-oldrel-macos-arm64
Version: 2.9.7
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘snpStats’
Flavor: r-oldrel-macos-arm64