CRAN Package Check Results for Package dartR.popgen

Last updated on 2024-12-25 05:48:32 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 23.07 157.80 180.87 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.0 15.36 123.02 138.38 OK
r-devel-linux-x86_64-fedora-clang 1.0.0 342.76 OK
r-devel-linux-x86_64-fedora-gcc 1.0.0 301.59 OK
r-devel-windows-x86_64 1.0.0 23.00 178.00 201.00 OK
r-patched-linux-x86_64 1.0.0 20.30 166.94 187.24 OK
r-release-linux-x86_64 1.0.0 18.92 167.58 186.50 OK
r-release-macos-arm64 1.0.0 80.00 OK
r-release-macos-x86_64 1.0.0 228.00 OK
r-release-windows-x86_64 1.0.0 23.00 171.00 194.00 OK
r-oldrel-macos-arm64 1.0.0 86.00 NOTE
r-oldrel-macos-x86_64 1.0.0 154.00 OK
r-oldrel-windows-x86_64 1.0.0 28.00 221.00 249.00 OK

Check Details

Version: 1.0.0
Check: examples
Result: ERROR Running examples in ‘dartR.popgen-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: gl.ld.haplotype > ### Title: Visualize patterns of linkage disequilibrium and identification > ### of haplotypes > ### Aliases: gl.ld.haplotype > > ### ** Examples > > require("dartR.data") > x <- platypus.gl > x <- gl.filter.callrate(x, threshold = 1) 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 > # only the first 15 individuals because of speed during tests > x <- gl.keep.pop(x, pop.list = "TENTERFIELD")[1:15, ] Starting gl.keep.pop Processing genlight object with SNP data Checking for presence of nominated populations Retaining only populations TENTERFIELD Warning: Resultant dataset may contain monomorphic loci Locus metrics not recalculated Completed: gl.keep.pop > x$chromosome <- as.factor(x$other$loc.metrics$Chrom_Platypus_Chrom_NCBIv1) > x$position <- x$other$loc.metrics$ChromPos_Platypus_Chrom_NCBIv1 > ld_res <- gl.ld.haplotype(x, + chrom_name = "NC_041728.1_chromosome_1", + ld_max_pairwise = 10000000 + ) Starting gl.ld.haplotype Processing genlight object with SNP data Calculating pairwise LD in population TENTERFIELD Analysing chromosome NC_041728.1_chromosome_1 The maximum distance at which LD should be calculated (ld_max_pairwise) is too short for chromosome NC_041728.1_chromosome_1 . Setting this distance to 40201976 bp Error in loadNamespace(x) : there is no package called ‘raster’ Calls: gl.ld.haplotype ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed gl.ld.distance 5.299 0.11 6.747 Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘snpStats’ Flavor: r-oldrel-macos-arm64

Version: 1.0.0
Check: Rd cross-references
Result: NOTE Package unavailable to check Rd xrefs: ‘snpStats’ Flavor: r-oldrel-macos-arm64