CRAN Package Check Results for Package paleobuddy

Last updated on 2024-11-03 03:49:44 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 3.41 99.35 102.76 OK
r-devel-linux-x86_64-debian-gcc 1.0.0 2.62 62.67 65.29 OK
r-devel-linux-x86_64-fedora-clang 1.0.0 173.69 OK
r-devel-linux-x86_64-fedora-gcc 1.0.0 174.65 OK
r-devel-windows-x86_64 1.0.0 4.00 108.00 112.00 OK
r-patched-linux-x86_64 1.0.0 3.88 93.80 97.68 OK
r-release-linux-x86_64 1.0.0 3.07 39.91 42.98 ERROR
r-release-macos-arm64 1.0.0 42.00 OK
r-release-macos-x86_64 1.0.0 60.00 OK
r-release-windows-x86_64 1.0.0 4.00 105.00 109.00 OK
r-oldrel-macos-arm64 1.0.0 44.00 OK
r-oldrel-macos-x86_64 1.0.0 73.00 OK
r-oldrel-windows-x86_64 1.0.0 6.00 121.00 127.00 OK

Check Details

Version: 1.0.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘ape’ Flavor: r-release-linux-x86_64

Version: 1.0.0
Check: examples
Result: ERROR Running examples in ‘paleobuddy-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: find.lineages > ### Title: Separate a paleobuddy simulation into monophyletic clades > ### Aliases: find.lineages > > ### ** Examples > > ### > # first, we run a simple simulation with one starting species > > # set seed > set.seed(1) > > # run simulation with a minimum of 20 species > sim <- bd.sim(n0 = 3, lambda = 0.1, mu = 0.1, tMax = 10, + nFinal = c(20, Inf)) > > # get a simulation object with the clade originating from species 2 > clades <- find.lineages(sim, S = 2) > > # now we can check to make sure the subclade was correctly separated > > # change NA to 0 on the clade's TE > clades[[1]]$sim$TE[clades[[1]]$sim$EXTANT] <- 0 > > # plot the phylogeny > if (requireNamespace("ape", quietly = TRUE)) { + plot <- ape::plot.phylo( + make.phylo(clades[[1]]$sim), + main = "red: extinction events \n blue: speciation events"); + ape::axisPhylo() + } > > # check speciation times > for (j in 2:length(clades[[1]]$sim$TS)) { + # the subtraction is just to adjust the wt with the plot scale + lines(x = c( + sort(clades[[1]]$sim$TS, decreasing = TRUE)[2] - + clades[[1]]$sim$TS[j], + sort(clades[[1]]$sim$TS, decreasing = TRUE)[2] - + clades[[1]]$sim$TS[j]), + y = c(plot$y.lim[1], plot$y.lim[2]), lwd = 2, col = "blue") + } Error in plot$y.lim : object of type 'closure' is not subsettable Calls: lines -> lines.default -> plot.xy -> xy.coords Execution halted Flavor: r-release-linux-x86_64

Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘overview.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/paleobuddy.Rcheck/vign_test/paleobuddy/vignettes/overview_files/figure-gfm/unnamed-chunk-3-1.png 2100x1500 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 38405 bytes Input file size = 39311 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33574 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 33273 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 33273 Output IDAT size = 33273 bytes (5132 bytes decrease) Output file size = 33351 bytes (5960 bytes = 15.16% decrease) Quitting from lines 76-86 [unnamed-chunk-4] (overview.Rmd) Error: processing vignette 'overview.Rmd' failed with diagnostics: there is no package called 'ape' --- failed re-building ‘overview.Rmd’ SUMMARY: processing the following file failed: ‘overview.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64