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 |
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