Last updated on 2026-10-02 05:51:17 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.1.6 | 3.26 | 49.72 | 52.98 | OK | |
| r-devel-linux-x86_64-debian-gcc | 4.1.6 | 2.83 | 37.99 | 40.82 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 4.1.6 | 37.15 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 4.1.6 | 41.57 | OK | |||
| r-devel-windows-x86_64 | 4.1.6 | 7.00 | 78.00 | 85.00 | OK | |
| r-patched-linux-x86_64 | 4.1.6 | 4.23 | 45.77 | 50.00 | OK | |
| r-release-linux-x86_64 | 4.1.6 | 3.26 | 45.27 | 48.53 | OK | |
| r-release-macos-arm64 | 4.1.6 | 1.00 | 19.00 | 20.00 | OK | |
| r-release-macos-x86_64 | 4.1.6 | 3.00 | 67.00 | 70.00 | OK | |
| r-release-windows-x86_64 | 4.1.6 | 6.00 | 72.00 | 78.00 | OK | |
| r-oldrel-macos-arm64 | 4.1.6 | 1.00 | 23.00 | 24.00 | OK | |
| r-oldrel-macos-x86_64 | 4.1.6 | 3.00 | 71.00 | 74.00 | OK | |
| r-oldrel-windows-x86_64 | 4.1.6 | 8.00 | 92.00 | 100.00 | OK |
Version: 4.1.6
Check: examples
Result: ERROR
Running examples in ‘bGMYC4-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bgmyc.multiphylo
> ### Title: Multi-tree GMYC analysis
> ### Aliases: bgmyc.multiphylo
>
> ### ** Examples
>
> # Load test data
> data(east10)
>
> # Single tree analysis
> result.single <- bgmyc.singlephy(
+ phylo = east10[[1]],
+ mcmc = 100, burnin = 1, thinning = 10
+ )
You are running bGMYC on a single phylogenetic tree.
This tree contains 215 tips.
The Yule process rate change parameter has a uniform prior ranging from 0 to 2.
The coalescent process rate change parameter has a uniform prior ranging from 0 to 2.
The threshold parameter, which is equal to the number of species, has a uniform prior ranging from 2 to 51. The upper bound of this prior should not be more than the number of tips in your trees.
The MCMC will start with the Yule parameter set to 1.
The MCMC will start with the coalescent parameter set to 0.5.
The MCMC will start with the threshold parameter set to 50. If this number is greater than the number of tips in your tree, an error will result.
Given your settings for mcmc, burnin and thinning, your analysis will result in 9.9 samples being retained.
10%
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acceptance rates py pc th: 0.63 0.54 0.38
> plot(result.single)
>
> # Multi-tree analysis (explicitly 2 trees to satisfy CRAN parallel limits)
> result.multi <- bgmyc.multiphylo(
+ multiphylo = east10[1:2],
+ mcmc = 100, burnin = 1, thinning = 10
+ )
You are running a multi tree analysis on 2 trees.
These trees each contain 215 tips.
The Yule process rate change parameter has a uniform prior ranging from 0 to 2.
The coalescent process rate change parameter has a uniform prior ranging from 0 to 2.
The threshold parameter, which is equal to the number of species, has a uniform prior ranging from 2 to 51. The upper bound of this prior should not be more than the number of tips in your trees.
The MCMC will start with the Yule parameter set to 1.
The MCMC will start with the coalescent parameter set to 0.5.
The MCMC will start with the threshold parameter set to 50. If this number is greater than the number of tips in your tree, an error will result.
Given your settings for mcmc, burnin and thinning, your analysis will result in 19.8 samples being retained.
[INFO] Starting parallel analysis (using 2 cores)...
Error in serverSocket(port = port) :
creation of server socket failed: port 11022 cannot be opened
Calls: bgmyc.multiphylo -> <Anonymous> -> makePSOCKcluster -> serverSocket
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc