Last updated on 2024-08-16 18:50:25 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3 | 11.13 | 86.34 | 97.47 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.3 | 8.04 | 62.18 | 70.22 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.3 | 158.03 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3 | 156.72 | ERROR | |||
| r-devel-windows-x86_64 | 0.3 | 14.00 | 107.00 | 121.00 | NOTE | |
| r-patched-linux-x86_64 | 0.3 | 16.27 | 90.70 | 106.97 | OK | |
| r-release-linux-x86_64 | 0.3 | 12.31 | 91.52 | 103.83 | OK | |
| r-release-macos-arm64 | 0.3 | 55.00 | OK | |||
| r-release-macos-x86_64 | 0.3 | 73.00 | OK | |||
| r-release-windows-x86_64 | 0.3 | 13.00 | 106.00 | 119.00 | OK | |
| r-oldrel-macos-arm64 | 0.3 | 51.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.3 | 87.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.3 | 18.00 | 129.00 | 147.00 | OK |
Version: 0.3
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘mvMORPH’
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
Version: 0.3
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
make_jive.Rd: make.simmap, as.phylo
plot_jive.Rd: vioplot
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: 0.3
Check: examples
Result: ERROR
Running examples in ‘bite-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_jive
> ### Title: Create a list that can be used as an input to mcmc_bite
> ### Aliases: make_jive
>
> ### ** Examples
>
>
> ## Load test data
> data(Anolis_traits)
> data(Anolis_tree)
> data(Anolis_map)
>
> ## JIVE object to run jive with single regimes
> my.jive <- make_jive(phy = Anolis_tree, traits = Anolis_traits[,-3],
+ model.priors = list(mean = "BM", logvar= c("OU", "root")))
mean prior model: BM [1]
logvar prior model: OU + root [1]
>
> ## JIVE object to run jive with multiple regimes
> my.jive <- make_jive(Anolis_tree, Anolis_traits[,-3], map = Anolis_map,
+ model.priors =list(mean = "BM", logvar = c("OU", "theta", "alpha")))
mean prior model: BM [1]
logvar prior model: OU + theta + alpha [2]
>
> ## JIVE object to run jive from an ancestral state reconstruction (stochastic mapping)
> # First generate simmap object
> library(phytools)
Loading required package: ape
Loading required package: maps
> n= length(Anolis_tree$tip.label)
> trait = rep(0,n)
> trait[c(4,3,14,16, 6,5)] = 1
> names(trait) = Anolis_tree$tip.label
>
> mapped_tree=make.simmap(Anolis_tree, trait, model='SYM')
make.simmap is sampling character histories conditioned on
the transition matrix
Q =
0 1
0 -0.01156974 0.01156974
1 0.01156974 -0.01156974
(estimated using likelihood);
and (mean) root node prior probabilities
pi =
0 1
0.5 0.5
Done.
> plotSimmap(mapped_tree)
no colors provided. using the following legend:
0 1
"black" "#DF536B"
>
> my.jive <- make_jive(mapped_tree, Anolis_traits[,-3]
+ , model.priors = list(mean = "OU" , logvar = c("OU", "theta")))
mean prior model: OU [1]
logvar prior model: OU + theta [2]
>
> ## Jive object using another model of trait evolution (EB from mvMORPH)
> library(mvMORPH)
Error in library(mvMORPH) : there is no package called ‘mvMORPH’
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.3
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘MASS’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3
Check: examples
Result: ERROR
Running examples in ‘bite-Ex.R’ failed
The error most likely occurred in:
> ### Name: make_jive
> ### Title: Create a list that can be used as an input to mcmc_bite
> ### Aliases: make_jive
>
> ### ** Examples
>
>
> ## Load test data
> data(Anolis_traits)
> data(Anolis_tree)
> data(Anolis_map)
>
> ## JIVE object to run jive with single regimes
> my.jive <- make_jive(phy = Anolis_tree, traits = Anolis_traits[,-3],
+ model.priors = list(mean = "BM", logvar= c("OU", "root")))
mean prior model: BM [1]
logvar prior model: OU + root [1]
>
> ## JIVE object to run jive with multiple regimes
> my.jive <- make_jive(Anolis_tree, Anolis_traits[,-3], map = Anolis_map,
+ model.priors =list(mean = "BM", logvar = c("OU", "theta", "alpha")))
mean prior model: BM [1]
logvar prior model: OU + theta + alpha [2]
>
> ## JIVE object to run jive from an ancestral state reconstruction (stochastic mapping)
> # First generate simmap object
> library(phytools)
Loading required package: ape
Loading required package: maps
> n= length(Anolis_tree$tip.label)
> trait = rep(0,n)
> trait[c(4,3,14,16, 6,5)] = 1
> names(trait) = Anolis_tree$tip.label
>
> mapped_tree=make.simmap(Anolis_tree, trait, model='SYM')
make.simmap is sampling character histories conditioned on
the transition matrix
Q =
0 1
0 -0.01156974 0.01156974
1 0.01156974 -0.01156974
(estimated using likelihood);
and (mean) root node prior probabilities
pi =
0 1
0.5 0.5
Done.
> plotSimmap(mapped_tree)
no colors provided. using the following legend:
0 1
"black" "#DF536B"
>
> my.jive <- make_jive(mapped_tree, Anolis_traits[,-3]
+ , model.priors = list(mean = "OU" , logvar = c("OU", "theta")))
mean prior model: OU [1]
logvar prior model: OU + theta [2]
>
> ## Jive object using another model of trait evolution (EB from mvMORPH)
> library(mvMORPH)
Error in library(mvMORPH) : there is no package called ‘mvMORPH’
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc