CRAN Package Check Results for Package bite

Last updated on 2024-08-23 07:49:25 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.3 10.94 85.00 95.94 ERROR
r-devel-linux-x86_64-debian-gcc 0.3 8.94 61.40 70.34 ERROR
r-devel-linux-x86_64-fedora-clang 0.3 158.03 ERROR
r-devel-linux-x86_64-fedora-gcc 0.3 153.42 ERROR
r-devel-windows-x86_64 0.3 13.00 107.00 120.00 NOTE
r-patched-linux-x86_64 0.3 15.03 90.04 105.07 OK
r-release-linux-x86_64 0.3 10.25 89.75 100.00 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 15.00 103.00 118.00 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 16.00 132.00 148.00 OK

Additional issues

noSuggests

Check Details

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