CRAN Package Check Results for Package BMhyb

Last updated on 2019-08-25 05:46:43 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.1.5 3.10 478.08 481.18 OK
r-devel-linux-x86_64-debian-gcc 2.1.5 3.14 279.11 282.25 OK
r-devel-linux-x86_64-fedora-clang 2.1.5 471.23 NOTE
r-devel-linux-x86_64-fedora-gcc 2.1.5 584.57 NOTE
r-devel-windows-ix86+x86_64 2.1.5 10.00 358.00 368.00 OK
r-patched-linux-x86_64 2.1.5 3.50 530.36 533.86 OK
r-patched-solaris-x86 2.1.5 511.20 NOTE
r-release-linux-x86_64 2.1.5 3.01 431.93 434.94 OK
r-release-windows-ix86+x86_64 2.1.5 14.00 466.00 480.00 OK
r-release-osx-x86_64 2.1.5 NOTE
r-oldrel-windows-ix86+x86_64 2.1.5 7.00 485.00 492.00 ERROR
r-oldrel-osx-x86_64 2.1.5 NOTE

Check Details

Version: 2.1.5
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘lhs’ ‘metR’ ‘methods’ ‘mvtnorm’ ‘numDeriv’ ‘viridis’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 2.1.5
Check: tests
Result: ERROR
     Running 'testthat.R' [430s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > test_check("BMhyb")
     Loading required package: BMhyb
     [1] "Now starting analysis"
     [1] "Starting with initial values"
     sigma.sq mu SE bt vh
     0.117682960 2.118832288 0.007956494 1.000000000 0.007956494
     Nelder-Mead direct search function minimizer
     function value for initial parameters = 24.088800
     Scaled convergence tolerance is 2.41888
     Stepsize computed as 0.211883
     BUILD 6 29.371482 24.088800
     HI-REDUCTION 8 26.889548 24.088800
     Exiting from Nelder Mead minimizer
     10 function evaluations used
     step negloglik sigma.sq mu SE bt
     1.000000000 24.088800143 0.117682960 2.118832288 0.007956494 1.000000000
     vh
     0.007956494
     Nelder-Mead direct search function minimizer
     function value for initial parameters = 24.088800
     Scaled convergence tolerance is 2.41888
     Stepsize computed as 0.211883
     BUILD 6 29.371482 24.088800
     HI-REDUCTION 8 26.889548 24.088800
     Exiting from Nelder Mead minimizer
     10 function evaluations used
     step negloglik sigma.sq mu SE bt
     2.000000000 24.088800143 0.117682960 2.118832288 0.007956494 1.000000000
     vh
     0.007956494
     Nelder-Mead direct search function minimizer
     function value for initial parameters = 24.257381
     Scaled convergence tolerance is 2.43574
     Stepsize computed as 0.200536
     BUILD 6 29.266206 24.257381
     HI-REDUCTION 8 26.922233 24.257381
     Exiting from Nelder Mead minimizer
     10 function evaluations used
     step negloglik sigma.sq mu SE bt
     3.000000000 24.088800143 0.117682960 2.118832288 0.007956494 1.000000000
     vh
     0.007956494
     [1] "100 of 100 done"
     [1] "Now starting analysis"
     [1] "Starting with initial values"
     sigma.sq mu SE bt vh
     1.22392255 -0.01140498 0.01223923 1.00000000 0.01223923
     Nelder-Mead direct search function minimizer
     function value for initial parameters = 5.069839
     Scaled convergence tolerance is 0.516984
     Stepsize computed as 0.122392
     Exiting from Nelder Mead minimizer
     6 function evaluations used
     step negloglik sigma.sq mu SE bt
     1.00000000 4.99367318 1.22392255 -0.01140498 0.13463148 1.00000000
     vh
     0.01223923
     Nelder-Mead direct search function minimizer
     function value for initial parameters = 4.993673
     Scaled convergence tolerance is 0.509367
     Stepsize computed as 0.122392
     Exiting from Nelder Mead minimizer
     6 function evaluations used
     step negloglik sigma.sq mu SE bt
     2.00000000 4.99367318 1.22392255 -0.01140498 0.13463148 1.00000000
     vh
     0.01223923
     Nelder-Mead direct search function minimizer
     -- 1. Error: Simulation works (@test_condition.R#31) --------------------------
     non-finite value supplied by optim
     1: BMhyb(phy.graph = network, traits = tips, confidence.points = 100, max.steps = 2,
     control = list(reltol = 0.1, trace = 6)) at testthat/test_condition.R:31
     2: OptimizeThoroughly(phy.graph = phy.graph, traits = traits, free.parameter.names = free.parameter.names,
     measurement.error = measurement.error, gamma = gamma, do.Higham.correction = do.Higham.correction,
     do.Brissette.correction = do.Brissette.correction, max.steps = max.steps, verbose = verbose,
     control = control)
     3: stats::optim(par = starting.values, fn = TryComputeLikelihood, traits = traits, phy.graph = phy.graph,
     measurement.error = measurement.error, gamma = gamma, do.Higham.correction = do.Higham.correction,
     do.Brissette.correction = do.Brissette.correction, control = control)
    
     == testthat results ===========================================================
     [ OK: 12 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
     1. Error: Simulation works (@test_condition.R#31)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64