CRAN Package Check Results for Package EpiNow2

Last updated on 2020-11-27 05:48:55 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.3.1 816.57 177.71 994.28 NOTE
r-devel-linux-x86_64-debian-gcc 1.3.1 1383.01 167.41 1550.42 NOTE
r-devel-linux-x86_64-fedora-clang 1.3.1 1353.43 NOTE
r-devel-linux-x86_64-fedora-gcc 1.3.1 1485.59 NOTE
r-devel-windows-ix86+x86_64 1.3.1 1598.00 423.00 2021.00 NOTE
r-patched-linux-x86_64 1.3.1 1146.39 244.94 1391.33 NOTE
r-patched-solaris-x86 1.3.1 1219.00 NOTE
r-release-linux-x86_64 1.3.1 1147.84 210.23 1358.07 NOTE
r-release-macos-x86_64 1.3.1 NOTE
r-release-windows-ix86+x86_64 1.3.1 1480.00 425.00 1905.00 NOTE
r-oldrel-macos-x86_64 1.3.1 ERROR
r-oldrel-windows-ix86+x86_64 1.3.1 1419.00 387.00 1806.00 NOTE

Check Details

Version: 1.3.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'EpiSoon'
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, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.3.1
Check: installed package size
Result: NOTE
     installed size is 128.6Mb
     sub-directories of 1Mb or more:
     libs 126.9Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.3.1
Check: examples
Result: ERROR
    Running examples in ‘EpiNow2-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: estimate_truncation
    > ### Title: Estimate Truncation of Observed Data
    > ### Aliases: estimate_truncation
    >
    > ### ** Examples
    >
    > #set number of cores to use
    > options(mc.cores = ifelse(interactive(), 4, 1))
    > # get example case counts
    > reported_cases <- example_confirmed[1:60]
    >
    > # define example truncation distribution (note not integer adjusted)
    > trunc_dist <- list(mean = convert_to_logmean(3, 2),
    + mean_sd = 0.1,
    + sd = convert_to_logsd(3, 2),
    + sd_sd = 0.1,
    + max = 10)
    >
    > # apply truncation to example data
    > construct_truncation <- function(index, cases, dist) {
    + set.seed(index)
    + cmf <- cumsum(
    + dlnorm(1:(dist$max + 1),
    + rnorm(1, dist$mean, dist$mean_sd),
    + rnorm(1, dist$sd, dist$sd_sd)))
    + cmf <- cmf / cmf[dist$max + 1]
    + cmf <- rev(cmf)[-1]
    + trunc_cases <- data.table::copy(cases)[1:(.N - index)]
    + trunc_cases[(.N - length(cmf) + 1):.N, confirm := as.integer(confirm * cmf)]
    + return(trunc_cases)
    + }
    > example_data <- purrr::map(c(20, 15, 10, 0),
    + construct_truncation,
    + cases = reported_cases,
    + dist = trunc_dist)
    >
    > # fit model to example data
    > est <- estimate_truncation(example_data, verbose = interactive(),
    + chains = 2, iter = 2000)
    [1] "Error in sampler$call_sampler(args_list[[i]]) : "
    [2] " c++ exception (unknown reason)"
    error occurred during calling the sampler; sampling not done
    Stan model 'estimate_truncation' does not contain samples.
    Error in round(rstan::summary(fit, pars = "logmean")$summary[1], 3) :
     non-numeric argument to mathematical function
    Calls: estimate_truncation
    Execution halted
Flavor: r-oldrel-macos-x86_64