CRAN Package Check Results for Package breathteststan

Last updated on 2018-11-15 06:47:15 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.4.7 189.80 104.19 293.99 NOTE
r-devel-linux-x86_64-debian-gcc 0.4.7 190.09 88.97 279.06 NOTE
r-devel-linux-x86_64-fedora-clang 0.4.7 403.53 NOTE
r-devel-linux-x86_64-fedora-gcc 0.4.7 412.62 NOTE
r-devel-windows-ix86+x86_64 0.4.7 331.00 184.00 515.00 NOTE
r-patched-linux-x86_64 0.4.7 221.08 99.43 320.51 NOTE
r-patched-solaris-x86 0.4.7 391.70 NOTE
r-release-linux-x86_64 0.4.7 207.76 98.87 306.63 NOTE
r-release-windows-ix86+x86_64 0.4.7 438.00 242.00 680.00 NOTE
r-release-osx-x86_64 0.4.7 ERROR
r-oldrel-windows-ix86+x86_64 0.4.7 435.00 258.00 693.00 NOTE
r-oldrel-osx-x86_64 0.4.7 ERROR

Check Details

Version: 0.4.7
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
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-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.4.7
Check: installed package size
Result: NOTE
     installed size is 41.2Mb
     sub-directories of 1Mb or more:
     libs 41.0Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.4.7
Check: examples
Result: ERROR
    Running examples in ‘breathteststan-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: stan_fit
    > ### Title: Bayesian Stan fit to 13C Breath Data
    > ### Aliases: stan_fit
    >
    > ### ** Examples
    >
    > library(breathtestcore)
    > suppressPackageStartupMessages(library(dplyr))
    > d = breathtestcore::simulate_breathtest_data(n_records = 3) # default 3 records
    > data = breathtestcore::cleanup_data(d$data)
    > # Use more than 80 iterations and 4 chains for serious fits
    > fit = stan_fit(data, chains = 1, iter = 80)
    error occurred during calling the sampler; sampling not done
    Stan model 'breath_test_1' does not contain samples.
    Stan model 'breath_test_1' does not contain samples.
    Stan model 'breath_test_1' does not contain samples.
    Error in data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2), :
     arguments imply differing number of rows: 120, 0
    Calls: stan_fit -> data.frame
    Execution halted
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.4.7
Check: tests
Result: ERROR
     Running ‘testthat.R’ [4s/4s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     arguments imply differing number of rows: 500, 0
     1: stan_fit(data, dose = dose, student_t_df = student_t_df, chains = chains, iter = iter) at testthat/test_stan_fit_2.R:21
     2: data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2), m = as.vector(rstan::extract(fit,
     permuted = TRUE, pars = "m")$m), beta = as.vector(rstan::extract(fit, permuted = TRUE,
     pars = "beta")$beta), k = as.vector(rstan::extract(fit, permuted = TRUE, pars = "k")$k))
     3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows),
     collapse = ", ")), domain = NA)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 4 SKIPPED: 7 FAILED: 2
     1. Error: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#16)
     2. Error: Data that cannot be fitted with nls_list/nlme work with stan_fit (@test_stan_fit_2.R#21)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-osx-x86_64

Version: 0.4.7
Check: tests
Result: ERROR
     Running ‘testthat.R’ [6s/6s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     arguments imply differing number of rows: 500, 0
     1: stan_fit(data, dose = dose, student_t_df = student_t_df, chains = chains, iter = iter) at testthat/test_stan_fit_2.R:21
     2: data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2), m = as.vector(rstan::extract(fit,
     permuted = TRUE, pars = "m")$m), beta = as.vector(rstan::extract(fit, permuted = TRUE,
     pars = "beta")$beta), k = as.vector(rstan::extract(fit, permuted = TRUE, pars = "k")$k))
     3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows),
     collapse = ", ")), domain = NA)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 4 SKIPPED: 7 FAILED: 2
     1. Error: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#16)
     2. Error: Data that cannot be fitted with nls_list/nlme work with stan_fit (@test_stan_fit_2.R#21)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-oldrel-osx-x86_64