CRAN Package Check Results for Package breathteststan

Last updated on 2019-02-19 22:51:21 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.4.7 181.33 95.46 276.79 NOTE
r-devel-linux-x86_64-debian-gcc 0.4.7 176.09 80.20 256.29 NOTE
r-devel-linux-x86_64-fedora-clang 0.4.7 409.33 NOTE
r-devel-linux-x86_64-fedora-gcc 0.4.7 311.81 NOTE
r-devel-windows-ix86+x86_64 0.4.7 431.00 251.00 682.00 NOTE
r-patched-linux-x86_64 0.4.7 202.32 99.64 301.96 NOTE
r-patched-solaris-x86 0.4.7 391.90 NOTE
r-release-linux-x86_64 0.4.7 201.03 100.32 301.35 NOTE
r-release-windows-ix86+x86_64 0.4.7 319.00 238.00 557.00 NOTE
r-release-osx-x86_64 0.4.7 ERROR
r-oldrel-windows-ix86+x86_64 0.4.7 362.00 7.00 369.00 ERROR
r-oldrel-osx-x86_64 0.4.7 ERROR

Check Details

Version: 0.4.7
Check: line endings in C/C++/Fortran sources/headers
Result: NOTE
    Found the following sources/headers with CR or CRLF line endings:
     inst/include/meta_header.hpp
    Some Unix compilers require LF line endings.
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

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-osx-x86_64

Version: 0.4.7
Check: installed package size
Result: NOTE
     installed size is 36.8Mb
     sub-directories of 1Mb or more:
     libs 36.7Mb
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: whether the package can be loaded
Result: ERROR
    Loading this package had a fatal error status code 1
    Loading log:
    Loading required package: Rcpp
    Error: package or namespace load failed for 'breathteststan' in namespaceExport(ns, exports):
     undefined exports: add_count, add_count_, add_rownames, add_tally, add_tally_, all_equal, all_vars, anti_join, any_vars, arrange, arrange_, arrange_all, arrange_at, arrange_if, as.tbl, as.tbl_cube, auto_copy, bench_tbls, between, bind_cols, bind_rows, case_when, changes, check_dbplyr, coalesce, collect, combine, common_by, compare_tbls, compare_tbls2, compute, copy_to, count, count_, cumall, cumany, cume_dist, cummean, current_vars, db_analyze, db_begin, db_commit, db_create_index, db_create_indexes, db_create_table, db_data_type, db_desc, db_drop_table, db_explain, db_has_table, db_insert_into, db_list_tables, db_query_fields, db_query_rows, db_rollback, db_save_query, db_write_table, dense_rank, desc, dim_desc, distinct, distinct_, distinct_all, distinct_at, distinct_if, distinct_prepare, do, do_, dr_dplyr, eval_tbls, eval_tbls2, explain, failwith, filter_, filter_all, filter_at, filter_if
    In addition: Warning message:
    S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
    Execution halted
    ** DONE
Flavor: r-oldrel-windows-ix86+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