Check results for 'distfreereg'

using R version 4.4.1 (2024-06-14)
using platform: aarch64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0
running under: macOS Ventura 13.4
using session charset: UTF-8
checking for file ‘distfreereg/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘distfreereg’ version ‘1.0’
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘distfreereg’ can be installed ... [1s/1s] OK See the install log for details.
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [0s/0s] OK
checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
checking whether the package can be unloaded cleanly ... [0s/0s] OK
checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
checking loading without being on the library search path ... [0s/0s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [2s/2s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [3s/3s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [33s/36s] ERROR Running ‘0_aggregator_matrix.R’ [0s/0s] Comparing ‘0_aggregator_matrix.Rout’ to ‘0_aggregator_matrix.Rout.save’ ... OK Running ‘0_combine_dfr_arg_lists_test.R’ [0s/0s] Comparing ‘0_combine_dfr_arg_lists_test.Rout’ to ‘0_combine_dfr_arg_lists_test.Rout.save’ ... OK Running ‘0_combine_lists_test.R’ [0s/0s] Comparing ‘0_combine_lists_test.Rout’ to ‘0_combine_lists_test.Rout.save’ ... OK Running ‘0_fill_covariance_list_test_01_matrix.R’ [0s/0s] Comparing ‘0_fill_covariance_list_test_01_matrix.Rout’ to ‘0_fill_covariance_list_test_01_matrix.Rout.save’ ... OK Running ‘0_fill_covariance_list_test_02_number.R’ [0s/0s] Comparing ‘0_fill_covariance_list_test_02_number.Rout’ to ‘0_fill_covariance_list_test_02_number.Rout.save’ ... OK Running ‘0_fill_covariance_list_test_03_vector.R’ [0s/0s] Comparing ‘0_fill_covariance_list_test_03_vector.Rout’ to ‘0_fill_covariance_list_test_03_vector.Rout.save’ ... OK Running ‘0_is_named_list_test.R’ [0s/0s] Comparing ‘0_is_named_list_test.Rout’ to ‘0_is_named_list_test.Rout.save’ ... OK Running ‘0_matrix_functions_test.R’ [0s/0s] Comparing ‘0_matrix_functions_test.Rout’ to ‘0_matrix_functions_test.Rout.save’ ... OK Running ‘0_scale_to_01_test.R’ [0s/0s] Comparing ‘0_scale_to_01_test.Rout’ to ‘0_scale_to_01_test.Rout.save’ ... OK Running ‘0_upstar_test.R’ [0s/0s] Comparing ‘0_upstar_test.Rout’ to ‘0_upstar_test.Rout.save’ ... OK Running ‘1_distfreereg_test_01_basic.R’ [1s/2s] Comparing ‘1_distfreereg_test_01_basic.Rout’ to ‘1_distfreereg_test_01_basic.Rout.save’ ...151c151 < [1] "Mean relative difference: 1.447528e-07" --- > [1] "Mean relative difference: 1.447316e-07" 153c153 < [1] "Mean relative difference: 1.447528e-07" --- > [1] "Mean relative difference: 1.447316e-07" 155c155 < [1] "Mean relative difference: 9.249522e-08" --- > [1] "Mean relative difference: 9.247401e-08" 159,160c159,160 < [1] "Component \"KS\": Mean relative difference: 3.224496e-08" < [2] "Component \"CvM\": Mean relative difference: 2.129433e-07" --- > [1] "Component \"KS\": Mean relative difference: 3.223872e-08" > [2] "Component \"CvM\": Mean relative difference: 2.129122e-07" 162,163c162,163 < [1] "Component \"KS\": Mean relative difference: 3.224496e-08" < [2] "Component \"CvM\": Mean relative difference: 2.129433e-07" --- > [1] "Component \"KS\": Mean relative difference: 3.223872e-08" > [2] "Component \"CvM\": Mean relative difference: 2.129122e-07" 165,166c165,166 < [1] "Component \"KS\": Mean relative difference: 2.001101e-08" < [2] "Component \"CvM\": Mean relative difference: 1.313586e-07" --- > [1] "Component \"KS\": Mean relative difference: 2.000477e-08" > [2] "Component \"CvM\": Mean relative difference: 1.313275e-07" Running ‘1_distfreereg_test_02_X_NULL.R’ [0s/0s] Comparing ‘1_distfreereg_test_02_X_NULL.Rout’ to ‘1_distfreereg_test_02_X_NULL.Rout.save’ ... OK Running ‘1_distfreereg_test_03_override_default.R’ [2s/2s] Comparing ‘1_distfreereg_test_03_override_default.Rout’ to ‘1_distfreereg_test_03_override_default.Rout.save’ ... OK Running ‘1_distfreereg_test_04_override_formula.R’ [2s/3s] Comparing ‘1_distfreereg_test_04_override_formula.Rout’ to ‘1_distfreereg_test_04_override_formula.Rout.save’ ... OK Running ‘1_distfreereg_test_05_override_function.R’ [2s/2s] Comparing ‘1_distfreereg_test_05_override_function.Rout’ to ‘1_distfreereg_test_05_override_function.Rout.save’ ... OK Running ‘1_distfreereg_test_06_override_lm.R’ [1s/1s] Comparing ‘1_distfreereg_test_06_override_lm.Rout’ to ‘1_distfreereg_test_06_override_lm.Rout.save’ ... OK Running ‘1_distfreereg_test_07_override_errors.R’ [0s/0s] Comparing ‘1_distfreereg_test_07_override_errors.Rout’ to ‘1_distfreereg_test_07_override_errors.Rout.save’ ... OK Running ‘1_distfreereg_test_08_external_f.R’ [1s/1s] Comparing ‘1_distfreereg_test_08_external_f.Rout’ to ‘1_distfreereg_test_08_external_f.Rout.save’ ... OK Running ‘1_distfreereg_test_09_ordering.R’ [7s/8s] Comparing ‘1_distfreereg_test_09_ordering.Rout’ to ‘1_distfreereg_test_09_ordering.Rout.save’ ... OK Running ‘1_distfreereg_test_10_ordering_errors.R’ [0s/0s] Comparing ‘1_distfreereg_test_10_ordering_errors.Rout’ to ‘1_distfreereg_test_10_ordering_errors.Rout.save’ ... OK Running ‘1_distfreereg_test_11_test_f_errors.R’ [0s/0s] Comparing ‘1_distfreereg_test_11_test_f_errors.Rout’ to ‘1_distfreereg_test_11_test_f_errors.Rout.save’ ... OK Running ‘1_distfreereg_test_12_update_function.R’ [3s/3s] Comparing ‘1_distfreereg_test_12_update_function.Rout’ to ‘1_distfreereg_test_12_update_function.Rout.save’ ... OK Running ‘1_distfreereg_test_13_predict.R’ [1s/1s] Comparing ‘1_distfreereg_test_13_predict.Rout’ to ‘1_distfreereg_test_13_predict.Rout.save’ ... OK Running ‘1_distfreereg_test_14_B.R’ [0s/0s] Comparing ‘1_distfreereg_test_14_B.Rout’ to ‘1_distfreereg_test_14_B.Rout.save’ ... OK Running ‘1_distfreereg_test_15_plot.R’ [1s/1s] Comparing ‘1_distfreereg_test_15_plot.Rout’ to ‘1_distfreereg_test_15_plot.Rout.save’ ... OK Running ‘1_distfreereg_test_16_stat_function_errors.R’ [0s/0s] Comparing ‘1_distfreereg_test_16_stat_function_errors.Rout’ to ‘1_distfreereg_test_16_stat_function_errors.Rout.save’ ... OK Running ‘1_distfreereg_test_17_covariance.R’ [1s/1s] Comparing ‘1_distfreereg_test_17_covariance.Rout’ to ‘1_distfreereg_test_17_covariance.Rout.save’ ... OK Running ‘1_distfreereg_test_18_optimization.R’ [1s/1s] Comparing ‘1_distfreereg_test_18_optimization.Rout’ to ‘1_distfreereg_test_18_optimization.Rout.save’ ...62c62 < 28 7 --- > 23 7 Running ‘1_distfreereg_test_19_symmetric.R’ [1s/1s] Comparing ‘1_distfreereg_test_19_symmetric.Rout’ to ‘1_distfreereg_test_19_symmetric.Rout.save’ ... OK Running ‘1_distfreereg_test_20_formula_method.R’ [0s/0s] Comparing ‘1_distfreereg_test_20_formula_method.Rout’ to ‘1_distfreereg_test_20_formula_method.Rout.save’ ...52c52 < [1] "Mean relative difference: 2.087567e-06" --- > [1] "Mean relative difference: 2.087606e-06" Running ‘1_distfreereg_test_21_update_default.R’ [1s/1s] Comparing ‘1_distfreereg_test_21_update_default.Rout’ to ‘1_distfreereg_test_21_update_default.Rout.save’ ...47,48c47,48 < [1] "Component \"KS\": Mean relative difference: 3.909002e-08" < [2] "Component \"CvM\": Mean relative difference: 1.108985e-07" --- > [1] "Component \"KS\": Mean relative difference: 3.909289e-08" > [2] "Component \"CvM\": Mean relative difference: 1.109057e-07" 71,72c71,72 < [1] "Component \"KS\": Mean relative difference: 1.162022e-07" < [2] "Component \"CvM\": Mean relative difference: 2.770613e-08" --- > [1] "Component \"KS\": Mean relative difference: 1.161913e-07" > [2] "Component \"CvM\": Mean relative difference: 2.769842e-08" Running ‘1_distfreereg_test_22_extra_argument_detection.R’ [0s/0s] Comparing ‘1_distfreereg_test_22_extra_argument_detection.Rout’ to ‘1_distfreereg_test_22_extra_argument_detection.Rout.save’ ... OK Running ‘1_distfreereg_test_23_lm_method.R’ [0s/0s] Comparing ‘1_distfreereg_test_23_lm_method.Rout’ to ‘1_distfreereg_test_23_lm_method.Rout.save’ ... OK Running ‘1_distfreereg_test_24_update_formula.R’ [1s/1s] Comparing ‘1_distfreereg_test_24_update_formula.Rout’ to ‘1_distfreereg_test_24_update_formula.Rout.save’ ... OK Running ‘1_distfreereg_test_25_update_lm.R’ [1s/1s] Comparing ‘1_distfreereg_test_25_update_lm.Rout’ to ‘1_distfreereg_test_25_update_lm.Rout.save’ ... OK Running ‘1_distfreereg_test_26_update_default.R’ [1s/1s] Running the tests in ‘tests/1_distfreereg_test_26_update_default.R’ failed. Complete output: > library(distfreereg) > set.seed(20240320) > n <- 1e2 > func <- function(x, theta) sum(theta*x) > Sig <- rWishart(1, df = n, Sigma = diag(n))[,,1] > theta <- c(2,5) > X <- cbind(`(Intercept)` = 1, matrix(rexp(n, rate = 1))) > Y <- distfreereg:::f2ftheta(f = func, X)(theta) + + as.vector(distfreereg:::rmvnorm(n = n, reps = 1, mean = rep(0,n), SqrtSigma = distfreereg:::matsqrt(Sig))) > > set.seed(20240320) > dfr_ref <- distfreereg(Y = Y, X = X, test_mean = func, covariance = list(Sigma = Sig), + theta_init = c(1,1), verbose = FALSE) > > J <- dfr_ref[["J"]] > fitted_values <- dfr_ref[["fitted_values"]] > > set.seed(20240320) > dfr_0 <- distfreereg(Y = Y, X = X, test_mean = NULL, covariance = list(Sigma = Sig), + verbose = FALSE, J = J, fitted_values = fitted_values) > > > set.seed(20240320) > dfr_1a <- distfreereg(Y = Y*Y, X = X, test_mean = NULL, covariance = list(Sigma = Sig), + verbose = FALSE, J = J, fitted_values = fitted_values) > dfr_1b <- update(dfr_0, Y = Y*Y) > identical(dfr_1a[-1], dfr_1b[-1])# TRUE [1] TRUE > > > set.seed(20240320) > dfr_2a <- distfreereg(Y = Y, X = X*X, test_mean = NULL, covariance = list(Sigma = Sig), + verbose = FALSE, J = J, fitted_values = fitted_values) > dfr_2b <- update(dfr_0, X = X*X) > identical(dfr_2a[-c(1,13,14)], dfr_2b[-c(1,13,14)])# TRUE; changing X requires recalculating ordering [1] TRUE > > set.seed(20240320) > dfr_3a <- distfreereg(Y = Y, X = X, test_mean = NULL, covariance = list(Sigma = Sig %*% Sig), + verbose = FALSE, J = J, fitted_values = fitted_values) Error in matsqrt(covariance_list[["P"]]) : covariance_list[["P"]] has eigenvalues less than the tolerance, the smallest of which is -3.4952795928114e-05 Calls: distfreereg ... distfreereg.default -> fill_covariance_list -> matsqrt Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [106s/106s] OK
checking PDF version of manual ... [3s/3s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '