Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-02-18 02:29:11 -0500 (Sun, 18 Feb 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4657 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4397 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4424 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4400 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1844/2244 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sccomp 1.7.5 (landing page) Stefano Mangiola
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the sccomp package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sccomp.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: sccomp |
Version: 1.7.5 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sccomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sccomp_1.7.5.tar.gz |
StartedAt: 2024-02-17 10:05:11 -0500 (Sat, 17 Feb 2024) |
EndedAt: 2024-02-17 10:45:12 -0500 (Sat, 17 Feb 2024) |
EllapsedTime: 2400.5 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: sccomp.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sccomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sccomp_1.7.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sccomp.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sccomp/DESCRIPTION’ ... OK * this is package ‘sccomp’ version ‘1.7.5’ * package encoding: UTF-8 * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘sccomp’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... OK Not all R platforms support C++17 * checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: data 1.1Mb figures 1.3Mb libs 4.9Mb * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... 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 ... NOTE alpha_to_CI: no visible binding for global variable ‘M’ alpha_to_CI: no visible binding for global variable ‘C_name’ alpha_to_CI: no visible binding for global variable ‘.lower’ alpha_to_CI: no visible binding for global variable ‘.median’ alpha_to_CI: no visible binding for global variable ‘.upper’ as_matrix: no visible binding for global variable ‘variable’ beta_to_CI: no visible binding for global variable ‘M’ beta_to_CI: no visible binding for global variable ‘C_name’ beta_to_CI: no visible binding for global variable ‘.lower’ beta_to_CI: no visible binding for global variable ‘.median’ beta_to_CI: no visible binding for global variable ‘.upper’ check_if_within_posterior: no visible binding for global variable ‘.lower’ check_if_within_posterior: no visible binding for global variable ‘.upper’ check_if_within_posterior: no visible binding for global variable ‘ppc’ check_random_intercept_design: no visible binding for global variable ‘factors’ check_random_intercept_design: no visible binding for global variable ‘groupings’ contrasts_to_enquos: no visible binding for global variable ‘.’ data_simulation_to_model_input: no visible binding for global variable ‘.’ data_simulation_to_model_input : <anonymous>: no visible global function definition for ‘sd’ data_spread_to_model_input: no visible global function definition for ‘as.formula’ data_spread_to_model_input: no visible binding for global variable ‘exposure’ data_spread_to_model_input: no visible binding for global variable ‘design’ data_spread_to_model_input: no visible binding for global variable ‘mat’ data_spread_to_model_input: no visible binding for global variable ‘factor___numeric’ data_spread_to_model_input: no visible binding for global variable ‘mean_idx’ data_spread_to_model_input: no visible binding for global variable ‘design_matrix’ data_spread_to_model_input: no visible binding for global variable ‘minus_sum’ data_spread_to_model_input: no visible binding for global variable ‘group___numeric’ data_spread_to_model_input: no visible binding for global variable ‘idx’ data_spread_to_model_input: no visible binding for global variable ‘group___label’ data_spread_to_model_input: no visible binding for global variable ‘parameter’ data_spread_to_model_input: no visible binding for global variable ‘design_matrix_col’ data_to_spread: no visible binding for global variable ‘exposure’ design_matrix_and_coefficients_to_dir_mult_simulation: no visible binding for global variable ‘cell_type’ design_matrix_and_coefficients_to_dir_mult_simulation: no visible binding for global variable ‘generated_counts’ design_matrix_and_coefficients_to_dir_mult_simulation: no visible binding for global variable ‘factor_1’ design_matrix_and_coefficients_to_simulation: no visible binding for global variable ‘cell_type’ design_matrix_and_coefficients_to_simulation: no visible binding for global variable ‘beta_1’ design_matrix_and_coefficients_to_simulation: no visible binding for global variable ‘beta_2’ dirichlet_multinomial_glm: no visible global function definition for ‘detect_cores’ dirichlet_multinomial_glm: no visible binding for global variable ‘glm_dirichlet_multinomial’ dirichlet_multinomial_glm: no visible binding for global variable ‘censoring_iteration’ dirichlet_multinomial_glm: no visible binding for global variable ‘.’ dirichlet_multinomial_glm: no visible binding for global variable ‘chains’ dirichlet_multinomial_glm: no visible binding for global variable ‘precision’ dirichlet_multinomial_glm: no visible binding for global variable ‘M’ do_inference_imputation: no visible binding for global variable ‘glm_dirichlet_multinomial_imputation’ draws_to_statistics: no visible binding for global variable ‘M’ draws_to_statistics: no visible binding for global variable ‘parameter’ draws_to_statistics: no visible binding for global variable ‘bigger_zero’ draws_to_statistics: no visible binding for global variable ‘smaller_zero’ draws_to_statistics: no visible binding for global variable ‘lower’ draws_to_statistics: no visible binding for global variable ‘effect’ draws_to_statistics: no visible binding for global variable ‘upper’ draws_to_statistics: no visible binding for global variable ‘pH0’ draws_to_statistics: no visible binding for global variable ‘FDR’ draws_to_statistics: no visible binding for global variable ‘n_eff’ draws_to_statistics: no visible binding for global variable ‘R_k_hat’ draws_to_tibble_x: no visible binding for global variable ‘.’ draws_to_tibble_x: no visible binding for global variable ‘dummy’ draws_to_tibble_x: no visible binding for global variable ‘.variable’ draws_to_tibble_x: no visible binding for global variable ‘.chain’ draws_to_tibble_x: no visible binding for global variable ‘.iteration’ draws_to_tibble_x: no visible binding for global variable ‘.draw’ draws_to_tibble_x: no visible binding for global variable ‘.value’ draws_to_tibble_x_y: no visible binding for global variable ‘.’ draws_to_tibble_x_y: no visible binding for global variable ‘dummy’ draws_to_tibble_x_y: no visible binding for global variable ‘.variable’ draws_to_tibble_x_y: no visible binding for global variable ‘.chain’ draws_to_tibble_x_y: no visible binding for global variable ‘.iteration’ draws_to_tibble_x_y: no visible binding for global variable ‘.draw’ draws_to_tibble_x_y: no visible binding for global variable ‘.value’ find_optimal_number_of_chains: no visible binding for global variable ‘chains’ find_optimal_number_of_chains: no visible binding for global variable ‘.’ fit_and_generate_quantities: no visible binding for global variable ‘N’ fit_and_generate_quantities: no visible binding for global variable ‘M’ fit_and_generate_quantities: no visible binding for global variable ‘precision’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘N’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘M’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘cores’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘additional_parameters_to_save’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘pass_fit’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘tol_rel_obj’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘glm_dirichlet_multinomial_generate_quantities’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.draw’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.chain’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.iteration’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.draw_imputation’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.variable’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘fit_list’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘n_eff’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘se_mean’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘sd’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘C_name’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.lower’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.median’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.upper’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘5%’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘95%’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘50%’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘precision’ fit_model_and_parse_out_no_missing_data: no visible binding for global variable ‘glm_dirichlet_multinomial_generate_quantities’ fit_to_counts_rng: no visible binding for global variable ‘.variable’ fit_to_counts_rng: no visible binding for global variable ‘S’ fit_to_counts_rng: no visible binding for global variable ‘G’ fit_to_counts_rng: no visible binding for global variable ‘.’ formula_to_random_effect_formulae: no visible binding for global variable ‘formula’ generate_quantities: no visible binding for global variable ‘N_M’ generate_quantities: no visible binding for global variable ‘generated_quantity’ generate_quantities: no visible binding for global variable ‘draw’ generate_quantities: no visible binding for global variable ‘N’ generate_quantities: no visible binding for global variable ‘M’ get_FDR: no visible binding for global variable ‘value’ get_FDR: no visible binding for global variable ‘name’ get_FDR: no visible binding for global variable ‘FDR’ get_abundance_contrast_draws: no visible binding for global variable ‘X’ get_abundance_contrast_draws: no visible binding for global variable ‘.value’ get_abundance_contrast_draws: no visible binding for global variable ‘.’ get_abundance_contrast_draws: no visible binding for global variable ‘N_random_intercepts’ get_abundance_contrast_draws: no visible binding for global variable ‘X_random_intercept’ get_abundance_contrast_draws: no visible binding for global variable ‘.variable’ get_abundance_contrast_draws: no visible binding for global variable ‘y’ get_abundance_contrast_draws: no visible binding for global variable ‘M’ get_abundance_contrast_draws: no visible binding for global variable ‘khat’ get_abundance_contrast_draws: no visible binding for global variable ‘parameter’ get_abundance_contrast_draws: no visible binding for global variable ‘n_eff’ get_abundance_contrast_draws: no visible binding for global variable ‘R_k_hat’ get_mean_precision: no visible binding for global variable ‘M’ get_mean_precision: no visible binding for global variable ‘2.5%’ get_mean_precision: no visible binding for global variable ‘97.5%’ get_mean_precision_association: no visible binding for global variable ‘.’ get_probability_non_zero: no visible binding for global variable ‘M’ get_probability_non_zero: no visible binding for global variable ‘C_name’ get_probability_non_zero: no visible binding for global variable ‘bigger_zero’ get_probability_non_zero: no visible binding for global variable ‘smaller_zero’ get_probability_non_zero_OLD: no visible binding for global variable ‘.’ get_probability_non_zero_OLD: no visible binding for global variable ‘.draw’ get_probability_non_zero_OLD: no visible binding for global variable ‘M’ get_probability_non_zero_OLD: no visible binding for global variable ‘C_name’ get_probability_non_zero_OLD: no visible binding for global variable ‘bigger_zero’ get_probability_non_zero_OLD: no visible binding for global variable ‘smaller_zero’ get_random_intercept_design: no visible binding for global variable ‘is_factor_continuous’ get_random_intercept_design: no visible binding for global variable ‘design’ get_random_intercept_design: no visible binding for global variable ‘max_mean_idx’ get_random_intercept_design: no visible binding for global variable ‘max_minus_sum’ get_random_intercept_design: no visible binding for global variable ‘max_factor_numeric’ get_random_intercept_design: no visible binding for global variable ‘max_group_numeric’ get_random_intercept_design: no visible binding for global variable ‘min_mean_idx’ get_random_intercept_design: no visible binding for global variable ‘min_minus_sum’ get_random_intercept_design2: no visible binding for global variable ‘formula’ get_variability_contrast_draws: no visible binding for global variable ‘XA’ get_variability_contrast_draws: no visible binding for global variable ‘.value’ get_variability_contrast_draws: no visible binding for global variable ‘.’ get_variability_contrast_draws: no visible binding for global variable ‘.variable’ get_variability_contrast_draws: no visible binding for global variable ‘y’ get_variability_contrast_draws: no visible binding for global variable ‘M’ get_variability_contrast_draws: no visible binding for global variable ‘khat’ get_variability_contrast_draws: no visible binding for global variable ‘parameter’ get_variability_contrast_draws: no visible binding for global variable ‘n_eff’ get_variability_contrast_draws: no visible binding for global variable ‘R_k_hat’ glm_multi_beta: no visible binding for global variable ‘.’ label_deleterious_outliers: no visible binding for global variable ‘.count’ label_deleterious_outliers: no visible binding for global variable ‘95%’ label_deleterious_outliers: no visible binding for global variable ‘5%’ label_deleterious_outliers: no visible binding for global variable ‘X’ label_deleterious_outliers: no visible binding for global variable ‘iteration’ label_deleterious_outliers: no visible binding for global variable ‘outlier_above’ label_deleterious_outliers: no visible binding for global variable ‘slope’ label_deleterious_outliers: no visible binding for global variable ‘is_group_right’ label_deleterious_outliers: no visible binding for global variable ‘outlier_below’ multi_beta_glm: no visible global function definition for ‘detect_cores’ parse_fit: no visible binding for global variable ‘M’ parse_formula: no visible binding for global variable ‘.’ parse_formula_random_intercept: no visible binding for global variable ‘formula’ parse_generated_quantities: no visible binding for global variable ‘.draw’ parse_generated_quantities: no visible binding for global variable ‘N’ parse_generated_quantities: no visible binding for global variable ‘.value’ parse_generated_quantities: no visible binding for global variable ‘generated_counts’ parse_generated_quantities: no visible binding for global variable ‘M’ parse_generated_quantities: no visible binding for global variable ‘generated_proportions’ plot.sccomp_tbl: no visible binding for global variable ‘parameter’ plot.sccomp_tbl: no visible binding for global variable ‘count_data’ plot.sccomp_tbl: no visible binding for global variable ‘multipanel_theme’ plot.sccomp_tbl: no visible binding for global variable ‘v_effect’ plot_1d_intervals: no visible binding for global variable ‘parameter’ plot_1d_intervals: no visible binding for global variable ‘estimate’ plot_1d_intervals: no visible binding for global variable ‘value’ plot_2d_intervals: no visible binding for global variable ‘v_effect’ plot_2d_intervals: no visible binding for global variable ‘parameter’ plot_2d_intervals: no visible binding for global variable ‘.’ plot_2d_intervals: no visible binding for global variable ‘c_effect’ plot_2d_intervals: no visible binding for global variable ‘c_lower’ plot_2d_intervals: no visible binding for global variable ‘c_upper’ plot_2d_intervals: no visible binding for global variable ‘c_FDR’ plot_2d_intervals: no visible binding for global variable ‘v_lower’ plot_2d_intervals: no visible binding for global variable ‘v_upper’ plot_2d_intervals: no visible binding for global variable ‘v_FDR’ plot_2d_intervals: no visible binding for global variable ‘cell_type_label’ plot_boxplot: no visible binding for global variable ‘stats_name’ plot_boxplot: no visible binding for global variable ‘parameter’ plot_boxplot: no visible binding for global variable ‘stats_value’ plot_boxplot: no visible binding for global variable ‘count_data’ plot_boxplot: no visible binding for global variable ‘generated_proportions’ plot_boxplot: no visible binding for global variable ‘proportion’ plot_boxplot: no visible binding for global variable ‘name’ plot_boxplot: no visible binding for global variable ‘outlier’ plot_scatterplot: no visible binding for global variable ‘stats_name’ plot_scatterplot: no visible binding for global variable ‘parameter’ plot_scatterplot: no visible binding for global variable ‘stats_value’ plot_scatterplot: no visible binding for global variable ‘count_data’ plot_scatterplot: no visible binding for global variable ‘generated_proportions’ plot_scatterplot: no visible binding for global variable ‘proportion’ plot_scatterplot: no visible binding for global variable ‘name’ plot_scatterplot: no visible binding for global variable ‘outlier’ replicate_data: no visible binding for global variable ‘glm_dirichlet_multinomial_generate_quantities’ replicate_data: no visible binding for global variable ‘count_data’ replicate_data: no visible binding for global variable ‘exposure’ replicate_data: no visible binding for global variable ‘dummy’ replicate_data: no visible global function definition for ‘tail’ replicate_data: no visible global function definition for ‘as.formula’ replicate_data: no visible binding for global variable ‘.’ replicate_data: no visible global function definition for ‘na.omit’ replicate_data: no visible binding for global variable ‘Xa’ replicate_data: no visible binding for global variable ‘intercept_in_design’ replicate_data: no visible binding for global variable ‘design’ replicate_data: no visible binding for global variable ‘design_matrix’ replicate_data: no visible binding for global variable ‘X_random_intercept’ sccomp_boxplot: no visible binding for global variable ‘parameter’ sccomp_boxplot: no visible binding for global variable ‘count_data’ sccomp_boxplot: no visible binding for global variable ‘multipanel_theme’ sccomp_boxplot: no visible binding for global variable ‘.x’ sccomp_glm_data_frame_counts: no visible binding for global variable ‘N’ sccomp_glm_data_frame_counts: no visible binding for global variable ‘M’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘count_data’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘M’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘N’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘2.5%’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘97.5%’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘count_data’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘N’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘M’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘5%’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘95%’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘truncation_up’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘truncation_down’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘.lower’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘.’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘50%’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘.upper’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘proportion_mean’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘y’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘observed_proportion’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘logit_residuals’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘exposure’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘adjusted_proportion’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘adjusted_counts’ sccomp_replicate.sccomp_tbl: no visible binding for global variable ‘N’ sccomp_replicate.sccomp_tbl: no visible binding for global variable ‘M’ sccomp_test.sccomp_tbl: no visible binding for global variable ‘design_matrix_col’ sccomp_test.sccomp_tbl: no visible binding for global variable ‘parameter’ sccomp_test.sccomp_tbl: no visible binding for global variable ‘M’ simulate_data.tbl: no visible binding for global variable ‘glm_dirichlet_multinomial_generate_quantities’ simulate_data.tbl: no visible binding for global variable ‘data___’ simulate_data.tbl: no visible binding for global variable ‘.exposure’ simulate_data.tbl: no visible binding for global variable ‘N’ simulate_data.tbl: no visible binding for global variable ‘M’ simulate_multinomial_logit_linear: no visible global function definition for ‘rnorm’ summary_to_tibble: no visible binding for global variable ‘.’ summary_to_tibble: no visible binding for global variable ‘.variable’ Undefined global functions or variables: . .chain .count .draw .draw_imputation .exposure .iteration .lower .median .upper .value .variable .x 2.5% 5% 50% 95% 97.5% C_name FDR G M N N_M N_random_intercepts R_k_hat S X XA X_random_intercept Xa additional_parameters_to_save adjusted_counts adjusted_proportion as.formula beta_1 beta_2 bigger_zero c_FDR c_effect c_lower c_upper cell_type cell_type_label censoring_iteration chains cores count_data data___ design design_matrix design_matrix_col detect_cores draw dummy effect estimate exposure factor_1 factor___numeric factors fit_list formula generated_counts generated_proportions generated_quantity glm_dirichlet_multinomial glm_dirichlet_multinomial_generate_quantities glm_dirichlet_multinomial_imputation group___label group___numeric groupings idx intercept_in_design is_factor_continuous is_group_right iteration khat logit_residuals lower mat max_factor_numeric max_group_numeric max_mean_idx max_minus_sum mean_idx min_mean_idx min_minus_sum minus_sum multipanel_theme n_eff na.omit name observed_proportion outlier outlier_above outlier_below pH0 parameter pass_fit ppc precision proportion proportion_mean rnorm sd se_mean slope smaller_zero stats_name stats_value tail tol_rel_obj truncation_down truncation_up upper v_FDR v_effect v_lower v_upper value variable y Consider adding importFrom("stats", "as.formula", "formula", "na.omit", "rnorm", "sd") importFrom("utils", "tail") to your NAMESPACE file. * checking Rd files ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sccomp_remove_outliers 343.724 18.687 554.347 sccomp_boxplot 50.483 1.814 98.198 test_contrasts 49.816 2.038 72.847 sccomp_estimate 49.534 1.478 81.536 sccomp_test 48.574 1.868 70.841 sccomp_glm 47.806 1.275 71.492 sccomp_remove_unwanted_variation 31.137 3.437 57.102 simulate_data 26.408 2.399 40.570 sccomp_predict 26.760 1.929 44.469 plot.sccomp_tbl 24.153 1.990 46.289 plot_summary 21.606 1.939 45.644 sccomp_replicate 20.693 1.792 36.512 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’
sccomp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sccomp ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘sccomp’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:28: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:28: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:28: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:28: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:28: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:28: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:28: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:28: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:28: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:36: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ 17 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_glm_multi_beta_binomial.cc -o stanExports_glm_multi_beta_binomial.o In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, const int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'const int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, const int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'const int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:36: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: ./stanExports_glm_multi_beta_binomial.h:546:9: warning: variable 'rows_X' set but not used [-Wunused-but-set-variable] int rows_X = std::numeric_limits<int>::min(); ^ ./stanExports_glm_multi_beta_binomial.h:2339:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 24 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_glm_multi_beta_binomial_generate_date.cc -o stanExports_glm_multi_beta_binomial_generate_date.o In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, const int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'const int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, const int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'const int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:36: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: ./stanExports_glm_multi_beta_binomial_generate_date.h:574:20: warning: unused variable 'jacobian__' [-Wunused-variable] constexpr bool jacobian__ = false; ^ ./stanExports_glm_multi_beta_binomial_generate_date.h:789:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 24 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_glm_multi_beta_binomial_simulate_data.cc -o stanExports_glm_multi_beta_binomial_simulate_data.o In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, const int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'const int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, const int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'const int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:36: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: ./stanExports_glm_multi_beta_binomial_simulate_data.h:534:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits<int>::min(); ^ ./stanExports_glm_multi_beta_binomial_simulate_data.h:568:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 24 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o sccomp.so RcppExports.o stanExports_glm_multi_beta_binomial.o stanExports_glm_multi_beta_binomial_generate_date.o stanExports_glm_multi_beta_binomial_simulate_data.o -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-sccomp/00new/sccomp/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sccomp)
sccomp.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(sccomp) > > test_check("sccomp") Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union sccomp says: estimation sccomp says: the composition design matrix has columns: typecancer, typehealthy sccomp says: the variability design matrix has columns: typecancer, typehealthy sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. sccomp says: outlier identification - step 1/2 sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. sccomp says: outlier-free model fitting - step 2/2 sccomp says: the composition design matrix has columns: typecancer, typehealthy sccomp says: the variability design matrix has columns: typecancer, typehealthy sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. sccomp says: calculating residuals sccomp says: regressing out unwanted factors cell_group parameter factor c_lower 1 B immature typecancer - typehealthy type -2.012895186 2 B immature typehealthy - typecancer type 0.924450420 3 B mem typecancer - typehealthy type -2.532439962 4 B mem typehealthy - typecancer type 1.040488015 5 CD4 cm S100A4 typecancer - typehealthy type -1.230736964 6 CD4 cm S100A4 typehealthy - typecancer type 0.456930775 7 CD4 cm high cytokine typecancer - typehealthy type 0.780883472 8 CD4 cm high cytokine typehealthy - typecancer type -3.198938201 9 CD4 cm ribosome typecancer - typehealthy type 0.320303625 10 CD4 cm ribosome typehealthy - typecancer type -1.804880631 11 CD4 em high cytokine typecancer - typehealthy type 0.279541279 12 CD4 em high cytokine typehealthy - typecancer type -2.214204883 13 CD4 naive typecancer - typehealthy type -1.321905058 14 CD4 naive typehealthy - typecancer type 0.247369316 15 CD4 ribosome typecancer - typehealthy type -2.605779590 16 CD4 ribosome typehealthy - typecancer type 1.448814089 17 CD8 em 1 typecancer - typehealthy type -0.851302992 18 CD8 em 1 typehealthy - typecancer type -0.445601395 19 CD8 em 2 typecancer - typehealthy type -1.087623898 20 CD8 em 2 typehealthy - typecancer type -1.317616272 21 CD8 em 3 typecancer - typehealthy type -1.631846282 22 CD8 em 3 typehealthy - typecancer type 0.003498518 23 CD8 naive typecancer - typehealthy type -0.454535717 24 CD8 naive typehealthy - typecancer type -0.788085494 25 CD8 transitional typecancer - typehealthy type -1.242591173 26 CD8 transitional typehealthy - typecancer type 0.204540584 27 MAIT typecancer - typehealthy type -1.875117011 28 MAIT typehealthy - typecancer type 0.482738863 29 Mac M1 typecancer - typehealthy type -1.132150422 30 Mac M1 typehealthy - typecancer type 0.071038090 31 Mac M1 FCER1A typecancer - typehealthy type 0.111760271 32 Mac M1 FCER1A typehealthy - typecancer type -1.769711647 33 Mono typecancer - typehealthy type -0.687142859 34 Mono typehealthy - typecancer type -0.828240074 35 Mono NKG7 1 typecancer - typehealthy type 0.472070419 36 Mono NKG7 1 typehealthy - typecancer type -2.976122145 37 Mono NKG7 2 typecancer - typehealthy type 0.597130488 38 Mono NKG7 2 typehealthy - typecancer type -2.389287253 39 Mono classic inflam typecancer - typehealthy type -0.030193767 40 Mono classic inflam typehealthy - typecancer type -1.235373470 41 Mono non-classic typecancer - typehealthy type -0.580501284 42 Mono non-classic typehealthy - typecancer type -0.621529833 43 Myeloid migratory typecancer - typehealthy type -0.132058557 44 Myeloid migratory typehealthy - typecancer type -1.356911630 45 NK typecancer - typehealthy type -1.241175902 46 NK typehealthy - typecancer type 0.253836144 47 NK cycling typecancer - typehealthy type -0.550919937 48 NK cycling typehealthy - typecancer type -0.895221188 49 NK high cytokine typecancer - typehealthy type -0.883939059 50 NK high cytokine typehealthy - typecancer type -1.296626146 51 Stem typecancer - typehealthy type 0.970251259 52 Stem typehealthy - typecancer type -2.920112149 53 T gd1 typecancer - typehealthy type -1.641005700 54 T gd1 typehealthy - typecancer type 0.055959802 55 T gd2 typecancer - typehealthy type -1.150228692 56 T gd2 typehealthy - typecancer type -0.389995310 57 cDC2 typecancer - typehealthy type -1.019267934 58 cDC2 typehealthy - typecancer type -0.421297750 59 pDC typecancer - typehealthy type -0.777859656 60 pDC typehealthy - typecancer type -0.619000279 c_effect c_upper c_pH0 c_FDR c_n_eff c_R_k_hat v_lower 1 -1.48138681 -0.924450420 0.000 0.0000000000 NA NA -0.6674120 2 1.48138681 2.012895186 0.000 0.0000000000 NA NA -1.1487536 3 -1.82337098 -1.040488015 0.000 0.0000000000 NA NA -0.2804766 4 1.82337098 2.532439962 0.000 0.0000000000 NA NA -1.5156986 5 -0.84283052 -0.456930775 0.001 0.0002500000 NA NA -1.2397154 6 0.84283052 1.230736964 0.001 0.0002500000 NA NA -0.8833201 7 2.00827191 3.198938201 0.007 0.0020000000 NA NA -1.5096608 8 -2.00827191 -0.780883472 0.007 0.0020000000 NA NA -0.6920000 9 1.09819791 1.804880631 0.012 0.0035000000 NA NA -1.4324200 10 -1.09819791 -0.320303625 0.012 0.0035000000 NA NA -0.4525842 11 1.33737688 2.214204883 0.020 0.0060000000 NA NA -1.2662642 12 -1.33737688 -0.279541279 0.020 0.0060000000 NA NA -0.7456472 13 -0.76169824 -0.247369316 0.022 0.0072307692 NA NA -0.9329118 14 0.76169824 1.321905058 0.022 0.0072307692 NA NA -0.8366409 15 -2.06589774 -1.448814089 0.000 0.0000000000 NA NA -1.2824474 16 2.06589774 2.605779590 0.000 0.0000000000 NA NA -0.6753537 17 -0.20210772 0.445601395 0.494 0.0933333333 NA NA -1.1041548 18 0.20210772 0.851302992 0.494 0.0933333333 NA NA -0.6661482 19 0.17144481 1.317616272 0.515 0.1250769231 NA NA -2.0440712 20 -0.17144481 1.087623898 0.515 0.1250769231 NA NA -0.4459925 21 -0.80061273 -0.003498518 0.065 0.0154705882 NA NA -0.9562369 22 0.80061273 1.631846282 0.065 0.0154705882 NA NA -1.1887174 23 0.20157513 0.788085494 0.497 0.1094800000 NA NA -1.6481739 24 -0.20157513 0.454535717 0.497 0.1094800000 NA NA -0.3724950 25 -0.68481784 -0.204540584 0.025 0.0085000000 NA NA -1.1701626 26 0.68481784 1.242591173 0.025 0.0085000000 NA NA -0.8061548 27 -1.13774742 -0.482738863 0.003 0.0008333333 NA NA -1.0673749 28 1.13774742 1.875117011 0.003 0.0008333333 NA NA -0.7656702 29 -0.59240836 -0.071038090 0.066 0.0182777778 NA NA -1.3537718 30 0.59240836 1.132150422 0.066 0.0182777778 NA NA -0.5847038 31 0.98329578 1.769711647 0.034 0.0102000000 NA NA -1.4923917 32 -0.98329578 -0.111760271 0.034 0.0102000000 NA NA -0.7368962 33 0.04735167 0.828240074 0.642 0.1747241379 NA NA -0.9094969 34 -0.04735167 0.687142859 0.642 0.1747241379 NA NA -1.1681687 35 1.76668359 2.976122145 0.007 0.0025555556 NA NA -0.9241161 36 -1.76668359 -0.472070419 0.007 0.0025555556 NA NA -1.5123042 37 1.53242231 2.389287253 0.004 0.0012857143 NA NA -1.8702867 38 -1.53242231 -0.597130488 0.004 0.0012857143 NA NA -0.2272445 39 0.61281800 1.235373470 0.105 0.0228421053 NA NA -1.7432768 40 -0.61281800 0.030193767 0.105 0.0228421053 NA NA -0.1770058 41 0.04929189 0.621529833 0.686 0.1917666667 NA NA -1.1663423 42 -0.04929189 0.580501284 0.686 0.1917666667 NA NA -0.6892361 43 0.60242695 1.356911630 0.127 0.0280500000 NA NA -1.4721079 44 -0.60242695 0.132058557 0.127 0.0280500000 NA NA -0.5281977 45 -0.73156223 -0.253836144 0.017 0.0047272727 NA NA -1.1098315 46 0.73156223 1.241175902 0.017 0.0047272727 NA NA -0.8969748 47 0.17169868 0.895221188 0.540 0.1404444444 NA NA -0.7836668 48 -0.17169868 0.550919937 0.540 0.1404444444 NA NA -1.4245593 49 0.25185849 1.296626146 0.463 0.0759130435 NA NA -1.3706085 50 -0.25185849 0.883939059 0.463 0.0759130435 NA NA -0.8139730 51 2.06233859 2.920112149 0.001 0.0004000000 NA NA -0.6971803 52 -2.06233859 -0.970251259 0.001 0.0004000000 NA NA -1.3521384 53 -0.81466664 -0.055959802 0.045 0.0123750000 NA NA -2.1498623 54 0.81466664 1.641005700 0.045 0.0123750000 NA NA -0.1385734 55 -0.38786752 0.389995310 0.322 0.0420476190 NA NA -0.5999218 56 0.38786752 1.150228692 0.322 0.0420476190 NA NA -1.3087391 57 -0.28157337 0.421297750 0.400 0.0583181818 NA NA -0.6724976 58 0.28157337 1.019267934 0.400 0.0583181818 NA NA -1.3228603 59 -0.08632541 0.619000279 0.633 0.1580357143 NA NA -0.3484608 60 0.08632541 0.777859656 0.633 0.1580357143 NA NA -1.8042943 v_effect v_upper v_pH0 v_FDR v_n_eff v_R_k_hat count_data 1 0.2557548 1.1487536 0.455 0.3001111 NA NA c("10x_6.... 2 -0.2557548 0.6674120 0.455 0.3001111 NA NA c("10x_6.... 3 0.6074578 1.5156986 0.188 0.1444000 NA NA c("10x_6.... 4 -0.6074578 0.2804766 0.188 0.1444000 NA NA c("10x_6.... 5 -0.1226882 0.8833201 0.566 0.3801034 NA NA c("10x_6.... 6 0.1226882 1.2397154 0.566 0.3801034 NA NA c("10x_6.... 7 -0.3652498 0.6920000 0.394 0.2367500 NA NA c("10x_6.... 8 0.3652498 1.5096608 0.394 0.2367500 NA NA c("10x_6.... 9 -0.4615031 0.4525842 0.300 0.1783750 NA NA c("10x_6.... 10 0.4615031 1.4324200 0.300 0.1783750 NA NA c("10x_6.... 11 -0.2358950 0.7456472 0.469 0.3293182 NA NA c("10x_6.... 12 0.2358950 1.2662642 0.469 0.3293182 NA NA c("10x_6.... 13 -0.0691784 0.8366409 0.609 0.3877333 NA NA c("10x_6.... 14 0.0691784 0.9329118 0.609 0.3877333 NA NA c("10x_6.... 15 -0.2990853 0.6753537 0.425 0.2823125 NA NA c("10x_6.... 16 0.2990853 1.2824474 0.425 0.2823125 NA NA c("10x_6.... 17 -0.2538093 0.6661482 0.457 0.3157500 NA NA c("10x_6.... 18 0.2538093 1.1041548 0.457 0.3157500 NA NA c("10x_6.... 19 -0.6713452 0.4459925 0.198 0.1533333 NA NA c("10x_6.... 20 0.6713452 2.0440712 0.198 0.1533333 NA NA c("10x_6.... 21 0.1631197 1.1887174 0.523 0.3447917 NA NA c("10x_6.... 22 -0.1631197 0.9562369 0.523 0.3447917 NA NA c("10x_6.... 23 -0.6030300 0.3724950 0.207 0.1610000 NA NA c("10x_6.... 24 0.6030300 1.6481739 0.207 0.1610000 NA NA c("10x_6.... 25 -0.1930191 0.8061548 0.507 0.3370435 NA NA c("10x_6.... 26 0.1930191 1.1701626 0.507 0.3370435 NA NA c("10x_6.... 27 -0.1411265 0.7656702 0.551 0.3667778 NA NA c("10x_6.... 28 0.1411265 1.0673749 0.551 0.3667778 NA NA c("10x_6.... 29 -0.3768545 0.5847038 0.348 0.2094000 NA NA c("10x_6.... 30 0.3768545 1.3537718 0.348 0.2094000 NA NA c("10x_6.... 31 -0.3243464 0.7368962 0.430 0.2910000 NA NA c("10x_6.... 32 0.3243464 1.4923917 0.430 0.2910000 NA NA c("10x_6.... 33 0.1541852 1.1681687 0.541 0.3596923 NA NA c("10x_6.... 34 -0.1541852 0.9094969 0.541 0.3596923 NA NA c("10x_6.... 35 0.2606584 1.5123042 0.456 0.3083158 NA NA c("10x_6.... 36 -0.2606584 0.9241161 0.456 0.3083158 NA NA c("10x_6.... 37 -0.8044376 0.2272445 0.137 0.1203333 NA NA c("10x_6.... 38 0.8044376 1.8702867 0.137 0.1203333 NA NA c("10x_6.... 39 -0.7694848 0.1770058 0.130 0.1120000 NA NA c("10x_6.... 40 0.7694848 1.7432768 0.130 0.1120000 NA NA c("10x_6.... 41 -0.1639814 0.6892361 0.536 0.3524400 NA NA c("10x_6.... 42 0.1639814 1.1663423 0.536 0.3524400 NA NA c("10x_6.... 43 -0.4517474 0.5281977 0.319 0.1940000 NA NA c("10x_6.... 44 0.4517474 1.4721079 0.319 0.1940000 NA NA c("10x_6.... 45 -0.1415536 0.8969748 0.554 0.3734643 NA NA c("10x_6.... 46 0.1415536 1.1098315 0.554 0.3734643 NA NA c("10x_6.... 47 0.3281948 1.4245593 0.417 0.2622143 NA NA c("10x_6.... 48 -0.3281948 0.7836668 0.417 0.2622143 NA NA c("10x_6.... 49 -0.2453478 0.8139730 0.461 0.3226667 NA NA c("10x_6.... 50 0.2453478 1.3706085 0.461 0.3226667 NA NA c("10x_6.... 51 0.3324718 1.3521384 0.413 0.2503077 NA NA c("10x_6.... 52 -0.3324718 0.6971803 0.413 0.2503077 NA NA c("10x_6.... 53 -0.9872568 0.1385734 0.094 0.0940000 NA NA c("10x_6.... 54 0.9872568 2.1498623 0.094 0.0940000 NA NA c("10x_6.... 55 0.3664687 1.3087391 0.353 0.2224545 NA NA c("10x_6.... 56 -0.3664687 0.5999218 0.353 0.2224545 NA NA c("10x_6.... 57 0.3112169 1.3228603 0.421 0.2728000 NA NA c("10x_6.... 58 -0.3112169 0.6724976 0.421 0.2728000 NA NA c("10x_6.... 59 0.6500937 1.8042943 0.173 0.1335000 NA NA c("10x_6.... 60 -0.6500937 0.3484608 0.173 0.1335000 NA NA c("10x_6.... sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), continuous_covariate, typehealthy, continuous_covariate:typehealthy sccomp says: the variability design matrix has columns: (Intercept) sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000517 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 5.17 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup) Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling) Chain 1: Iteration: 1300 / 1300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 7.763 seconds (Warm-up) Chain 1: 18.266 seconds (Sampling) Chain 1: 26.029 seconds (Total) Chain 1: sccomp says: estimation sccomp says: the composition design matrix has columns: typecancer, typehealthy, continuous_covariate sccomp says: the variability design matrix has columns: (Intercept) sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000453 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.53 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup) Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling) Chain 1: Iteration: 1300 / 1300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 6.253 seconds (Warm-up) Chain 1: 11.389 seconds (Sampling) Chain 1: 17.642 seconds (Total) Chain 1: sccomp says: estimation sccomp says: the composition design matrix has columns: typecancer, typehealthy sccomp says: the variability design matrix has columns: (Intercept) sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000994 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 9.94 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup) Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling) Chain 1: Iteration: 1300 / 1300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 9.61 seconds (Warm-up) Chain 1: 19.825 seconds (Sampling) Chain 1: 29.435 seconds (Total) Chain 1: sccomp says: outlier identification - step 1/2 sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.001733 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 17.33 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup) Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling) Chain 1: Iteration: 1300 / 1300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 7.082 seconds (Warm-up) Chain 1: 12.322 seconds (Sampling) Chain 1: 19.404 seconds (Total) Chain 1: sccomp says: outlier-free model fitting - step 2/2 sccomp says: the composition design matrix has columns: (Intercept), continuous_covariate, typehealthy, continuous_covariate:typehealthy sccomp says: the variability design matrix has columns: (Intercept) sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000655 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.55 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup) Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling) Chain 1: Iteration: 1300 / 1300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 7.109 seconds (Warm-up) Chain 1: 11.785 seconds (Sampling) Chain 1: 18.894 seconds (Total) Chain 1: sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), typehealthy sccomp says: the variability design matrix has columns: (Intercept) sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000904 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 9.04 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup) Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling) Chain 1: Iteration: 1300 / 1300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 12.291 seconds (Warm-up) Chain 1: 27.271 seconds (Sampling) Chain 1: 39.562 seconds (Total) Chain 1: sccomp says: estimation sccomp says: the composition design matrix has columns: typecancer, typehealthy sccomp says: the variability design matrix has columns: (Intercept) sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000577 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 5.77 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup) Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling) Chain 1: Iteration: 1300 / 1300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 10.037 seconds (Warm-up) Chain 1: 18.583 seconds (Sampling) Chain 1: 28.62 seconds (Total) Chain 1: sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), continuous_covariate sccomp says: the variability design matrix has columns: (Intercept) sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000617 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.17 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup) Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling) Chain 1: Iteration: 1300 / 1300 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 13.795 seconds (Warm-up) Chain 1: 50.515 seconds (Sampling) Chain 1: 64.31 seconds (Total) Chain 1: Loading required package: ttservice Attaching package: 'ttservice' The following objects are masked from 'package:dplyr': bind_cols, bind_rows Loading required package: SeuratObject Loading required package: sp Attaching package: 'SeuratObject' The following object is masked from 'package:base': intersect ======================================== tidyseurat version 0.8.0 If you use TIDYSEURAT in published research, please cite: Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021. This message can be suppressed by: suppressPackageStartupMessages(library(tidyseurat)) To restore the Seurat default display use options("restore_Seurat_show" = TRUE) ======================================== Attaching package: 'tidyseurat' The following object is masked from 'package:ttservice': plot_ly sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), typehealthy, batch sccomp says: the variability design matrix has columns: (Intercept) sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. Chain 1: ------------------------------------------------------------ Chain 1: EXPERIMENTAL ALGORITHM: Chain 1: This procedure has not been thoroughly tested and may be unstable Chain 1: or buggy. The interface is subject to change. Chain 1: ------------------------------------------------------------ Chain 1: Chain 1: Chain 1: Chain 1: Gradient evaluation took 0.000612 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.12 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Begin eta adaptation. Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation) Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation) Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation) Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation) Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation) Chain 1: Success! Found best value [eta = 1] earlier than expected. Chain 1: Chain 1: Begin stochastic gradient ascent. Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes Chain 1: 100 -3250.691 1.000 1.000 Chain 1: 200 -3210.906 0.506 1.000 Chain 1: 300 -3201.548 0.338 0.012 Chain 1: 400 -3196.916 0.254 0.012 Chain 1: 500 -3199.336 0.204 0.003 MEDIAN ELBO CONVERGED Chain 1: Chain 1: Drawing a sample of size 1000 from the approximate posterior... Chain 1: COMPLETED. sccomp says: calculating residuals sccomp says: regressing out unwanted factors sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), typehealthy sccomp says: the variability design matrix has columns: (Intercept) sccomp says: the number of draws used to defined quantiles of the posterior distribution is capped to 20K. Chain 1: ------------------------------------------------------------ Chain 1: EXPERIMENTAL ALGORITHM: Chain 1: This procedure has not been thoroughly tested and may be unstable Chain 1: or buggy. The interface is subject to change. Chain 1: ------------------------------------------------------------ Chain 1: Chain 1: Chain 1: Chain 1: Gradient evaluation took 0.000446 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.46 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Begin eta adaptation. Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation) Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation) Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation) Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation) Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation) Chain 1: Success! Found best value [eta = 1] earlier than expected. Chain 1: Chain 1: Begin stochastic gradient ascent. Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes Chain 1: 100 -3413.749 1.000 1.000 Chain 1: 200 -3158.083 0.540 1.000 Chain 1: 300 -3152.839 0.361 0.081 Chain 1: 400 -3149.457 0.271 0.081 Chain 1: 500 -3147.490 0.217 0.002 MEDIAN ELBO CONVERGED Chain 1: Chain 1: Drawing a sample of size 1000 from the approximate posterior... Chain 1: COMPLETED.
sccomp.Rcheck/sccomp-Ex.timings
name | user | system | elapsed | |
plot.sccomp_tbl | 24.153 | 1.990 | 46.289 | |
plot_summary | 21.606 | 1.939 | 45.644 | |
sccomp_boxplot | 50.483 | 1.814 | 98.198 | |
sccomp_estimate | 49.534 | 1.478 | 81.536 | |
sccomp_glm | 47.806 | 1.275 | 71.492 | |
sccomp_predict | 26.760 | 1.929 | 44.469 | |
sccomp_remove_outliers | 343.724 | 18.687 | 554.347 | |
sccomp_remove_unwanted_variation | 31.137 | 3.437 | 57.102 | |
sccomp_replicate | 20.693 | 1.792 | 36.512 | |
sccomp_test | 48.574 | 1.868 | 70.841 | |
simulate_data | 26.408 | 2.399 | 40.570 | |
test_contrasts | 49.816 | 2.038 | 72.847 | |