Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-10-24 11:41:29 -0400 (Tue, 24 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4724 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4459 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4473 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4461 |
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 1862/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sccomp 1.5.1 (landing page) Stefano Mangiola
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.3.1 Ventura / arm64 | see weekly results here | ||||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: sccomp |
Version: 1.5.1 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:sccomp.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings sccomp_1.5.1.tar.gz |
StartedAt: 2023-10-24 12:28:38 -0000 (Tue, 24 Oct 2023) |
EndedAt: 2023-10-24 13:07:34 -0000 (Tue, 24 Oct 2023) |
EllapsedTime: 2336.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sccomp.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:sccomp.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings sccomp_1.5.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sccomp.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * checking for file ‘sccomp/DESCRIPTION’ ... OK * this is package ‘sccomp’ version ‘1.5.1’ * 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: ‘g++ (GCC) 10.3.1’ * checking C++ specification ... OK Not all R platforms support C++17 * checking installed package size ... NOTE installed size is 135.7Mb sub-directories of 1Mb or more: data 1.1Mb libs 133.1Mb * 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 loading without being on the library search path ... 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_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 ‘is_factor_continuous’ data_spread_to_model_input: no visible binding for global variable ‘design_matrix’ data_spread_to_model_input: no visible binding for global variable ‘.’ data_spread_to_model_input: no visible binding for global variable ‘minus_sum’ data_spread_to_model_input: no visible binding for global variable ‘mean_idx’ 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’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘N’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘M’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘5%’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘95%’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘truncation_up’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘truncation_down’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘.lower’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘.’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘50%’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘.upper’ 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: no visible binding for global variable ‘.’ 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 ‘.’ 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 ‘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_design_matrix: no visible binding for global variable ‘.’ 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_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 ‘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 global function definition for ‘terms’ parse_formula: no visible binding for global variable ‘.’ parse_formula_random_intercept: no visible global function definition for ‘terms’ 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_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_summary: no visible binding for global variable ‘parameter’ plot_summary: no visible binding for global variable ‘count_data’ plot_summary: no visible binding for global variable ‘v_effect’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘proportion_mean’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘y’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘observed_proportion’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘logit_residuals’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘exposure’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘adjusted_proportion’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘adjusted_counts’ replicate_data: no visible binding for global variable ‘count_data’ replicate_data: no visible binding for global variable ‘exposure’ 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 ‘is_factor_continuous’ replicate_data: no visible binding for global variable ‘design_matrix’ replicate_data: no visible binding for global variable ‘X_random_intercept’ sccomp_predict.data.frame: no visible binding for global variable ‘count_data’ sccomp_predict.data.frame: no visible binding for global variable ‘M’ sccomp_predict.data.frame: no visible binding for global variable ‘N’ sccomp_predict.data.frame: no visible binding for global variable ‘2.5%’ sccomp_predict.data.frame: no visible binding for global variable ‘97.5%’ sccomp_replicate.data.frame: no visible binding for global variable ‘N’ sccomp_replicate.data.frame: no visible binding for global variable ‘M’ simulate_data.data.frame: no visible binding for global variable ‘data___’ simulate_data.data.frame: no visible binding for global variable ‘.exposure’ simulate_data.data.frame: no visible binding for global variable ‘N’ simulate_data.data.frame: 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’ test_contrasts.data.frame: no visible binding for global variable ‘design_matrix_col’ test_contrasts.data.frame: no visible binding for global variable ‘parameter’ test_contrasts.data.frame: no visible binding for global variable ‘M’ test_contrasts.data.frame: no visible binding for global variable ‘N’ test_contrasts.data.frame: no visible binding for global variable ‘.variable’ test_contrasts.data.frame: no visible binding for global variable ‘se_mean’ test_contrasts.data.frame: no visible binding for global variable ‘sd’ test_contrasts.data.frame: no visible binding for global variable ‘n_eff’ Undefined global functions or variables: . .chain .count .draw .draw_imputation .exposure .iteration .lower .median .upper .value .variable 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 factors fit_list 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 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 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 terms 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", "na.omit", "rnorm", "sd", "terms") 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 test_contrasts 56.108 0.220 56.435 sccomp_glm 53.647 0.147 53.905 remove_unwanted_variation 43.071 0.535 43.678 simulate_data 41.156 0.415 41.646 sccomp_predict 38.114 0.543 38.735 plot_summary 34.856 0.663 35.625 sccomp_replicate 33.404 0.336 33.808 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘introduction.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/sccomp.Rcheck/00check.log’ for details.
sccomp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL sccomp ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘sccomp’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-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'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-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'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_glm_multi_beta_binomial.cc -o stanExports_glm_multi_beta_binomial.o In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/callbacks/writer.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/filtered_values.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:110, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp: In function ‘Eigen::Matrix<typename stan::value_type<T>::type, EigMat::ColsAtCompileTime, EigMat::RowsAtCompileTime> stan::math::generalized_inverse(const EigMat&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp:34:9: warning: typedef ‘using value_t = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs] 34 | using value_t = value_type_t<EigMat>; | ^~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:319, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/tail.hpp: In function ‘std::vector<T> stan::math::tail(const std::vector<T>&, size_t)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/tail.hpp:46:9: warning: typedef ‘using idx_t = stan::math::index_type_t<std::vector<T> >’ locally defined but not used [-Wunused-local-typedefs] 46 | using idx_t = index_type_t<std::vector<T>>; | ^~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/include/make_fused.hpp:11, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp: At global scope: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::bernoulli_logit_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp:59:9: warning: typedef ‘using T_y_val = std::conditional_t<stan::is_vector<T2>::value, Eigen::Matrix<typename stan::partials_return_type<T_y>::type, -1, 1>, typename stan::partials_return_type<T_y>::type>’ locally defined but not used [-Wunused-local-typedefs] 59 | using T_y_val = | ^~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:31, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::beta_lpdf(const T_y&, const T_scale_succ&, const T_scale_fail&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp:50:9: warning: typedef ‘using T_partials_matrix = class Eigen::Matrix<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 50 | using T_partials_matrix = Eigen::Matrix<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:37, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::beta_proportion_lpdf(const T_y&, const T_loc&, const T_prec&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp:55:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 55 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:63, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::cauchy_lpdf(const T_y&, const T_loc&, const T_scale&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp:45:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 45 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:74, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpdf(const T_prob&, const T_prior_size&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_n, T_prob>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 60 | using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>; | ^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:91, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::double_exponential_lpdf(const T_y&, const T_loc&, const T_scale&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp:44:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 44 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:111, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp: In function ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::frechet_cdf(const T_y&, const T_shape&, const T_scale&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp:30:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 30 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:245, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp: In function ‘stan::return_type_t<T_shared_param, T_job_param> stan::math::ordered_logistic_lpmf(const T_y&, const T_loc&, const T_cut&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp:76:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_loc, T_cut>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 76 | using T_partials_array = Eigen::Array<T_partials_return, -1, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:277, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp:62:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T_prob>::value, Eigen::Array<typename stan::partials_return_type<T_cut>::type, -1, 1>, typename stan::partials_return_type<T_cut>::type>’ locally defined but not used [-Wunused-local-typedefs] 62 | using T_alpha_val = typename std::conditional_t< | ^~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:32, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp: In lambda function: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp:83:11: warning: typedef ‘using Block_ = class Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>’ locally defined but not used [-Wunused-local-typedefs] 83 | using Block_ = Eigen::Block<Eigen::MatrixXd>; | ^~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:34, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp: In function ‘stan::math::var_value<Eigen::Matrix<double, -1, -1> > stan::math::cholesky_factor_constrain(const T&, int, int)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp:32:9: warning: typedef ‘using T_scalar = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs] 32 | using T_scalar = value_type_t<T>; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:71, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp: In function ‘auto stan::math::generalized_inverse(const VarMat&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp:64:9: warning: typedef ‘using value_t = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs] 64 | using value_t = value_type_t<VarMat>; | ^~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:15, from stanExports_glm_multi_beta_binomial.h:25, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp: In function ‘void stan::model::assign(Mat1&&, const stan::model::cons_index_list<stan::model::index_multi, stan::model::cons_index_list<stan::model::index_multi, stan::model::nil_index_list> >&, const Mat2&, const char*, int)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp:349:9: warning: typedef ‘using pair_type = struct std::pair<int, std::vector<int, stan::math::arena_allocator<int> > >’ locally defined but not used [-Wunused-local-typedefs] 349 | using pair_type = std::pair<int, arena_vec>; | ^~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:96:75: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:73:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for (int i = 0; i < dims.size(); i++) { | ~~^~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:117:75: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:73:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’: stanExports_glm_multi_beta_binomial.cc:30:89: required from here /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 158 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, -1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, -1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, -1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:222:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 222 | for (size_t i = 0; i < x.rows(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:223:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 223 | for (size_t j = 0; j < x.cols(); j++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 158 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’: /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:30:89: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:89:22: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 89 | if (p_names.size() != draws.cols()) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:107:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 107 | for (size_t i = 0; i < draws.rows(); ++i) { | ~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_cholesky_factor.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘static void stan::math::internal::less_or_equal<T_y, T_high, is_vec>::check(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int; bool is_vec = false]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:74:74: required from ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:78:36: required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:117:75: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:23:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘std::decay_t<long int>’ {aka ‘long int’} [-Wsign-compare] 23 | if (!(y <= high_vec[n])) { | ~~~^~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:8, from stanExports_glm_multi_beta_binomial.h:25, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp: In instantiation of ‘T stan::io::reader<T>::scalar() [with T = double]’: stanExports_glm_multi_beta_binomial.h:1980:22: required from ‘void model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::write_array_impl(RNG&, VecR&, VecI&, VecVar&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; VecR = std::vector<double>; VecI = std::vector<int>; VecVar = std::vector<double>; stan::require_vector_like_vt<std::is_floating_point, VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::require_std_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3019:23: required from ‘void model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::write_array(RNG&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1105:23: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::constrain_pars(SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:26:89: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp:139:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Map<const Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare] 139 | if (pos_ >= data_r_.size()) { | ~~~~~^~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp: In instantiation of ‘T stan::io::reader<T>::scalar() [with T = stan::math::var_value<double>]’: stanExports_glm_multi_beta_binomial.h:1541:22: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:23:88: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp:139:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Map<const Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing.hpp:9, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:15, from stanExports_glm_multi_beta_binomial.h:25, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp: In instantiation of ‘stan::plain_type_t<T> stan::model::rvalue(EigVec&&, const stan::model::cons_index_list<stan::model::index_multi, stan::model::nil_index_list>&, const char*, int) [with EigVec = Eigen::Matrix<stan::math::var_value<double>, -1, 1>&; stan::require_eigen_vector_t<C>* <anonymous> = 0; stan::plain_type_t<T> = Eigen::Matrix<stan::math::var_value<double>, -1, 1>]’: stanExports_glm_multi_beta_binomial.h:1790:23: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:23:88: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:143:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 143 | for (int i = 0; i < idxs.head_.ns_.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:140:14: warning: unused variable ‘v_size’ [-Wunused-variable] 140 | const auto v_size = v.size(); | ^~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:2128:35: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 299 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:240, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 543 | std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing.hpp:9, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:15, from stanExports_glm_multi_beta_binomial.h:25, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp: In instantiation of ‘stan::plain_type_t<T> stan::model::rvalue(EigVec&&, const stan::model::cons_index_list<stan::model::index_multi, stan::model::nil_index_list>&, const char*, int) [with EigVec = Eigen::Matrix<double, -1, 1>&; stan::require_eigen_vector_t<C>* <anonymous> = 0; stan::plain_type_t<T> = Eigen::Matrix<double, -1, 1>]’: stanExports_glm_multi_beta_binomial.h:1790:23: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector<double>; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = double; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T__ = double; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:55:47: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::__cxx11::basic_string<char> >&, RNG_t&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::call_sampler(SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:15:87: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:143:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 143 | for (int i = 0; i < idxs.head_.ns_.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:140:14: warning: unused variable ‘v_size’ [-Wunused-variable] 140 | const auto v_size = v.size(); | ^~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t<T>::result_type boost::math::detail::ibeta_fraction2_t<T>::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t<T>::result_type = std::pair<double, double>]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:729:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1367:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1404:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1543:93: required from ‘typename boost::math::tools::promote_args<RT1, RT2, A>::type boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2, A>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:28:56: required from here /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:692:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 692 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive_finite<Eigen::Matrix<stan::math::var_value<double>, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_positive_finite.hpp:24:20: required from ‘void stan::math::check_positive_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_binomial_lpmf.hpp:62:24: required from ‘stan::return_type_t<T_size1, T_size2> stan::math::beta_binomial_lpmf(const T_n&, const T_N&, const T_size1&, const T_size2&) [with bool propto = false; T_n = std::vector<int>; T_N = std::vector<int>; T_size1 = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_size2 = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; stan::return_type_t<T_size1, T_size2> = stan::math::var_value<double>]’ stanExports_glm_multi_beta_binomial.h:1782:38: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:23:88: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<stan::math::var_value<double>, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 158 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:69:16: required from ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Block<Eigen::Matrix<stan::math::var_value<double>, -1, -1>, 1, -1, false>; T_loc = Eigen::Matrix<stan::math::var_value<double>, 1, -1>; T_scale = int; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T_x, T_alpha, T_beta> = stan::math::var_value<double>]’ stanExports_glm_multi_beta_binomial.h:1826:40: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:23:88: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Array<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:70:15: required from ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Block<Eigen::Matrix<stan::math::var_value<double>, -1, -1>, 1, -1, false>; T_loc = Eigen::Matrix<stan::math::var_value<double>, 1, -1>; T_scale = int; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T_x, T_alpha, T_beta> = stan::math::var_value<double>]’ stanExports_glm_multi_beta_binomial.h:1826:40: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:23:88: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Array<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Block<Eigen::Matrix<stan::math::var_value<double>, -1, -1>, -1, 1, true> >::<lambda(double)>; T = Eigen::Block<Eigen::Matrix<stan::math::var_value<double>, -1, -1>, -1, 1, true>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Block<Eigen::Matrix<stan::math::var_value<double>, -1, -1>, -1, 1, true>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t<T2> stan::math::std_normal_lpdf(const T_y&) [with bool propto = true; T_y = Eigen::Block<Eigen::Matrix<stan::math::var_value<double>, -1, -1>, -1, 1, true>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y>* <anonymous> = 0; stan::return_type_t<T2> = stan::math::var_value<double>]’ stanExports_glm_multi_beta_binomial.h:1916:40: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:23:88: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Block<Eigen::Matrix<stan::math::var_value<double>, -1, -1>, -1, 1, true> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<stan::math::var_value<double>, 1, -1> >::<lambda(double)>; T = Eigen::Matrix<stan::math::var_value<double>, 1, -1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<stan::math::var_value<double>, 1, -1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t<T2> stan::math::std_normal_lpdf(const T_y&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, 1, -1>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y>* <anonymous> = 0; stan::return_type_t<T2> = stan::math::var_value<double>]’ stanExports_glm_multi_beta_binomial.h:1923:38: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:23:88: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<stan::math::var_value<double>, 1, -1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_positive_finite.hpp:24:20: required from ‘void stan::math::check_positive_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_binomial_lpmf.hpp:62:24: required from ‘stan::return_type_t<T_size1, T_size2> stan::math::beta_binomial_lpmf(const T_n&, const T_N&, const T_size1&, const T_size2&) [with bool propto = false; T_n = std::vector<int>; T_N = std::vector<int>; T_size1 = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const Eigen::Matrix<double, -1, 1> >; T_size2 = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > > >, const Eigen::Matrix<double, -1, 1> >; stan::return_type_t<T_size1, T_size2> = double]’ stanExports_glm_multi_beta_binomial.h:1782:38: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector<double>; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = double; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T__ = double; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:55:47: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::__cxx11::basic_string<char> >&, RNG_t&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::call_sampler(SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:15:87: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:69:16: required from ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_loc = int; T_scale = int; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T_x, T_alpha, T_beta> = double]’ stanExports_glm_multi_beta_binomial.h:1864:40: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector<double>; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = double; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T__ = double; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:55:47: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::__cxx11::basic_string<char> >&, RNG_t&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::call_sampler(SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:15:87: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true> >::<lambda(double)>; T = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t<T2> stan::math::std_normal_lpdf(const T_y&) [with bool propto = false; T_y = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y>* <anonymous> = 0; stan::return_type_t<T2> = double]’ stanExports_glm_multi_beta_binomial.h:1916:40: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector<double>; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = double; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T__ = double; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:55:47: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::__cxx11::basic_string<char> >&, RNG_t&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::call_sampler(SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:15:87: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, 1, -1> >::<lambda(double)>; T = Eigen::Matrix<double, 1, -1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, 1, -1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t<T2> stan::math::std_normal_lpdf(const T_y&) [with bool propto = false; T_y = Eigen::Matrix<double, 1, -1>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y>* <anonymous> = 0; stan::return_type_t<T2> = double]’ stanExports_glm_multi_beta_binomial.h:1923:38: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector<double>; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = double; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T__ = double; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:55:47: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::__cxx11::basic_string<char> >&, RNG_t&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::call_sampler(SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:15:87: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, -1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::ArrayWrapper<const Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > >]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:69:16: required from ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, 1, -1>; T_loc = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::ArrayWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Matrix<double, 1, -1> > >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, 1, -1, 1, 1, -1> > > >; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T_x, T_alpha, T_beta> = double]’ stanExports_glm_multi_beta_binomial.h:627:30: required from ‘stan::promote_args_t<typename stan::value_type<T, void>::type, typename stan::value_type<T_actual, void>::type, T2__, T3__, T5__> model_glm_multi_beta_binomial_namespace::abundance_variability_regression(const T0__&, const T1__&, const std::vector<T_l>&, const T3__&, const int&, const T5__&, std::ostream*) [with T0__ = Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>; T1__ = Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>; T2__ = double; T3__ = double; T5__ = double; stan::promote_args_t<typename stan::value_type<T, void>::type, typename stan::value_type<T_actual, void>::type, T2__, T3__, T5__> = double; typename stan::value_type<T>::type = double; typename stan::value_type<T_actual, void>::type = double; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:1814:49: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector<double>; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = double; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial.h:3031:49: required from ‘T__ model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T__ = double; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:55:47: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::__cxx11::basic_string<char> >&, RNG_t&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::call_sampler(SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial.cc:15:87: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::ArrayWrapper<const Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > > >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:18, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial.h:23, from stanExports_glm_multi_beta_binomial.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-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'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_glm_multi_beta_binomial_generate_date.cc -o stanExports_glm_multi_beta_binomial_generate_date.o In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_generate_date.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_generate_date.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_generate_date.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_generate_date.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_generate_date.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_generate_date.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_generate_date.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/callbacks/writer.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/filtered_values.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:110, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp: In function ‘Eigen::Matrix<typename stan::value_type<T>::type, EigMat::ColsAtCompileTime, EigMat::RowsAtCompileTime> stan::math::generalized_inverse(const EigMat&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp:34:9: warning: typedef ‘using value_t = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs] 34 | using value_t = value_type_t<EigMat>; | ^~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:319, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/tail.hpp: In function ‘std::vector<T> stan::math::tail(const std::vector<T>&, size_t)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/tail.hpp:46:9: warning: typedef ‘using idx_t = stan::math::index_type_t<std::vector<T> >’ locally defined but not used [-Wunused-local-typedefs] 46 | using idx_t = index_type_t<std::vector<T>>; | ^~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/include/make_fused.hpp:11, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp: At global scope: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_generate_date.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::bernoulli_logit_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp:59:9: warning: typedef ‘using T_y_val = std::conditional_t<stan::is_vector<T2>::value, Eigen::Matrix<typename stan::partials_return_type<T_y>::type, -1, 1>, typename stan::partials_return_type<T_y>::type>’ locally defined but not used [-Wunused-local-typedefs] 59 | using T_y_val = | ^~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:31, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::beta_lpdf(const T_y&, const T_scale_succ&, const T_scale_fail&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp:50:9: warning: typedef ‘using T_partials_matrix = class Eigen::Matrix<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 50 | using T_partials_matrix = Eigen::Matrix<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:37, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::beta_proportion_lpdf(const T_y&, const T_loc&, const T_prec&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp:55:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 55 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:63, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::cauchy_lpdf(const T_y&, const T_loc&, const T_scale&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp:45:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 45 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:74, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpdf(const T_prob&, const T_prior_size&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_n, T_prob>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 60 | using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>; | ^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:91, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::double_exponential_lpdf(const T_y&, const T_loc&, const T_scale&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp:44:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 44 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:111, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp: In function ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::frechet_cdf(const T_y&, const T_shape&, const T_scale&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp:30:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 30 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:245, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp: In function ‘stan::return_type_t<T_shared_param, T_job_param> stan::math::ordered_logistic_lpmf(const T_y&, const T_loc&, const T_cut&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp:76:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_loc, T_cut>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 76 | using T_partials_array = Eigen::Array<T_partials_return, -1, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:277, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp:62:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T_prob>::value, Eigen::Array<typename stan::partials_return_type<T_cut>::type, -1, 1>, typename stan::partials_return_type<T_cut>::type>’ locally defined but not used [-Wunused-local-typedefs] 62 | using T_alpha_val = typename std::conditional_t< | ^~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:32, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp: In lambda function: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp:83:11: warning: typedef ‘using Block_ = class Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>’ locally defined but not used [-Wunused-local-typedefs] 83 | using Block_ = Eigen::Block<Eigen::MatrixXd>; | ^~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:34, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp: In function ‘stan::math::var_value<Eigen::Matrix<double, -1, -1> > stan::math::cholesky_factor_constrain(const T&, int, int)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp:32:9: warning: typedef ‘using T_scalar = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs] 32 | using T_scalar = value_type_t<T>; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:71, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp: In function ‘auto stan::math::generalized_inverse(const VarMat&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp:64:9: warning: typedef ‘using value_t = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs] 64 | using value_t = value_type_t<VarMat>; | ^~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:15, from stanExports_glm_multi_beta_binomial_generate_date.h:25, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp: In function ‘void stan::model::assign(Mat1&&, const stan::model::cons_index_list<stan::model::index_multi, stan::model::cons_index_list<stan::model::index_multi, stan::model::nil_index_list> >&, const Mat2&, const char*, int)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp:349:9: warning: typedef ‘using pair_type = struct std::pair<int, std::vector<int, stan::math::arena_allocator<int> > >’ locally defined but not used [-Wunused-local-typedefs] 349 | using pair_type = std::pair<int, arena_vec>; | ^~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:96:75: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:73:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for (int i = 0; i < dims.size(); i++) { | ~~^~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:117:75: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:73:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing.hpp:9, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:15, from stanExports_glm_multi_beta_binomial_generate_date.h:25, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp: In instantiation of ‘stan::plain_type_t<T> stan::model::rvalue(EigMat&&, const stan::model::cons_index_list<stan::model::index_multi, stan::model::nil_index_list>&, const char*, int) [with EigMat = Eigen::Matrix<double, -1, -1>&; stan::require_eigen_dense_dynamic_t<Mat>* <anonymous> = 0; stan::plain_type_t<T> = Eigen::Matrix<double, -1, -1>]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:641:16: required from ‘auto stan::model::rvalue(Mat&&, const stan::model::cons_index_list<Idx, stan::model::cons_index_list<stan::model::index_omni, stan::model::nil_index_list> >&, const char*, int) [with Mat = Eigen::Matrix<double, -1, -1>&; Idx = stan::model::index_multi; stan::require_dense_dynamic_t<Mat>* <anonymous> = 0]’ stanExports_glm_multi_beta_binomial_generate_date.h:683:63: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:281:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 281 | for (int i = 0; i < idxs.head_.ns_.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’: stanExports_glm_multi_beta_binomial_generate_date.cc:30:89: required from here /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 158 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, -1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, -1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, -1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:222:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 222 | for (size_t i = 0; i < x.rows(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:223:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 223 | for (size_t j = 0; j < x.cols(); j++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 158 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’: /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial_generate_date.cc:30:89: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:89:22: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 89 | if (p_names.size() != draws.cols()) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:107:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 107 | for (size_t i = 0; i < draws.rows(); ++i) { | ~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_cholesky_factor.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘static void stan::math::internal::less_or_equal<T_y, T_high, is_vec>::check(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int; bool is_vec = false]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:74:74: required from ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:78:36: required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:117:75: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:23:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘std::decay_t<long int>’ {aka ‘long int’} [-Wsign-compare] 23 | if (!(y <= high_vec[n])) { | ~~~^~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing.hpp:9, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:15, from stanExports_glm_multi_beta_binomial_generate_date.h:25, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp: In instantiation of ‘stan::plain_type_t<T> stan::model::rvalue(EigMat&&, const stan::model::cons_index_list<Idx, stan::model::cons_index_list<stan::model::index_multi, stan::model::nil_index_list> >&, const char*, int) [with EigMat = const Eigen::Matrix<double, -1, -1>&; Idx = stan::model::index_omni; stan::require_eigen_dense_dynamic_t<Mat>* <anonymous> = 0; stan::require_not_same_t<typename std::decay<_Tp2>::type, stan::model::index_uni>* <anonymous> = 0; stan::plain_type_t<T> = Eigen::Matrix<double, -1, -1>]’: stanExports_glm_multi_beta_binomial_generate_date.h:757:23: required from ‘void model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date::write_array_impl(RNG&, VecR&, VecI&, VecVar&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; VecR = std::vector<double>; VecI = std::vector<int>; VecVar = std::vector<double>; stan::require_vector_like_vt<std::is_floating_point, VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::require_std_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial_generate_date.h:1231:23: required from ‘void model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date::write_array(RNG&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1105:23: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::constrain_pars(SEXP) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial_generate_date.cc:26:89: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:612:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 612 | for (int j = 0; j < idxs.tail_.head_.ns_.size(); ++j) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:610:13: warning: unused variable ‘cols’ [-Wunused-variable] 610 | const int cols = rvalue_index_size(idxs.tail_.head_, x_ref.cols()); | ^~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:2128:35: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 299 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:240, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 543 | std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_positive_finite.hpp:24:20: required from ‘void stan::math::check_positive_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_binomial_rng.hpp:46:24: required from ‘typename stan::VectorBuilder<true, int, T_N, T_shape1, T_shape2>::type stan::math::beta_binomial_rng(const T_N&, const T_shape1&, const T_shape2&, RNG&) [with T_N = int; T_shape1 = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true>, const Eigen::MatrixWrapper<const Eigen::CwiseUnaryOp<Eigen::internal::scalar_exp_op<double>, const Eigen::ArrayWrapper<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true> > > > >; T_shape2 = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true> > > >, const Eigen::MatrixWrapper<const Eigen::CwiseUnaryOp<Eigen::internal::scalar_exp_op<double>, const Eigen::ArrayWrapper<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true> > > > >; RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; typename stan::VectorBuilder<true, int, T_N, T_shape1, T_shape2>::type = std::vector<int>]’ stanExports_glm_multi_beta_binomial_generate_date.h:787:28: required from ‘void model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date::write_array_impl(RNG&, VecR&, VecI&, VecVar&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; VecR = std::vector<double>; VecI = std::vector<int>; VecVar = std::vector<double>; stan::require_vector_like_vt<std::is_floating_point, VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::require_std_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial_generate_date.h:1231:23: required from ‘void model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date::write_array(RNG&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1105:23: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::constrain_pars(SEXP) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial_generate_date.cc:26:89: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 158 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t<T>::result_type boost::math::detail::ibeta_fraction2_t<T>::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t<T>::result_type = std::pair<double, double>]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:729:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1367:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1404:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1543:93: required from ‘typename boost::math::tools::promote_args<RT1, RT2, A>::type boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2, A>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:28:56: required from here /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:692:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 692 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:18, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_generate_date.h:23, from stanExports_glm_multi_beta_binomial_generate_date.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-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'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_glm_multi_beta_binomial_simulate_data.cc -o stanExports_glm_multi_beta_binomial_simulate_data.o In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_simulate_data.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_simulate_data.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_simulate_data.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_simulate_data.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr<Y> & r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_simulate_data.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr<Y> && r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_simulate_data.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_simulate_data.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/callbacks/writer.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/filtered_values.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:23, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:110, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp: In function ‘Eigen::Matrix<typename stan::value_type<T>::type, EigMat::ColsAtCompileTime, EigMat::RowsAtCompileTime> stan::math::generalized_inverse(const EigMat&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp:34:9: warning: typedef ‘using value_t = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs] 34 | using value_t = value_type_t<EigMat>; | ^~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:319, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/tail.hpp: In function ‘std::vector<T> stan::math::tail(const std::vector<T>&, size_t)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/tail.hpp:46:9: warning: typedef ‘using idx_t = stan::math::index_type_t<std::vector<T> >’ locally defined but not used [-Wunused-local-typedefs] 46 | using idx_t = index_type_t<std::vector<T>>; | ^~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/include/make_fused.hpp:11, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp: At global scope: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27, from stanExports_glm_multi_beta_binomial_simulate_data.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template<typename> class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::bernoulli_logit_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp:59:9: warning: typedef ‘using T_y_val = std::conditional_t<stan::is_vector<T2>::value, Eigen::Matrix<typename stan::partials_return_type<T_y>::type, -1, 1>, typename stan::partials_return_type<T_y>::type>’ locally defined but not used [-Wunused-local-typedefs] 59 | using T_y_val = | ^~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:31, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::beta_lpdf(const T_y&, const T_scale_succ&, const T_scale_fail&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp:50:9: warning: typedef ‘using T_partials_matrix = class Eigen::Matrix<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 50 | using T_partials_matrix = Eigen::Matrix<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:37, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::beta_proportion_lpdf(const T_y&, const T_loc&, const T_prec&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp:55:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 55 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:63, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::cauchy_lpdf(const T_y&, const T_loc&, const T_scale&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp:45:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 45 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:74, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpdf(const T_prob&, const T_prior_size&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_n, T_prob>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 60 | using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>; | ^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:91, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::double_exponential_lpdf(const T_y&, const T_loc&, const T_scale&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp:44:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 44 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:111, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp: In function ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::frechet_cdf(const T_y&, const T_shape&, const T_scale&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp:30:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 30 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:245, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp: In function ‘stan::return_type_t<T_shared_param, T_job_param> stan::math::ordered_logistic_lpmf(const T_y&, const T_loc&, const T_cut&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp:76:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_loc, T_cut>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs] 76 | using T_partials_array = Eigen::Array<T_partials_return, -1, 1>; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_log.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:277, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp:62:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T_prob>::value, Eigen::Array<typename stan::partials_return_type<T_cut>::type, -1, 1>, typename stan::partials_return_type<T_cut>::type>’ locally defined but not used [-Wunused-local-typedefs] 62 | using T_alpha_val = typename std::conditional_t< | ^~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:32, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp: In lambda function: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp:83:11: warning: typedef ‘using Block_ = class Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>’ locally defined but not used [-Wunused-local-typedefs] 83 | using Block_ = Eigen::Block<Eigen::MatrixXd>; | ^~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:34, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp: In function ‘stan::math::var_value<Eigen::Matrix<double, -1, -1> > stan::math::cholesky_factor_constrain(const T&, int, int)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp:32:9: warning: typedef ‘using T_scalar = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs] 32 | using T_scalar = value_type_t<T>; | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:71, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp: In function ‘auto stan::math::generalized_inverse(const VarMat&)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp:64:9: warning: typedef ‘using value_t = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs] 64 | using value_t = value_type_t<VarMat>; | ^~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing.hpp:8, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:15, from stanExports_glm_multi_beta_binomial_simulate_data.h:25, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp: In function ‘void stan::model::assign(Mat1&&, const stan::model::cons_index_list<stan::model::index_multi, stan::model::cons_index_list<stan::model::index_multi, stan::model::nil_index_list> >&, const Mat2&, const char*, int)’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp:349:9: warning: typedef ‘using pair_type = struct std::pair<int, std::vector<int, stan::math::arena_allocator<int> > >’ locally defined but not used [-Wunused-local-typedefs] 349 | using pair_type = std::pair<int, arena_vec>; | ^~~~~~~~~ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: stanExports_glm_multi_beta_binomial_simulate_data.h: In member function ‘void model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::transform_inits_impl(const stan::io::var_context&, VecI&, VecVar&, std::ostream*) const’: stanExports_glm_multi_beta_binomial_simulate_data.h:614:11: warning: typedef ‘using local_scalar_t__ = double’ locally defined but not used [-Wunused-local-typedefs] 614 | using local_scalar_t__ = double; | ^~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:96:75: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:73:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | for (int i = 0; i < dims.size(); i++) { | ~~^~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:117:75: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:73:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: stanExports_glm_multi_beta_binomial_simulate_data.h: In instantiation of ‘void model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::transform_inits_impl(const stan::io::var_context&, VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector<double>; VecI = std::vector<int>; stan::require_std_vector_t<T>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’: stanExports_glm_multi_beta_binomial_simulate_data.h:880:68: required from here stanExports_glm_multi_beta_binomial_simulate_data.h:619:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] 619 | int pos__; | ^~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’: stanExports_glm_multi_beta_binomial_simulate_data.cc:30:89: required from here /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 158 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, -1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, -1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, -1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:222:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 222 | for (size_t i = 0; i < x.rows(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:223:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 223 | for (size_t j = 0; j < x.cols(); j++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 158 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’: /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial_simulate_data.cc:30:89: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:89:22: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 89 | if (p_names.size() != draws.cols()) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:107:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 107 | for (size_t i = 0; i < draws.rows(); ++i) { | ~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_cholesky_factor.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘static void stan::math::internal::less_or_equal<T_y, T_high, is_vec>::check(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int; bool is_vec = false]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:74:74: required from ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:78:36: required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:117:75: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:23:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘std::decay_t<long int>’ {aka ‘long int’} [-Wsign-compare] 23 | if (!(y <= high_vec[n])) { | ~~~^~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:8, from stanExports_glm_multi_beta_binomial_simulate_data.h:25, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp: In instantiation of ‘T stan::io::reader<T>::scalar() [with T = double]’: stanExports_glm_multi_beta_binomial_simulate_data.h:422:22: required from ‘void model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::write_array_impl(RNG&, VecR&, VecI&, VecVar&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; VecR = std::vector<double>; VecI = std::vector<int>; VecVar = std::vector<double>; stan::require_vector_like_vt<std::is_floating_point, VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::require_std_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial_simulate_data.h:860:23: required from ‘void model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::write_array(RNG&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1105:23: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::constrain_pars(SEXP) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial_simulate_data.cc:26:89: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp:139:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Map<const Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare] 139 | if (pos_ >= data_r_.size()) { | ~~~~~^~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp: In instantiation of ‘T stan::io::reader<T>::scalar() [with T = stan::math::var_value<double>]’: stanExports_glm_multi_beta_binomial_simulate_data.h:373:22: required from ‘stan::scalar_type_t<T2> model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial_simulate_data.h:872:49: required from ‘T__ model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial_simulate_data.cc:23:88: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp:139:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Map<const Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:2128:35: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 299 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:240, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 543 | std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’: /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_positive_finite.hpp:24:20: required from ‘void stan::math::check_positive_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_binomial_rng.hpp:46:24: required from ‘typename stan::VectorBuilder<true, int, T_N, T_shape1, T_shape2>::type stan::math::beta_binomial_rng(const T_N&, const T_shape1&, const T_shape2&, RNG&) [with T_N = int; T_shape1 = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true>, const Eigen::MatrixWrapper<const Eigen::CwiseUnaryOp<Eigen::internal::scalar_exp_op<double>, const Eigen::ArrayWrapper<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true> > > > >; T_shape2 = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true> > > >, const Eigen::MatrixWrapper<const Eigen::CwiseUnaryOp<Eigen::internal::scalar_exp_op<double>, const Eigen::ArrayWrapper<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true> > > > >; RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; typename stan::VectorBuilder<true, int, T_N, T_shape1, T_shape2>::type = std::vector<int>]’ stanExports_glm_multi_beta_binomial_simulate_data.h:531:28: required from ‘void model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::write_array_impl(RNG&, VecR&, VecI&, VecVar&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; VecR = std::vector<double>; VecI = std::vector<int>; VecVar = std::vector<double>; stan::require_vector_like_vt<std::is_floating_point, VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::require_std_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’ stanExports_glm_multi_beta_binomial_simulate_data.h:860:23: required from ‘void model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::write_array(RNG&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; std::ostream = std::basic_ostream<char>]’ /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1105:23: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::constrain_pars(SEXP) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’ stanExports_glm_multi_beta_binomial_simulate_data.cc:26:89: required from here /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] 158 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t<T>::result_type boost::math::detail::ibeta_fraction2_t<T>::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t<T>::result_type = std::pair<double, double>]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:729:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1367:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1404:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1543:93: required from ‘typename boost::math::tools::promote_args<RT1, RT2, A>::type boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = 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>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2, A>::type = double]’ /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:28:56: required from here /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:692:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 692 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:18, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_glm_multi_beta_binomial_simulate_data.h:23, from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’: /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/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/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-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 version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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: (Intercept), typehealthy sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` sccomp says: estimation sccomp says: the composition design matrix has columns: typecancer, typehealthy sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` sccomp says: The QR deconposition resulted in extreme values, probably for the correlation structure of your design matrix. Omitting QR decomposition. sccomp says: outlier identification first pass - step 1/3 Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` 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 0.000562 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 5.62 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 -3376.709 1.000 1.000 Chain 1: 200 -3159.175 0.534 1.000 Chain 1: 300 -3153.584 0.357 0.069 Chain 1: 400 -3148.099 0.268 0.069 Chain 1: 500 -3148.407 0.214 0.002 MEDIAN ELBO CONVERGED Chain 1: Chain 1: Drawing a sample of size 1000 from the approximate posterior... Chain 1: COMPLETED. sccomp says: outlier identification second pass - step 2/3 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 0.000547 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 5.47 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 -3043.897 1.000 1.000 Chain 1: 200 -2826.565 0.538 1.000 Chain 1: 300 -2823.670 0.359 0.077 Chain 1: 400 -2816.603 0.270 0.077 Chain 1: 500 -2816.948 0.216 0.003 MEDIAN ELBO CONVERGED Chain 1: Chain 1: Drawing a sample of size 1000 from the approximate posterior... Chain 1: COMPLETED. sccomp says: outlier-free model fitting - step 3/3 sccomp says: the composition design matrix has columns: (Intercept), typehealthy sccomp says: the variability design matrix has columns: (Intercept) 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 0.000534 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 5.34 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 -3210.777 1.000 1.000 Chain 1: 200 -3004.012 0.534 1.000 Chain 1: 300 -3000.277 0.357 0.069 Chain 1: 400 -2993.941 0.268 0.069 Chain 1: 500 -2994.680 0.214 0.002 MEDIAN ELBO CONVERGED Chain 1: Chain 1: Drawing a sample of size 1000 from the approximate posterior... Chain 1: COMPLETED. sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), typehealthy sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` sccomp says: The QR deconposition resulted in extreme values, probably for the correlation structure of your design matrix. Omitting QR decomposition. sccomp says: estimation sccomp says: the composition design matrix has columns: typecancer, typehealthy sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` sccomp says: The QR deconposition resulted in extreme values, probably for the correlation structure of your design matrix. Omitting QR decomposition. sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), continuous_covariate sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` sccomp says: The QR deconposition resulted in extreme values, probably for the correlation structure of your design matrix. Omitting QR decomposition. sccomp says: estimation sccomp says: the composition design matrix has columns: typecancer, typehealthy, continuous_covariate sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` sccomp says: The QR deconposition resulted in extreme values, probably for the correlation structure of your design matrix. Omitting QR decomposition. sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), typehealthy sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` sccomp says: estimation sccomp says: the composition design matrix has columns: typecancer, typehealthy sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` sccomp says: estimation sccomp says: the composition design matrix has columns: typecancer, typehealthy sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` 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 ======================================== tidyseurat version 0.7.4 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) ======================================== sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), typehealthy, batch sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` 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) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), typehealthy sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), typehealthy sccomp says: the variability design matrix has columns: (Intercept), typehealthy Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` Joining with `by = join_by(cell_group, sample)` Joining with `by = join_by(cell_group, type)` Joining with `by = join_by(cell_group, sample)` Joining with `by = join_by(cell_group, type)` sccomp says: estimation sccomp says: the composition design matrix has columns: (Intercept), typehealthy sccomp says: the variability design matrix has columns: (Intercept) Joining with `by = join_by(sample)` Joining with `by = join_by(cell_group)` [ FAIL 0 | WARN 284 | SKIP 5 | PASS 17 ] ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • empty test (5): 'test-sccomp_.R:86:1', 'test-sccomp_.R:335:1', 'test-sccomp_.R:437:1', 'test-sccomp_.R:444:1', 'test-sccomp_.R:451:1' [ FAIL 0 | WARN 284 | SKIP 5 | PASS 17 ] > > proc.time() user system elapsed 299.271 3.220 303.014
sccomp.Rcheck/sccomp-Ex.timings
name | user | system | elapsed | |
plot_summary | 34.856 | 0.663 | 35.625 | |
remove_unwanted_variation | 43.071 | 0.535 | 43.678 | |
sccomp_glm | 53.647 | 0.147 | 53.905 | |
sccomp_predict | 38.114 | 0.543 | 38.735 | |
sccomp_replicate | 33.404 | 0.336 | 33.808 | |
simulate_data | 41.156 | 0.415 | 41.646 | |
test_contrasts | 56.108 | 0.220 | 56.435 | |