Stefano Mangiola
| Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024) |
| git_url: https://git.bioconductor.org/packages/sccomp |
| git_branch: devel |
| git_last_commit: 13c5322 |
| git_last_commit_date: 2024-04-30 11:39:15 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-15 13:46:42 -0400 (Wed, 15 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4663 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 1823/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sccomp 1.9.0 (landing page) Stefano Mangiola
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.8.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:sccomp.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings sccomp_1.8.0.tar.gz |
| StartedAt: 2024-05-09 11:37:10 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 11:55:40 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 1109.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sccomp.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:sccomp.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings sccomp_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sccomp.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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
* using option ‘--no-vignettes’
* checking for file ‘sccomp/DESCRIPTION’ ... OK
* this is package ‘sccomp’ version ‘1.8.0’
* 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 159.5Mb
sub-directories of 1Mb or more:
data 1.1Mb
figures 1.2Mb
libs 156.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... 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_simulation_to_model_input : <anonymous>: no visible global
function definition for ‘sd’
data_spread_to_model_input: no visible global function definition for
‘as.formula’
data_spread_to_model_input: no visible binding for global variable
‘exposure’
data_spread_to_model_input: no visible binding for global variable
‘design’
data_spread_to_model_input: no visible binding for global variable
‘mat’
data_spread_to_model_input: no visible binding for global variable
‘factor___numeric’
data_spread_to_model_input: no visible binding for global variable
‘mean_idx’
data_spread_to_model_input: no visible binding for global variable
‘design_matrix’
data_spread_to_model_input: no visible binding for global variable
‘minus_sum’
data_spread_to_model_input: no visible binding for global variable
‘group___numeric’
data_spread_to_model_input: no visible binding for global variable
‘idx’
data_spread_to_model_input: no visible binding for global variable
‘group___label’
data_spread_to_model_input: no visible binding for global variable
‘parameter’
data_spread_to_model_input: no visible binding for global variable
‘group’
data_spread_to_model_input: no visible binding for global variable
‘design_matrix_col’
data_to_spread: no visible binding for global variable ‘exposure’
design_matrix_and_coefficients_to_dir_mult_simulation: no visible
binding for global variable ‘cell_type’
design_matrix_and_coefficients_to_dir_mult_simulation: no visible
binding for global variable ‘generated_counts’
design_matrix_and_coefficients_to_dir_mult_simulation: no visible
binding for global variable ‘factor_1’
design_matrix_and_coefficients_to_simulation: no visible binding for
global variable ‘cell_type’
design_matrix_and_coefficients_to_simulation: no visible binding for
global variable ‘beta_1’
design_matrix_and_coefficients_to_simulation: no visible binding for
global variable ‘beta_2’
dirichlet_multinomial_glm: no visible global function definition for
‘detect_cores’
dirichlet_multinomial_glm: no visible binding for global variable
‘glm_dirichlet_multinomial’
dirichlet_multinomial_glm: no visible binding for global variable
‘censoring_iteration’
dirichlet_multinomial_glm: no visible binding for global variable ‘.’
dirichlet_multinomial_glm: no visible binding for global variable
‘chains’
dirichlet_multinomial_glm: no visible binding for global variable
‘precision’
dirichlet_multinomial_glm: no visible binding for global variable ‘M’
do_inference_imputation: no visible binding for global variable
‘glm_dirichlet_multinomial_imputation’
draws_to_statistics: no visible binding for global variable ‘M’
draws_to_statistics: no visible binding for global variable ‘parameter’
draws_to_statistics: no visible binding for global variable
‘bigger_zero’
draws_to_statistics: no visible binding for global variable
‘smaller_zero’
draws_to_statistics: no visible binding for global variable ‘lower’
draws_to_statistics: no visible binding for global variable ‘effect’
draws_to_statistics: no visible binding for global variable ‘upper’
draws_to_statistics: no visible binding for global variable ‘pH0’
draws_to_statistics: no visible binding for global variable ‘FDR’
draws_to_statistics: no visible binding for global variable ‘n_eff’
draws_to_statistics: no visible binding for global variable ‘R_k_hat’
draws_to_tibble_x: no visible binding for global variable ‘.’
draws_to_tibble_x: no visible binding for global variable ‘dummy’
draws_to_tibble_x: no visible binding for global variable ‘.variable’
draws_to_tibble_x: no visible binding for global variable ‘.chain’
draws_to_tibble_x: no visible binding for global variable ‘.iteration’
draws_to_tibble_x: no visible binding for global variable ‘.draw’
draws_to_tibble_x: no visible binding for global variable ‘.value’
draws_to_tibble_x_y: no visible binding for global variable ‘.’
draws_to_tibble_x_y: no visible binding for global variable ‘dummy’
draws_to_tibble_x_y: no visible binding for global variable ‘.variable’
draws_to_tibble_x_y: no visible binding for global variable ‘.chain’
draws_to_tibble_x_y: no visible binding for global variable
‘.iteration’
draws_to_tibble_x_y: no visible binding for global variable ‘.draw’
draws_to_tibble_x_y: no visible binding for global variable ‘.value’
find_optimal_number_of_chains: no visible binding for global variable
‘chains’
find_optimal_number_of_chains: no visible binding for global variable
‘.’
fit_and_generate_quantities: no visible binding for global variable ‘N’
fit_and_generate_quantities: no visible binding for global variable ‘M’
fit_and_generate_quantities: no visible binding for global variable
‘precision’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘N’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘M’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘cores’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘additional_parameters_to_save’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘pass_fit’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘tol_rel_obj’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘glm_dirichlet_multinomial_generate_quantities’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘.draw’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘.chain’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘.iteration’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘.draw_imputation’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘.variable’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘fit_list’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘n_eff’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘se_mean’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘sd’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘.’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘C_name’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘.lower’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘.median’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘.upper’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘5%’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘95%’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘50%’
fit_model_and_parse_out_missing_data: no visible binding for global
variable ‘precision’
fit_model_and_parse_out_no_missing_data: no visible binding for global
variable ‘glm_dirichlet_multinomial_generate_quantities’
fit_to_counts_rng: no visible binding for global variable ‘.variable’
fit_to_counts_rng: no visible binding for global variable ‘S’
fit_to_counts_rng: no visible binding for global variable ‘G’
fit_to_counts_rng: no visible binding for global variable ‘.’
formula_to_random_effect_formulae: no visible binding for global
variable ‘formula’
generate_quantities: no visible binding for global variable ‘N_M’
generate_quantities: no visible binding for global variable
‘generated_quantity’
generate_quantities: no visible binding for global variable ‘draw’
generate_quantities: no visible binding for global variable ‘N’
generate_quantities: no visible binding for global variable ‘M’
get_FDR: no visible binding for global variable ‘value’
get_FDR: no visible binding for global variable ‘name’
get_FDR: no visible binding for global variable ‘FDR’
get_abundance_contrast_draws: no visible binding for global variable
‘X’
get_abundance_contrast_draws: no visible binding for global variable
‘.value’
get_abundance_contrast_draws: no visible binding for global variable
‘.’
get_abundance_contrast_draws: no visible binding for global variable
‘N_random_intercepts’
get_abundance_contrast_draws: no visible binding for global variable
‘X_random_intercept’
get_abundance_contrast_draws: no visible binding for global variable
‘.variable’
get_abundance_contrast_draws: no visible binding for global variable
‘y’
get_abundance_contrast_draws: no visible binding for global variable
‘M’
get_abundance_contrast_draws: no visible binding for global variable
‘khat’
get_abundance_contrast_draws: no visible binding for global variable
‘parameter’
get_abundance_contrast_draws: no visible binding for global variable
‘n_eff’
get_abundance_contrast_draws: no visible binding for global variable
‘R_k_hat’
get_mean_precision: no visible binding for global variable ‘M’
get_mean_precision: no visible binding for global variable ‘2.5%’
get_mean_precision: no visible binding for global variable ‘97.5%’
get_mean_precision_association: no visible binding for global variable
‘.’
get_probability_non_zero: no visible binding for global variable ‘M’
get_probability_non_zero: no visible binding for global variable
‘C_name’
get_probability_non_zero: no visible binding for global variable
‘bigger_zero’
get_probability_non_zero: no visible binding for global variable
‘smaller_zero’
get_probability_non_zero_OLD: no visible binding for global variable
‘.’
get_probability_non_zero_OLD: no visible binding for global variable
‘.draw’
get_probability_non_zero_OLD: no visible binding for global variable
‘M’
get_probability_non_zero_OLD: no visible binding for global variable
‘C_name’
get_probability_non_zero_OLD: no visible binding for global variable
‘bigger_zero’
get_probability_non_zero_OLD: no visible binding for global variable
‘smaller_zero’
get_random_intercept_design: no visible binding for global variable
‘is_factor_continuous’
get_random_intercept_design: no visible binding for global variable
‘design’
get_random_intercept_design: no visible binding for global variable
‘max_mean_idx’
get_random_intercept_design: no visible binding for global variable
‘max_minus_sum’
get_random_intercept_design: no visible binding for global variable
‘max_factor_numeric’
get_random_intercept_design: no visible binding for global variable
‘max_group_numeric’
get_random_intercept_design: no visible binding for global variable
‘min_mean_idx’
get_random_intercept_design: no visible binding for global variable
‘min_minus_sum’
get_random_intercept_design2: no visible binding for global variable
‘formula’
get_variability_contrast_draws: no visible binding for global variable
‘XA’
get_variability_contrast_draws: no visible binding for global variable
‘.value’
get_variability_contrast_draws: no visible binding for global variable
‘.’
get_variability_contrast_draws: no visible binding for global variable
‘.variable’
get_variability_contrast_draws: no visible binding for global variable
‘y’
get_variability_contrast_draws: no visible binding for global variable
‘M’
get_variability_contrast_draws: no visible binding for global variable
‘khat’
get_variability_contrast_draws: no visible binding for global variable
‘parameter’
get_variability_contrast_draws: no visible binding for global variable
‘n_eff’
get_variability_contrast_draws: no visible binding for global variable
‘R_k_hat’
glm_multi_beta: no visible binding for global variable ‘.’
label_deleterious_outliers: no visible binding for global variable
‘.count’
label_deleterious_outliers: no visible binding for global variable
‘95%’
label_deleterious_outliers: no visible binding for global variable ‘5%’
label_deleterious_outliers: no visible binding for global variable ‘X’
label_deleterious_outliers: no visible binding for global variable
‘iteration’
label_deleterious_outliers: no visible binding for global variable
‘outlier_above’
label_deleterious_outliers: no visible binding for global variable
‘slope’
label_deleterious_outliers: no visible binding for global variable
‘is_group_right’
label_deleterious_outliers: no visible binding for global variable
‘outlier_below’
multi_beta_glm: no visible global function definition for
‘detect_cores’
parse_fit: no visible binding for global variable ‘M’
parse_formula: no visible binding for global variable ‘.’
parse_formula_random_intercept: no visible binding for global variable
‘formula’
parse_generated_quantities: no visible binding for global variable
‘.draw’
parse_generated_quantities: no visible binding for global variable ‘N’
parse_generated_quantities: no visible binding for global variable
‘.value’
parse_generated_quantities: no visible binding for global variable
‘generated_counts’
parse_generated_quantities: no visible binding for global variable ‘M’
parse_generated_quantities: no visible binding for global variable
‘generated_proportions’
plot.sccomp_tbl: no visible binding for global variable ‘parameter’
plot.sccomp_tbl: no visible binding for global variable ‘count_data’
plot.sccomp_tbl: no visible binding for global variable
‘multipanel_theme’
plot.sccomp_tbl: no visible binding for global variable ‘v_effect’
plot_1d_intervals: no visible binding for global variable ‘parameter’
plot_1d_intervals: no visible binding for global variable ‘estimate’
plot_1d_intervals: no visible binding for global variable ‘value’
plot_2d_intervals: no visible binding for global variable ‘v_effect’
plot_2d_intervals: no visible binding for global variable ‘parameter’
plot_2d_intervals: no visible binding for global variable ‘.’
plot_2d_intervals: no visible binding for global variable ‘c_effect’
plot_2d_intervals: no visible binding for global variable ‘c_lower’
plot_2d_intervals: no visible binding for global variable ‘c_upper’
plot_2d_intervals: no visible binding for global variable ‘c_FDR’
plot_2d_intervals: no visible binding for global variable ‘v_lower’
plot_2d_intervals: no visible binding for global variable ‘v_upper’
plot_2d_intervals: no visible binding for global variable ‘v_FDR’
plot_2d_intervals: no visible binding for global variable
‘cell_type_label’
plot_boxplot: no visible binding for global variable ‘stats_name’
plot_boxplot: no visible binding for global variable ‘parameter’
plot_boxplot: no visible binding for global variable ‘stats_value’
plot_boxplot: no visible binding for global variable ‘count_data’
plot_boxplot: no visible binding for global variable
‘generated_proportions’
plot_boxplot: no visible binding for global variable ‘proportion’
plot_boxplot: no visible binding for global variable ‘name’
plot_boxplot: no visible binding for global variable ‘outlier’
plot_scatterplot: no visible binding for global variable ‘stats_name’
plot_scatterplot: no visible binding for global variable ‘parameter’
plot_scatterplot: no visible binding for global variable ‘stats_value’
plot_scatterplot: no visible binding for global variable ‘count_data’
plot_scatterplot: no visible binding for global variable
‘generated_proportions’
plot_scatterplot: no visible binding for global variable ‘proportion’
plot_scatterplot: no visible binding for global variable ‘name’
plot_scatterplot: no visible binding for global variable ‘outlier’
replicate_data: no visible binding for global variable
‘glm_dirichlet_multinomial_generate_quantities’
replicate_data: no visible binding for global variable ‘count_data’
replicate_data: no visible binding for global variable ‘exposure’
replicate_data: no visible binding for global variable ‘dummy’
replicate_data: no visible global function definition for ‘tail’
replicate_data: no visible global function definition for ‘as.formula’
replicate_data: no visible binding for global variable ‘.’
replicate_data: no visible global function definition for ‘na.omit’
replicate_data: no visible binding for global variable ‘Xa’
replicate_data: no visible binding for global variable
‘intercept_in_design’
replicate_data: no visible binding for global variable ‘design’
replicate_data: no visible binding for global variable ‘design_matrix’
replicate_data: no visible binding for global variable
‘X_random_intercept’
sccomp_boxplot: no visible binding for global variable ‘parameter’
sccomp_boxplot: no visible binding for global variable ‘count_data’
sccomp_boxplot: no visible binding for global variable
‘multipanel_theme’
sccomp_glm_data_frame_counts: no visible binding for global variable
‘N’
sccomp_glm_data_frame_counts: no visible binding for global variable
‘M’
sccomp_glm_data_frame_counts: no visible global function definition for
‘na.omit’
sccomp_predict.sccomp_tbl: no visible binding for global variable
‘count_data’
sccomp_predict.sccomp_tbl: no visible binding for global variable ‘M’
sccomp_predict.sccomp_tbl: no visible binding for global variable ‘N’
sccomp_predict.sccomp_tbl: no visible binding for global variable
‘2.5%’
sccomp_predict.sccomp_tbl: no visible binding for global variable
‘97.5%’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘count_data’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘N’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘M’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘5%’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘95%’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘truncation_up’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘truncation_down’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘.lower’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘.’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘50%’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
variable ‘.upper’
sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for
global variable ‘proportion_mean’
sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for
global variable ‘y’
sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for
global variable ‘observed_proportion’
sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for
global variable ‘logit_residuals’
sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for
global variable ‘exposure’
sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for
global variable ‘adjusted_proportion’
sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for
global variable ‘adjusted_counts’
sccomp_replicate.sccomp_tbl: no visible binding for global variable ‘N’
sccomp_replicate.sccomp_tbl: no visible binding for global variable ‘M’
sccomp_test.sccomp_tbl: no visible binding for global variable
‘design_matrix_col’
sccomp_test.sccomp_tbl: no visible binding for global variable
‘parameter’
sccomp_test.sccomp_tbl: no visible binding for global variable ‘M’
simulate_data.tbl: no visible binding for global variable
‘glm_dirichlet_multinomial_generate_quantities’
simulate_data.tbl: no visible binding for global variable ‘data___’
simulate_data.tbl: no visible binding for global variable ‘.exposure’
simulate_data.tbl: no visible binding for global variable ‘N’
simulate_data.tbl: no visible binding for global variable ‘M’
simulate_multinomial_logit_linear: no visible global function
definition for ‘rnorm’
summary_to_tibble: no visible binding for global variable ‘.’
summary_to_tibble: no visible binding for global variable ‘.variable’
Undefined global functions or variables:
. .chain .count .draw .draw_imputation .exposure .iteration .lower
.median .upper .value .variable 2.5% 5% 50% 95% 97.5% C_name FDR G M
N N_M N_random_intercepts R_k_hat S X XA X_random_intercept Xa
additional_parameters_to_save adjusted_counts adjusted_proportion
as.formula beta_1 beta_2 bigger_zero c_FDR c_effect c_lower c_upper
cell_type cell_type_label censoring_iteration chains cores count_data
data___ design design_matrix design_matrix_col detect_cores draw
dummy effect estimate exposure factor_1 factor___numeric factors
fit_list formula generated_counts generated_proportions
generated_quantity glm_dirichlet_multinomial
glm_dirichlet_multinomial_generate_quantities
glm_dirichlet_multinomial_imputation group group___label
group___numeric groupings idx intercept_in_design
is_factor_continuous is_group_right iteration khat logit_residuals
lower mat max_factor_numeric max_group_numeric max_mean_idx
max_minus_sum mean_idx min_mean_idx min_minus_sum minus_sum
multipanel_theme n_eff na.omit name observed_proportion outlier
outlier_above outlier_below pH0 parameter pass_fit ppc precision
proportion proportion_mean rnorm sd se_mean slope smaller_zero
stats_name stats_value tail tol_rel_obj truncation_down truncation_up
upper v_FDR v_effect v_lower v_upper value variable y
Consider adding
importFrom("stats", "as.formula", "formula", "na.omit", "rnorm", "sd")
importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
test_contrasts 58.313 0.163 58.598
sccomp_glm 57.039 0.184 57.345
sccomp_remove_outliers 45.188 0.395 45.660
sccomp_remove_unwanted_variation 22.667 0.180 22.895
sccomp_predict 15.907 0.204 16.179
simulate_data 13.313 0.116 13.454
plot.sccomp_tbl 12.306 0.260 12.594
sccomp_boxplot 12.031 0.224 12.281
plot_summary 11.509 0.171 11.705
sccomp_test 11.404 0.096 11.525
sccomp_estimate 11.204 0.223 11.450
sccomp_replicate 10.918 0.183 11.147
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/sccomp.Rcheck/00check.log’
for details.
sccomp.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL sccomp
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector<int>&, const int&, const int&, const int&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
73 | for (std::size_t i = 0; i < p - 1; i++) {
| ~~^~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
79 | } while (k < x);
| ~~^~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector<std::vector<double> >&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
105 | for (std::size_t j = 0; j != k; j++) {
| ~~^~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector<bool>&, const int&, const double&, const std::vector<int>&, std::vector<double>&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
126 | for (std::size_t j = 0; j != k; j++) {
| ~~^~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
132 | while ((first_zero < index.size()) && index[first_zero]) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
135 | if (first_zero == index.size()) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
143 | for (std::size_t i = 0; i != first_zero + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector<std::vector<double> >&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::dump::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
694 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
707 | real_iter < val_i->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp:85:40: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
85 | for (Eigen::Index pos = 0; pos < l_tri_size; pos++) {
| ~~~~^~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::random_var_context::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
111 | for (comp_iter = 0, real_iter = 0; real_iter < val_r.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::array_var_context::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
304 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
317 | real_iter < val_i->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6,
from stanExports_glm_multi_beta_binomial.h:25,
from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer<T>::read(Eigen::Index, Sizes ...) [with Ret = std::vector<Eigen::Matrix<double, -1, 1> >; Sizes = {int}; stan::require_std_vector_t<Ret>* <anonymous> = 0; stan::require_not_same_t<typename stan::value_type<S, void>::type, T>* <anonymous> = 0; T = double; Eigen::Index = long int]’:
stanExports_glm_multi_beta_binomial.h:2469:71: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
337 | for (size_t i = 0; i < m; ++i) {
| ~~^~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: 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]
74 | for (int i = 0; i < dims.size(); i++) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: 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.cc:5:
stanExports_glm_multi_beta_binomial.h: In instantiation of ‘void model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector<double>; VecI = std::vector<int>; stan::require_vector_t<T_y>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_glm_multi_beta_binomial.h:3450:36: required from here
stanExports_glm_multi_beta_binomial.h:2724:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
2724 | int pos__ = std::numeric_limits<int>::min();
| ^~~~~
stanExports_glm_multi_beta_binomial.h: In instantiation of ‘void model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix<double, -1, 1>; VecI = std::vector<int>; stan::require_vector_t<T_y>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_glm_multi_beta_binomial.h:3460:36: required from here
stanExports_glm_multi_beta_binomial.h:2724:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
207 | for (size_t i = 0; i < x.rows(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
208 | for (size_t j = 0; j < x.cols(); j++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t<U, V>* <anonymous> = 0; Idxs = {}]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare]
39 | if (unlikely(!(y <= high))) {
| ~~~^~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’
9 | #define unlikely(x) __builtin_expect(!!(x), 0)
| ^
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: 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]
55 | if (p_names.size() != draws.cols()) {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
71 | for (size_t i = 0; i < draws.rows(); ++i) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::detail::hypergeometric_pFq_checked_series_impl(const Seq&, const Seq&, const Real&, const Policy&, const Terminal&, long long int&) [with Seq = std::vector<double>; Real = 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>; Terminal = boost::math::detail::iteration_terminator]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:107: required from ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector<double>; Real = 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<Real, typename Seq::value_type>::type = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:72:35: required from ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*) [with Seq = std::vector<double>; Real = double; typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:55:41: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, -1, 1>; Tb = Eigen::Matrix<double, -1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector<double>; Tb = std::vector<double>; Tz = double; stan::require_all_vector_t<T_y, T_high>* <anonymous> = 0; stan::require_stan_scalar_t<T2>* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Up>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t<Ta, Tb, Tz>* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp:122:28: 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
122 | std::pair<Real, Real> hypergeometric_pFq_checked_series_impl(const Seq& aj, const Seq& bj, const Real& z, const Policy& pol, const Terminal& termination, long long& log_scale)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6,
from stanExports_glm_multi_beta_binomial.h:25,
from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer<T>::read(Eigen::Index, Sizes ...) [with Ret = std::vector<Eigen::Matrix<stan::math::var_value<double>, -1, 1>, std::allocator<Eigen::Matrix<stan::math::var_value<double>, -1, 1> > >; Sizes = {int}; stan::require_std_vector_t<Ret>* <anonymous> = 0; stan::require_not_same_t<typename stan::value_type<S, void>::type, T>* <anonymous> = 0; T = stan::math::var_value<double>; Eigen::Index = long int]’:
stanExports_glm_multi_beta_binomial.h:2104:78: 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:3423:47: 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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
337 | for (size_t i = 0; i < m; ++i) {
| ~~^~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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, 2, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 2, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 2, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, 1, 0, 1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 2, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 2, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, 1, 0, 1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1721,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp: In instantiation of ‘boost::math::detail::temme_root_finder<T>::temme_root_finder(T, T) [with T = double]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: required from ‘T boost::math::detail::temme_method_2_ibeta_inverse(T, T, T, T, T, const Policy&) [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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:48: required from ‘T boost::math::detail::ibeta_inv_imp(T, T, T, T, 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:30: required from ‘boost::math::tools::promote_args_t<T1, T2, T3, T4> boost::math::ibeta_inv(T1, T2, T3, T4*, const Policy&) [with T1 = double; T2 = double; T3 = double; T4 = 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>; boost::math::tools::promote_args_t<T1, T2, T3, T4> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:20: required from ‘boost::math::tools::promote_args_t<RT1, RT2, A> boost::math::ibeta_inv(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>; boost::math::tools::promote_args_t<RT1, RT2, A> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable ‘x_extrema’ [-Wunused-variable]
29 | const T x_extrema = 1 / (1 + a);
| ^~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35: required from ‘boost::math::tools::promote_args_t<RT1, RT2> 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>; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘boost::math::tools::promote_args_t<RT1, RT2> 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>; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘boost::math::tools::promote_args_t<RT1, RT2> boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:830:54: 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1472:36: 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1509:20: 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1663:93: required from ‘boost::math::tools::promote_args_t<RT1, RT2, A> 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>; boost::math::tools::promote_args_t<RT1, RT2, A> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:793:16: 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
793 | result_type operator()()
| ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/beta_binomial_lpmf.hpp:63:24: 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::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_n, T_N, T_size1, T_size2>* <anonymous> = 0; stan::return_type_t<T_size1, T_size2> = stan::math::var_value<double>]’
stanExports_glm_multi_beta_binomial.h:2199:63: 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:3423:47: 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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t<T, L, U> 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, L, U> = stan::math::var_value<double>]’
stanExports_glm_multi_beta_binomial.h:2248:65: 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:3423:47: 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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:63:15: required from ‘stan::return_type_t<T, L, U> 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, L, U> = stan::math::var_value<double>]’
stanExports_glm_multi_beta_binomial.h:2248:65: 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:3423:47: 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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t<T> 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<T> = stan::math::var_value<double>]’
stanExports_glm_multi_beta_binomial.h:2352:65: 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:3423:47: 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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t<T> 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<T> = stan::math::var_value<double>]’
stanExports_glm_multi_beta_binomial.h:2361:65: 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:3423:47: 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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/beta_binomial_lpmf.hpp:63:24: 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::CwiseNullaryOp<stan::model::rvalue<Eigen::Matrix<double, -1, 1>&, 0>::<lambda(auto:703&)> [with auto:703 = Eigen::Matrix<double, -1, 1>]::<lambda(Eigen::Index)>, Eigen::Matrix<double, -1, 1> >, const Eigen::CwiseNullaryOp<stan::model::rvalue<Eigen::Matrix<double, -1, 1>&, 0>::<lambda(auto:703&)> [with auto:703 = Eigen::Matrix<double, -1, 1>]::<lambda(Eigen::Index)>, 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::CwiseNullaryOp<stan::model::rvalue<Eigen::Matrix<double, -1, 1>&, 0>::<lambda(auto:703&)> [with auto:703 = Eigen::Matrix<double, -1, 1>]::<lambda(Eigen::Index)>, Eigen::Matrix<double, -1, 1> > > > >, const Eigen::CwiseNullaryOp<stan::model::rvalue<Eigen::Matrix<double, -1, 1>&, 0>::<lambda(auto:703&)> [with auto:703 = Eigen::Matrix<double, -1, 1>]::<lambda(Eigen::Index)>, Eigen::Matrix<double, -1, 1> > >; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_n, T_N, T_size1, T_size2>* <anonymous> = 0; stan::return_type_t<T_size1, T_size2> = double]’
stanExports_glm_multi_beta_binomial.h:2199:63: 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:3423:47: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: 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; bool jacobian = false]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t<T, L, U> 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, L, U> = double]’
stanExports_glm_multi_beta_binomial.h:2278:65: 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:3423:47: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: 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; bool jacobian = false]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t<T> 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<T> = double]’
stanExports_glm_multi_beta_binomial.h:2352:65: 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:3423:47: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: 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; bool jacobian = false]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/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<Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > > >::<lambda(double)>; T = Eigen::ArrayWrapper<Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > >; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > >]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t<T, L, U> 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, L, U> = double]’
stanExports_glm_multi_beta_binomial.h:735:42: required from ‘stan::promote_args_t<typename stan::base_type<T, void>::type, typename stan::base_type<T1__, 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::require_all_t<stan::is_row_vector<Row>, stan::is_vt_not_complex<T0__>, stan::is_row_vector<Vec>, stan::is_vt_not_complex<T1__>, stan::is_stan_scalar<T2__>, stan::is_stan_scalar<T3__>, stan::is_stan_scalar<T5__> >* <anonymous> = 0; stan::promote_args_t<typename stan::base_type<T, void>::type, typename stan::base_type<T1__, void>::type, T2__, T3__, T5__> = double; typename stan::base_type<T>::type = double; typename stan::base_type<T1__, void>::type = double; std::ostream = std::basic_ostream<char>]’
stanExports_glm_multi_beta_binomial.h:2224:60: 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:3423:47: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: 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; bool jacobian = false]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::ArrayWrapper<Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > > >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp: In function ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector<double>; Real = 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:44: 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
61 | std::pair<value_type, value_type> r = boost::math::detail::hypergeometric_pFq_checked_series_impl(aj, bj, value_type(z), pol, boost::math::detail::iteration_terminator(boost::math::policies::get_max_series_iterations<forwarding_policy>()), scale);
| ^
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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<double>; U = double]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: 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
217 | value_type v = g();
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector<int>&, const int&, const int&, const int&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
73 | for (std::size_t i = 0; i < p - 1; i++) {
| ~~^~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
79 | } while (k < x);
| ~~^~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector<std::vector<double> >&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
105 | for (std::size_t j = 0; j != k; j++) {
| ~~^~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector<bool>&, const int&, const double&, const std::vector<int>&, std::vector<double>&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
126 | for (std::size_t j = 0; j != k; j++) {
| ~~^~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
132 | while ((first_zero < index.size()) && index[first_zero]) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
135 | if (first_zero == index.size()) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
143 | for (std::size_t i = 0; i != first_zero + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector<std::vector<double> >&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::dump::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
694 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
707 | real_iter < val_i->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp:85:40: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
85 | for (Eigen::Index pos = 0; pos < l_tri_size; pos++) {
| ~~~~^~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::random_var_context::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
111 | for (comp_iter = 0, real_iter = 0; real_iter < val_r.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::array_var_context::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
304 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
317 | real_iter < val_i->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: 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]
74 | for (int i = 0; i < dims.size(); i++) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:13,
from stanExports_glm_multi_beta_binomial_generate_date.h:25,
from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp: In instantiation of ‘stan::plain_type_t<T> stan::model::rvalue(EigMat&&, const char*, const stan::model::index_multi&) [with EigMat = Eigen::Matrix<double, -1, -1>&; stan::require_eigen_dense_dynamic_t<M>* <anonymous> = 0; stan::plain_type_t<T> = std::decay<const Eigen::Matrix<double, -1, -1>&>::type]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:583:16: required from ‘auto stan::model::rvalue(Mat&&, const char*, const Idx&, stan::model::index_omni) [with Mat = Eigen::Matrix<double, -1, -1>&; Idx = stan::model::index_multi; stan::require_dense_dynamic_t<T_y>* <anonymous> = 0]’
stanExports_glm_multi_beta_binomial_generate_date.h:615:36: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:268:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
268 | for (int i = 0; i < idx.ns_.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
stanExports_glm_multi_beta_binomial_generate_date.h: In instantiation of ‘void model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector<double>; VecI = std::vector<int>; stan::require_vector_t<T_y>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_glm_multi_beta_binomial_generate_date.h:1165:36: required from here
stanExports_glm_multi_beta_binomial_generate_date.h:780:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
780 | int pos__ = std::numeric_limits<int>::min();
| ^~~~~
stanExports_glm_multi_beta_binomial_generate_date.h: In instantiation of ‘void model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix<double, -1, 1>; VecI = std::vector<int>; stan::require_vector_t<T_y>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_glm_multi_beta_binomial_generate_date.h:1175:36: required from here
stanExports_glm_multi_beta_binomial_generate_date.h:780:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
207 | for (size_t i = 0; i < x.rows(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
208 | for (size_t j = 0; j < x.cols(); j++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t<U, V>* <anonymous> = 0; Idxs = {}]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare]
39 | if (unlikely(!(y <= high))) {
| ~~~^~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’
9 | #define unlikely(x) __builtin_expect(!!(x), 0)
| ^
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: 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]
55 | if (p_names.size() != draws.cols()) {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
71 | for (size_t i = 0; i < draws.rows(); ++i) {
| ~~^~~~~~~~~~~~~~
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
stanExports_glm_multi_beta_binomial_generate_date.h: In instantiation of ‘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_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_glm_multi_beta_binomial_generate_date.h:1127:21: 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-beta-2024-04-15_r86425/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
stanExports_glm_multi_beta_binomial_generate_date.h:567:20: warning: unused variable ‘jacobian__’ [-Wunused-variable]
567 | constexpr bool jacobian__ = false;
| ^~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::detail::hypergeometric_pFq_checked_series_impl(const Seq&, const Seq&, const Real&, const Policy&, const Terminal&, long long int&) [with Seq = std::vector<double>; Real = 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>; Terminal = boost::math::detail::iteration_terminator]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:107: required from ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector<double>; Real = 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<Real, typename Seq::value_type>::type = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:72:35: required from ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*) [with Seq = std::vector<double>; Real = double; typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:55:41: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, -1, 1>; Tb = Eigen::Matrix<double, -1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector<double>; Tb = std::vector<double>; Tz = double; stan::require_all_vector_t<T_y, T_high>* <anonymous> = 0; stan::require_stan_scalar_t<T2>* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Up>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t<Ta, Tb, Tz>* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp:122:28: 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
122 | std::pair<Real, Real> hypergeometric_pFq_checked_series_impl(const Seq& aj, const Seq& bj, const Real& z, const Policy& pol, const Terminal& termination, long long& log_scale)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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, 2, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 2, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 2, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, 1, 0, 1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 2, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 2, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, 1, 0, 1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1721,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp: In instantiation of ‘boost::math::detail::temme_root_finder<T>::temme_root_finder(T, T) [with T = double]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: required from ‘T boost::math::detail::temme_method_2_ibeta_inverse(T, T, T, T, T, const Policy&) [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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:48: required from ‘T boost::math::detail::ibeta_inv_imp(T, T, T, T, 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:30: required from ‘boost::math::tools::promote_args_t<T1, T2, T3, T4> boost::math::ibeta_inv(T1, T2, T3, T4*, const Policy&) [with T1 = double; T2 = double; T3 = double; T4 = 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>; boost::math::tools::promote_args_t<T1, T2, T3, T4> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:20: required from ‘boost::math::tools::promote_args_t<RT1, RT2, A> boost::math::ibeta_inv(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>; boost::math::tools::promote_args_t<RT1, RT2, A> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable ‘x_extrema’ [-Wunused-variable]
29 | const T x_extrema = 1 / (1 + a);
| ^~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35: required from ‘boost::math::tools::promote_args_t<RT1, RT2> 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>; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘boost::math::tools::promote_args_t<RT1, RT2> 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>; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘boost::math::tools::promote_args_t<RT1, RT2> boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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:707:40: 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_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’
stanExports_glm_multi_beta_binomial_generate_date.h:1127:21: 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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:830:54: 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1472:36: 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1509:20: 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1663:93: required from ‘boost::math::tools::promote_args_t<RT1, RT2, A> 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>; boost::math::tools::promote_args_t<RT1, RT2, A> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:793:16: 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
793 | result_type operator()()
| ^~~~~~~~
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
stanExports_glm_multi_beta_binomial_generate_date.h: In instantiation of ‘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 = Eigen::Matrix<double, -1, 1>; VecI = std::vector<int>; VecVar = Eigen::Matrix<double, -1, 1>; 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_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_glm_multi_beta_binomial_generate_date.h:1108:21: required from ‘void model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date::write_array(RNG&, Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&, 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:140:61: required from ‘void stan::model::model_base_crtp<M>::write_array(boost::random::ecuyer1988&, Eigen::VectorXd&, Eigen::VectorXd&, bool, bool, std::ostream*) const [with M = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; boost::random::ecuyer1988 = 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> >; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:136:8: required from here
stanExports_glm_multi_beta_binomial_generate_date.h:567:20: warning: unused variable ‘jacobian__’ [-Wunused-variable]
567 | constexpr bool jacobian__ = false;
| ^~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp: In function ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector<double>; Real = 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:44: 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
61 | std::pair<value_type, value_type> r = boost::math::detail::hypergeometric_pFq_checked_series_impl(aj, bj, value_type(z), pol, boost::math::detail::iteration_terminator(boost::math::policies::get_max_series_iterations<forwarding_policy>()), scale);
| ^
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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<double>; U = double]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: 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
217 | value_type v = g();
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
251 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
508 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
521 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
604 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
613 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
615 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector<int>&, const int&, const int&, const int&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
73 | for (std::size_t i = 0; i < p - 1; i++) {
| ~~^~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
79 | } while (k < x);
| ~~^~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector<std::vector<double> >&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
105 | for (std::size_t j = 0; j != k; j++) {
| ~~^~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector<bool>&, const int&, const double&, const std::vector<int>&, std::vector<double>&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
126 | for (std::size_t j = 0; j != k; j++) {
| ~~^~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
132 | while ((first_zero < index.size()) && index[first_zero]) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
135 | if (first_zero == index.size()) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
143 | for (std::size_t i = 0; i != first_zero + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector<std::vector<double> >&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::dump::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
694 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
707 | real_iter < val_i->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp:85:40: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
85 | for (Eigen::Index pos = 0; pos < l_tri_size; pos++) {
| ~~~~^~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::random_var_context::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
111 | for (comp_iter = 0, real_iter = 0; real_iter < val_r.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::array_var_context::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
304 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
317 | real_iter < val_i->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: 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]
74 | for (int i = 0; i < dims.size(); i++) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: 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&, VecVar&, std::ostream*) const [with VecVar = std::vector<double>; stan::require_vector_t<T_y>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_glm_multi_beta_binomial_simulate_data.h:797:50: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:568:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
568 | int pos__ = std::numeric_limits<int>::min();
| ^~~~~
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::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector<double>; VecI = std::vector<int>; stan::require_vector_t<T_y>* <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:807:36: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:534:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
534 | int pos__ = std::numeric_limits<int>::min();
| ^~~~~
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::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix<double, -1, 1>; VecI = std::vector<int>; stan::require_vector_t<T_y>* <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:817:36: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:534:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
207 | for (size_t i = 0; i < x.rows(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
208 | for (size_t j = 0; j < x.cols(); j++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:10,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t<U, V>* <anonymous> = 0; Idxs = {}]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare]
39 | if (unlikely(!(y <= high))) {
| ~~~^~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’
9 | #define unlikely(x) __builtin_expect(!!(x), 0)
| ^
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: 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]
55 | if (p_names.size() != draws.cols()) {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
71 | for (size_t i = 0; i < draws.rows(); ++i) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::detail::hypergeometric_pFq_checked_series_impl(const Seq&, const Seq&, const Real&, const Policy&, const Terminal&, long long int&) [with Seq = std::vector<double>; Real = 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>; Terminal = boost::math::detail::iteration_terminator]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:107: required from ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector<double>; Real = 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<Real, typename Seq::value_type>::type = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:72:35: required from ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*) [with Seq = std::vector<double>; Real = double; typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:55:41: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, -1, 1>; Tb = Eigen::Matrix<double, -1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector<double>; Tb = std::vector<double>; Tz = double; stan::require_all_vector_t<T_y, T_high>* <anonymous> = 0; stan::require_stan_scalar_t<T2>* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Up>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t<Ta, Tb, Tz>* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp:122:28: 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
122 | std::pair<Real, Real> hypergeometric_pFq_checked_series_impl(const Seq& aj, const Seq& bj, const Real& z, const Policy& pol, const Terminal& termination, long long& log_scale)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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, 2, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 2, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 2, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, 1, 0, 1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 2, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 2, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, 1, 0, 1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1721,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp: In instantiation of ‘boost::math::detail::temme_root_finder<T>::temme_root_finder(T, T) [with T = double]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: required from ‘T boost::math::detail::temme_method_2_ibeta_inverse(T, T, T, T, T, const Policy&) [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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:48: required from ‘T boost::math::detail::ibeta_inv_imp(T, T, T, T, 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:30: required from ‘boost::math::tools::promote_args_t<T1, T2, T3, T4> boost::math::ibeta_inv(T1, T2, T3, T4*, const Policy&) [with T1 = double; T2 = double; T3 = double; T4 = 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>; boost::math::tools::promote_args_t<T1, T2, T3, T4> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:20: required from ‘boost::math::tools::promote_args_t<RT1, RT2, A> boost::math::ibeta_inv(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>; boost::math::tools::promote_args_t<RT1, RT2, A> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable ‘x_extrema’ [-Wunused-variable]
29 | const T x_extrema = 1 / (1 + a);
| ^~~~~~~~~
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
stanExports_glm_multi_beta_binomial_simulate_data.h: In instantiation of ‘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__ = 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_simulate_data.h:780:47: 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__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: 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_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; bool jacobian = false]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_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> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_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:15:87: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:319:24: warning: variable ‘prec_sd’ set but not used [-Wunused-but-set-variable]
319 | local_scalar_t__ prec_sd = DUMMY_VAR__;
| ^~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35: required from ‘boost::math::tools::promote_args_t<RT1, RT2> 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>; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘boost::math::tools::promote_args_t<RT1, RT2> 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>; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘boost::math::tools::promote_args_t<RT1, RT2> boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/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 stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
stanExports_glm_multi_beta_binomial_simulate_data.h: In instantiation of ‘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__ = false; bool jacobian__ = true; 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_simulate_data.h:780:47: 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__ = false; bool jacobian__ = true; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:129:58: required from ‘std::vector<double> stan::services::util::initialize(Model&, const InitContext&, RNG&, double, bool, stan::callbacks::logger&, stan::callbacks::writer&) [with bool Jacobian = true; Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; InitContext = stan::io::var_context; 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> >]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:53: required from ‘int stan::services::diagnose::diagnose(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, double, double, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:481:53: 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_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> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_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:15:87: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:319:24: warning: variable ‘prec_sd’ set but not used [-Wunused-but-set-variable]
319 | local_scalar_t__ prec_sd = DUMMY_VAR__;
| ^~~~~~~
stanExports_glm_multi_beta_binomial_simulate_data.h: In instantiation of ‘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__ = false; bool jacobian__ = true; VecR = Eigen::Matrix<double, -1, 1>; VecI = Eigen::Matrix<int, -1, 1>; 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_simulate_data.h:775:47: required from ‘T_ model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = true; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/advi.hpp:514:52: required from ‘int stan::variational::advi<Model, Q, BaseRNG>::run(double, bool, int, double, int, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) const [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; Q = stan::variational::normal_fullrank; BaseRNG = 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> >]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/experimental/advi/fullrank.hpp:82:15: required from ‘int stan::services::experimental::advi::fullrank(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, int, int, double, double, bool, int, int, int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:890:17: 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_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> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_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:15:87: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:319:24: warning: variable ‘prec_sd’ set but not used [-Wunused-but-set-variable]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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:462:40: 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_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’
stanExports_glm_multi_beta_binomial_simulate_data.h:769:21: 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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:830:54: 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1472:36: 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1509:20: 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1663:93: required from ‘boost::math::tools::promote_args_t<RT1, RT2, A> 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>; boost::math::tools::promote_args_t<RT1, RT2, A> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:793:16: 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
793 | result_type operator()()
| ^~~~~~~~
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
stanExports_glm_multi_beta_binomial_simulate_data.h: In instantiation of ‘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__ = false; bool jacobian__ = false; VecR = Eigen::Matrix<double, -1, 1>; VecI = Eigen::Matrix<int, -1, 1>; 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_simulate_data.h:775:47: required from ‘T_ model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:93:80: required from ‘double stan::model::model_base_crtp<M>::log_prob(Eigen::VectorXd&, std::ostream*) const [with M = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:91:17: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:319:24: warning: variable ‘prec_sd’ set but not used [-Wunused-but-set-variable]
319 | local_scalar_t__ prec_sd = DUMMY_VAR__;
| ^~~~~~~
stanExports_glm_multi_beta_binomial_simulate_data.h: In instantiation of ‘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__ = false; VecR = Eigen::Matrix<double, -1, 1>; VecI = Eigen::Matrix<int, -1, 1>; 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_simulate_data.h:775:47: required from ‘T_ model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:115:71: required from ‘double stan::model::model_base_crtp<M>::log_prob_propto(Eigen::VectorXd&, std::ostream*) const [with M = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:113:17: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:319:24: warning: variable ‘prec_sd’ set but not used [-Wunused-but-set-variable]
stanExports_glm_multi_beta_binomial_simulate_data.h: In instantiation of ‘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 = Eigen::Matrix<double, -1, 1>; VecI = Eigen::Matrix<int, -1, 1>; 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_simulate_data.h:775:47: required from ‘T_ model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:126:70: required from ‘double stan::model::model_base_crtp<M>::log_prob_propto_jacobian(Eigen::VectorXd&, std::ostream*) const [with M = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:124:17: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:319:24: warning: variable ‘prec_sd’ set but not used [-Wunused-but-set-variable]
stanExports_glm_multi_beta_binomial_simulate_data.h: In instantiation of ‘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__ = 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_simulate_data.h:780:47: 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__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:182:71: required from ‘double stan::model::model_base_crtp<M>::log_prob_propto(std::vector<double>&, std::vector<int>&, std::ostream*) const [with 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:179:17: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:319:24: warning: variable ‘prec_sd’ set but not used [-Wunused-but-set-variable]
stanExports_glm_multi_beta_binomial_simulate_data.h: In instantiation of ‘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<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_simulate_data.h:780:47: 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_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:195:70: required from ‘double stan::model::model_base_crtp<M>::log_prob_propto_jacobian(std::vector<double>&, std::vector<int>&, std::ostream*) const [with 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_base_crtp.hpp:192:17: required from here
stanExports_glm_multi_beta_binomial_simulate_data.h:319:24: warning: variable ‘prec_sd’ set but not used [-Wunused-but-set-variable]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp: In function ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector<double>; Real = 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:44: 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
61 | std::pair<value_type, value_type> r = boost::math::detail::hypergeometric_pFq_checked_series_impl(aj, bj, value_type(z), pol, boost::math::detail::iteration_terminator(boost::math::policies::get_max_series_iterations<forwarding_policy>()), scale);
| ^
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:18,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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<double>; U = double]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: 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
217 | value_type v = g();
| ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: typecancer, typehealthy
sccomp says: the variability design matrix has columns: typecancer, typehealthy
sccomp says: From version 1.7.7 the model by default is fit with the variational inference method (variational_inference = TRUE; much faster). For a full Bayesian inference (HMC method; the gold standard) use variational_inference = FALSE.
This message is displayed once per session.
sccomp says: outlier identification - step 1/2
sccomp says: outlier-free model fitting - step 2/2
sccomp says: the composition design matrix has columns: typecancer, typehealthy
sccomp says: the variability design matrix has columns: typecancer, typehealthy
sccomp says: calculating residuals
sccomp says: regressing out unwanted factors
Joining with `by = join_by(cell_group, sample)`
Joining with `by = join_by(cell_group, type)`
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), continuous_covariate, typehealthy, continuous_covariate:typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
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 0.000655 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.55 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: 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: Iteration: 250 / 250 [100%] (Adaptation)
Chain 1: Success! Found best value [eta = 0.1].
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -4905.096 1.000 1.000
Chain 1: 200 -4077.463 0.601 1.000
Chain 1: 300 -3745.212 0.431 0.203
Chain 1: 400 -3562.547 0.336 0.203
Chain 1: 500 -3465.209 0.274 0.089
Chain 1: 600 -3399.343 0.232 0.089
Chain 1: 700 -3359.020 0.200 0.051
Chain 1: 800 -3328.728 0.176 0.051
Chain 1: 900 -3311.712 0.157 0.028
Chain 1: 1000 -3284.990 0.142 0.028
Chain 1: 1100 -3271.539 0.043 0.019
Chain 1: 1200 -3264.321 0.023 0.012
Chain 1: 1300 -3256.480 0.014 0.009 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), continuous_covariate, typehealthy, continuous_covariate:typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000657 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.57 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup)
Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling)
Chain 1: Iteration: 1300 / 1300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 4.495 seconds (Warm-up)
Chain 1: 8.348 seconds (Sampling)
Chain 1: 12.843 seconds (Total)
Chain 1:
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: typecancer, typehealthy, continuous_covariate
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 0.000642 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.42 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 -3277.756 1.000 1.000
Chain 1: 200 -3196.968 0.513 1.000
Chain 1: 300 -3191.089 0.342 0.025
Chain 1: 400 -3187.829 0.257 0.025
Chain 1: 500 -3191.394 0.206 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: typecancer, typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000793 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.93 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup)
Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling)
Chain 1: Iteration: 1300 / 1300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 11.107 seconds (Warm-up)
Chain 1: 29.091 seconds (Sampling)
Chain 1: 40.198 seconds (Total)
Chain 1:
sccomp says: outlier identification - step 1/2
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 0.000623 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.23 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: Iteration: 250 / 250 [100%] (Adaptation)
Chain 1: Success! Found best value [eta = 0.1].
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -4781.171 1.000 1.000
Chain 1: 200 -3971.009 0.602 1.000
Chain 1: 300 -3637.424 0.432 0.204
Chain 1: 400 -3505.688 0.333 0.204
Chain 1: 500 -3389.983 0.273 0.092
Chain 1: 600 -3317.783 0.232 0.092
Chain 1: 700 -3260.582 0.201 0.038
Chain 1: 800 -3226.832 0.177 0.038
Chain 1: 900 -3194.633 0.159 0.034
Chain 1: 1000 -3177.027 0.143 0.034
Chain 1: 1100 -3158.273 0.044 0.022
Chain 1: 1200 -3146.812 0.024 0.018
Chain 1: 1300 -3134.948 0.015 0.010
Chain 1: 1400 -3128.273 0.012 0.010
Chain 1: 1500 -3120.540 0.008 0.006 MEAN ELBO CONVERGED 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 2/2
sccomp says: the composition design matrix has columns: (Intercept), continuous_covariate, typehealthy, continuous_covariate:typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
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 0.000628 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.28 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: Iteration: 250 / 250 [100%] (Adaptation)
Chain 1: Success! Found best value [eta = 0.1].
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -4909.820 1.000 1.000
Chain 1: 200 -4040.130 0.608 1.000
Chain 1: 300 -3717.911 0.434 0.215
Chain 1: 400 -3557.971 0.337 0.215
Chain 1: 500 -3449.401 0.276 0.087
Chain 1: 600 -3374.351 0.233 0.087
Chain 1: 700 -3314.721 0.203 0.045
Chain 1: 800 -3281.373 0.179 0.045
Chain 1: 900 -3253.520 0.160 0.031
Chain 1: 1000 -3230.971 0.144 0.031
Chain 1: 1100 -3208.439 0.045 0.022
Chain 1: 1200 -3201.840 0.024 0.018
Chain 1: 1300 -3189.201 0.016 0.010
Chain 1: 1400 -3177.696 0.011 0.009 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
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 0.000727 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.27 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 -3259.836 1.000 1.000
Chain 1: 200 -3170.846 0.514 1.000
Chain 1: 300 -3163.996 0.343 0.028
Chain 1: 400 -3161.271 0.258 0.028
Chain 1: 500 -3161.564 0.206 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), continuous_covariate
sccomp says: the variability design matrix has columns: (Intercept)
SAMPLING FOR MODEL 'glm_multi_beta_binomial' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000811 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 8.11 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Iteration: 1 / 1300 [ 0%] (Warmup)
Chain 1: Iteration: 301 / 1300 [ 23%] (Sampling)
Chain 1: Iteration: 1300 / 1300 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 14.955 seconds (Warm-up)
Chain 1: 41.825 seconds (Sampling)
Chain 1: 56.78 seconds (Total)
Chain 1:
Loading required package: ttservice
Attaching package: 'ttservice'
The following objects are masked from 'package:dplyr':
bind_cols, bind_rows
Loading required package: SeuratObject
Loading required package: sp
Attaching package: 'SeuratObject'
The following object is masked from 'package:base':
intersect
========================================
tidyseurat version 0.8.0
If you use TIDYSEURAT in published research, please cite:
Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.
This message can be suppressed by:
suppressPackageStartupMessages(library(tidyseurat))
To restore the Seurat default display use options("restore_Seurat_show" = TRUE)
========================================
Attaching package: 'tidyseurat'
The following object is masked from 'package:ttservice':
plot_ly
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typehealthy, batch
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 0.000616 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.16 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: Iteration: 250 / 250 [100%] (Adaptation)
Chain 1: Success! Found best value [eta = 0.1].
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -4522.444 1.000 1.000
Chain 1: 200 -3799.209 0.595 1.000
Chain 1: 300 -3510.725 0.424 0.190
Chain 1: 400 -3386.013 0.327 0.190
Chain 1: 500 -3321.092 0.266 0.082
Chain 1: 600 -3286.420 0.223 0.082
Chain 1: 700 -3258.831 0.193 0.037
Chain 1: 800 -3239.101 0.169 0.037
Chain 1: 900 -3230.705 0.151 0.020
Chain 1: 1000 -3216.965 0.136 0.020
Chain 1: 1100 -3213.073 0.036 0.011
Chain 1: 1200 -3206.270 0.017 0.008 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
sccomp says: calculating residuals
sccomp says: regressing out unwanted factors
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
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 0.000614 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.14 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 -3247.354 1.000 1.000
Chain 1: 200 -3162.277 0.513 1.000
Chain 1: 300 -3151.517 0.343 0.027
Chain 1: 400 -3150.089 0.258 0.027
Chain 1: 500 -3147.767 0.206 0.003 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
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 0.000586 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 5.86 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 -3218.250 1.000 1.000
Chain 1: 200 -3154.922 0.510 1.000
Chain 1: 300 -3153.512 0.340 0.020
Chain 1: 400 -3148.086 0.256 0.020
Chain 1: 500 -3148.325 0.204 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept), typehealthy
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 0.000591 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 5.91 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 -3248.662 1.000 1.000
Chain 1: 200 -3168.815 0.513 1.000
Chain 1: 300 -3164.832 0.342 0.025
Chain 1: 400 -3159.578 0.257 0.025
Chain 1: 500 -3159.231 0.206 0.002 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
Joining with `by = join_by(cell_group, sample)`
Joining with `by = join_by(cell_group, sample, continuous_covariate)`
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)`
[ FAIL 0 | WARN 168 | SKIP 8 | PASS 21 ]
══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• empty test (8): 'test-old_framework.R:36:1', 'test-old_framework.R:43:1',
'test-sccomp_.R:148:1', 'test-sccomp_.R:156:1', 'test-sccomp_.R:288:1',
'test-sccomp_.R:317:1', 'test-sccomp_.R:369:1', 'test-sccomp_.R:398:1'
[ FAIL 0 | WARN 168 | SKIP 8 | PASS 21 ]
>
> proc.time()
user system elapsed
485.900 4.211 491.160
sccomp.Rcheck/sccomp-Ex.timings
| name | user | system | elapsed | |
| plot.sccomp_tbl | 12.306 | 0.260 | 12.594 | |
| plot_summary | 11.509 | 0.171 | 11.705 | |
| sccomp_boxplot | 12.031 | 0.224 | 12.281 | |
| sccomp_estimate | 11.204 | 0.223 | 11.450 | |
| sccomp_glm | 57.039 | 0.184 | 57.345 | |
| sccomp_predict | 15.907 | 0.204 | 16.179 | |
| sccomp_remove_outliers | 45.188 | 0.395 | 45.660 | |
| sccomp_remove_unwanted_variation | 22.667 | 0.180 | 22.895 | |
| sccomp_replicate | 10.918 | 0.183 | 11.147 | |
| sccomp_test | 11.404 | 0.096 | 11.525 | |
| simulate_data | 13.313 | 0.116 | 13.454 | |
| test_contrasts | 58.313 | 0.163 | 58.598 | |