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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:sccomp.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings sccomp_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sccomp.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘sccomp/DESCRIPTION’ ... OK
* this is package ‘sccomp’ version ‘1.5.0’
* 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 125.7Mb
  sub-directories of 1Mb or more:
    data    1.2Mb
    libs  123.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alpha_to_CI: no visible binding for global variable ‘M’
alpha_to_CI: no visible binding for global variable ‘C_name’
alpha_to_CI: no visible binding for global variable ‘.lower’
alpha_to_CI: no visible binding for global variable ‘.median’
alpha_to_CI: no visible binding for global variable ‘.upper’
as_matrix: no visible binding for global variable ‘variable’
beta_to_CI: no visible binding for global variable ‘M’
beta_to_CI: no visible binding for global variable ‘C_name’
beta_to_CI: no visible binding for global variable ‘.lower’
beta_to_CI: no visible binding for global variable ‘.median’
beta_to_CI: no visible binding for global variable ‘.upper’
check_if_within_posterior: no visible binding for global variable
  ‘.lower’
check_if_within_posterior: no visible binding for global variable
  ‘.upper’
check_if_within_posterior: no visible binding for global variable ‘ppc’
check_random_intercept_design: no visible binding for global variable
  ‘factors’
check_random_intercept_design: no visible binding for global variable
  ‘groupings’
contrasts_to_enquos: no visible binding for global variable ‘.’
data_simulation_to_model_input: no visible binding for global variable
  ‘.’
data_spread_to_model_input: no visible global function definition for
  ‘as.formula’
data_spread_to_model_input: no visible binding for global variable
  ‘exposure’
data_spread_to_model_input: no visible binding for global variable
  ‘design’
data_spread_to_model_input: no visible binding for global variable
  ‘mat’
data_spread_to_model_input: no visible binding for global variable
  ‘is_factor_continuous’
data_spread_to_model_input: no visible binding for global variable
  ‘design_matrix’
data_spread_to_model_input: no visible binding for global variable ‘.’
data_spread_to_model_input: no visible binding for global variable
  ‘minus_sum’
data_spread_to_model_input: no visible binding for global variable
  ‘mean_idx’
data_spread_to_model_input: no visible binding for global variable
  ‘group___numeric’
data_spread_to_model_input: no visible binding for global variable
  ‘idx’
data_spread_to_model_input: no visible binding for global variable
  ‘group___label’
data_spread_to_model_input: no visible binding for global variable
  ‘parameter’
data_spread_to_model_input: no visible binding for global variable
  ‘design_matrix_col’
data_to_spread: no visible binding for global variable ‘exposure’
design_matrix_and_coefficients_to_dir_mult_simulation: no visible
  binding for global variable ‘cell_type’
design_matrix_and_coefficients_to_dir_mult_simulation: no visible
  binding for global variable ‘generated_counts’
design_matrix_and_coefficients_to_dir_mult_simulation: no visible
  binding for global variable ‘factor_1’
design_matrix_and_coefficients_to_simulation: no visible binding for
  global variable ‘cell_type’
design_matrix_and_coefficients_to_simulation: no visible binding for
  global variable ‘beta_1’
design_matrix_and_coefficients_to_simulation: no visible binding for
  global variable ‘beta_2’
dirichlet_multinomial_glm: no visible global function definition for
  ‘detect_cores’
dirichlet_multinomial_glm: no visible binding for global variable
  ‘glm_dirichlet_multinomial’
dirichlet_multinomial_glm: no visible binding for global variable
  ‘censoring_iteration’
dirichlet_multinomial_glm: no visible binding for global variable ‘.’
dirichlet_multinomial_glm: no visible binding for global variable
  ‘chains’
dirichlet_multinomial_glm: no visible binding for global variable
  ‘precision’
dirichlet_multinomial_glm: no visible binding for global variable ‘M’
do_inference_imputation: no visible binding for global variable
  ‘glm_dirichlet_multinomial_imputation’
draws_to_statistics: no visible binding for global variable ‘M’
draws_to_statistics: no visible binding for global variable ‘parameter’
draws_to_statistics: no visible binding for global variable
  ‘bigger_zero’
draws_to_statistics: no visible binding for global variable
  ‘smaller_zero’
draws_to_statistics: no visible binding for global variable ‘lower’
draws_to_statistics: no visible binding for global variable ‘effect’
draws_to_statistics: no visible binding for global variable ‘upper’
draws_to_statistics: no visible binding for global variable ‘pH0’
draws_to_statistics: no visible binding for global variable ‘FDR’
draws_to_statistics: no visible binding for global variable ‘n_eff’
draws_to_statistics: no visible binding for global variable ‘R_k_hat’
draws_to_tibble_x: no visible binding for global variable ‘.’
draws_to_tibble_x: no visible binding for global variable ‘dummy’
draws_to_tibble_x: no visible binding for global variable ‘.variable’
draws_to_tibble_x: no visible binding for global variable ‘.chain’
draws_to_tibble_x: no visible binding for global variable ‘.iteration’
draws_to_tibble_x: no visible binding for global variable ‘.draw’
draws_to_tibble_x: no visible binding for global variable ‘.value’
draws_to_tibble_x_y: no visible binding for global variable ‘.’
draws_to_tibble_x_y: no visible binding for global variable ‘dummy’
draws_to_tibble_x_y: no visible binding for global variable ‘.variable’
draws_to_tibble_x_y: no visible binding for global variable ‘.chain’
draws_to_tibble_x_y: no visible binding for global variable
  ‘.iteration’
draws_to_tibble_x_y: no visible binding for global variable ‘.draw’
draws_to_tibble_x_y: no visible binding for global variable ‘.value’
estimate_multi_beta_binomial_glm: no visible binding for global
  variable ‘N’
estimate_multi_beta_binomial_glm: no visible binding for global
  variable ‘M’
estimate_multi_beta_binomial_glm: no visible binding for global
  variable ‘5%’
estimate_multi_beta_binomial_glm: no visible binding for global
  variable ‘95%’
estimate_multi_beta_binomial_glm: no visible binding for global
  variable ‘truncation_up’
estimate_multi_beta_binomial_glm: no visible binding for global
  variable ‘truncation_down’
estimate_multi_beta_binomial_glm: no visible binding for global
  variable ‘.lower’
estimate_multi_beta_binomial_glm: no visible binding for global
  variable ‘.’
estimate_multi_beta_binomial_glm: no visible binding for global
  variable ‘50%’
estimate_multi_beta_binomial_glm: no visible binding for global
  variable ‘.upper’
find_optimal_number_of_chains: no visible binding for global variable
  ‘chains’
find_optimal_number_of_chains: no visible binding for global variable
  ‘.’
fit_and_generate_quantities: no visible binding for global variable ‘N’
fit_and_generate_quantities: no visible binding for global variable ‘M’
fit_and_generate_quantities: no visible binding for global variable
  ‘precision’
fit_model: no visible binding for global variable ‘.’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘N’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘M’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘cores’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘additional_parameters_to_save’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘pass_fit’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘tol_rel_obj’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘glm_dirichlet_multinomial_generate_quantities’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘.draw’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘.chain’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘.iteration’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘.draw_imputation’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘.variable’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘fit_list’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘n_eff’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘se_mean’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘sd’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘.’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘C_name’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘.lower’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘.median’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘.upper’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘5%’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘95%’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘50%’
fit_model_and_parse_out_missing_data: no visible binding for global
  variable ‘precision’
fit_model_and_parse_out_no_missing_data: no visible binding for global
  variable ‘glm_dirichlet_multinomial_generate_quantities’
fit_to_counts_rng: no visible binding for global variable ‘.variable’
fit_to_counts_rng: no visible binding for global variable ‘S’
fit_to_counts_rng: no visible binding for global variable ‘G’
fit_to_counts_rng: no visible binding for global variable ‘.’
generate_quantities: no visible binding for global variable ‘N_M’
generate_quantities: no visible binding for global variable
  ‘generated_quantity’
generate_quantities: no visible binding for global variable ‘draw’
generate_quantities: no visible binding for global variable ‘N’
generate_quantities: no visible binding for global variable ‘M’
get_FDR: no visible binding for global variable ‘value’
get_FDR: no visible binding for global variable ‘name’
get_FDR: no visible binding for global variable ‘FDR’
get_abundance_contrast_draws: no visible binding for global variable
  ‘X’
get_abundance_contrast_draws: no visible binding for global variable
  ‘.value’
get_abundance_contrast_draws: no visible binding for global variable
  ‘.’
get_abundance_contrast_draws: no visible binding for global variable
  ‘X_random_intercept’
get_abundance_contrast_draws: no visible binding for global variable
  ‘.variable’
get_abundance_contrast_draws: no visible binding for global variable
  ‘y’
get_abundance_contrast_draws: no visible binding for global variable
  ‘M’
get_abundance_contrast_draws: no visible binding for global variable
  ‘parameter’
get_abundance_contrast_draws: no visible binding for global variable
  ‘n_eff’
get_abundance_contrast_draws: no visible binding for global variable
  ‘R_k_hat’
get_design_matrix: no visible binding for global variable ‘.’
get_mean_precision: no visible binding for global variable ‘M’
get_mean_precision: no visible binding for global variable ‘2.5%’
get_mean_precision: no visible binding for global variable ‘97.5%’
get_mean_precision_association: no visible binding for global variable
  ‘.’
get_probability_non_zero: no visible binding for global variable ‘M’
get_probability_non_zero: no visible binding for global variable
  ‘C_name’
get_probability_non_zero: no visible binding for global variable
  ‘bigger_zero’
get_probability_non_zero: no visible binding for global variable
  ‘smaller_zero’
get_probability_non_zero_OLD: no visible binding for global variable
  ‘.’
get_probability_non_zero_OLD: no visible binding for global variable
  ‘.draw’
get_probability_non_zero_OLD: no visible binding for global variable
  ‘M’
get_probability_non_zero_OLD: no visible binding for global variable
  ‘C_name’
get_probability_non_zero_OLD: no visible binding for global variable
  ‘bigger_zero’
get_probability_non_zero_OLD: no visible binding for global variable
  ‘smaller_zero’
get_random_intercept_design: no visible binding for global variable
  ‘is_factor_continuous’
get_random_intercept_design: no visible binding for global variable
  ‘design’
get_random_intercept_design: no visible binding for global variable
  ‘max_mean_idx’
get_random_intercept_design: no visible binding for global variable
  ‘max_minus_sum’
get_random_intercept_design: no visible binding for global variable
  ‘max_factor_numeric’
get_random_intercept_design: no visible binding for global variable
  ‘max_group_numeric’
get_random_intercept_design: no visible binding for global variable
  ‘min_mean_idx’
get_random_intercept_design: no visible binding for global variable
  ‘min_minus_sum’
get_variability_contrast_draws: no visible binding for global variable
  ‘XA’
get_variability_contrast_draws: no visible binding for global variable
  ‘.value’
get_variability_contrast_draws: no visible binding for global variable
  ‘.’
get_variability_contrast_draws: no visible binding for global variable
  ‘.variable’
get_variability_contrast_draws: no visible binding for global variable
  ‘y’
get_variability_contrast_draws: no visible binding for global variable
  ‘M’
get_variability_contrast_draws: no visible binding for global variable
  ‘parameter’
get_variability_contrast_draws: no visible binding for global variable
  ‘n_eff’
get_variability_contrast_draws: no visible binding for global variable
  ‘R_k_hat’
glm_multi_beta: no visible binding for global variable ‘.’
label_deleterious_outliers: no visible binding for global variable
  ‘.count’
label_deleterious_outliers: no visible binding for global variable
  ‘95%’
label_deleterious_outliers: no visible binding for global variable ‘5%’
label_deleterious_outliers: no visible binding for global variable ‘X’
label_deleterious_outliers: no visible binding for global variable
  ‘iteration’
label_deleterious_outliers: no visible binding for global variable
  ‘outlier_above’
label_deleterious_outliers: no visible binding for global variable
  ‘slope’
label_deleterious_outliers: no visible binding for global variable
  ‘is_group_right’
label_deleterious_outliers: no visible binding for global variable
  ‘outlier_below’
multi_beta_glm: no visible global function definition for
  ‘detect_cores’
parse_fit: no visible binding for global variable ‘M’
parse_formula: no visible global function definition for ‘terms’
parse_formula: no visible binding for global variable ‘.’
parse_formula_random_intercept: no visible global function definition
  for ‘terms’
parse_generated_quantities: no visible binding for global variable
  ‘.draw’
parse_generated_quantities: no visible binding for global variable ‘N’
parse_generated_quantities: no visible binding for global variable
  ‘.value’
parse_generated_quantities: no visible binding for global variable
  ‘generated_counts’
parse_generated_quantities: no visible binding for global variable ‘M’
parse_generated_quantities: no visible binding for global variable
  ‘generated_proportions’
plot_1d_intervals: no visible binding for global variable ‘parameter’
plot_1d_intervals: no visible binding for global variable ‘estimate’
plot_1d_intervals: no visible binding for global variable ‘value’
plot_2d_intervals: no visible binding for global variable ‘v_effect’
plot_2d_intervals: no visible binding for global variable ‘parameter’
plot_2d_intervals: no visible binding for global variable ‘.’
plot_2d_intervals: no visible binding for global variable ‘c_effect’
plot_2d_intervals: no visible binding for global variable ‘c_lower’
plot_2d_intervals: no visible binding for global variable ‘c_upper’
plot_2d_intervals: no visible binding for global variable ‘c_FDR’
plot_2d_intervals: no visible binding for global variable ‘v_lower’
plot_2d_intervals: no visible binding for global variable ‘v_upper’
plot_2d_intervals: no visible binding for global variable ‘v_FDR’
plot_2d_intervals: no visible binding for global variable
  ‘cell_type_label’
plot_boxplot: no visible binding for global variable ‘stats_name’
plot_boxplot: no visible binding for global variable ‘parameter’
plot_boxplot: no visible binding for global variable ‘stats_value’
plot_boxplot: no visible binding for global variable ‘count_data’
plot_boxplot: no visible binding for global variable
  ‘generated_proportions’
plot_boxplot: no visible binding for global variable ‘proportion’
plot_boxplot: no visible binding for global variable ‘name’
plot_boxplot: no visible binding for global variable ‘outlier’
plot_summary: no visible binding for global variable ‘parameter’
plot_summary: no visible binding for global variable ‘count_data’
plot_summary: no visible binding for global variable ‘v_effect’
remove_unwanted_variation.data.frame: no visible binding for global
  variable ‘proportion_mean’
remove_unwanted_variation.data.frame: no visible binding for global
  variable ‘y’
remove_unwanted_variation.data.frame: no visible binding for global
  variable ‘observed_proportion’
remove_unwanted_variation.data.frame: no visible binding for global
  variable ‘logit_residuals’
remove_unwanted_variation.data.frame: no visible binding for global
  variable ‘exposure’
remove_unwanted_variation.data.frame: no visible binding for global
  variable ‘adjusted_proportion’
remove_unwanted_variation.data.frame: no visible binding for global
  variable ‘adjusted_counts’
replicate_data: no visible binding for global variable ‘count_data’
replicate_data: no visible binding for global variable ‘exposure’
replicate_data: no visible global function definition for ‘tail’
replicate_data: no visible global function definition for ‘as.formula’
replicate_data: no visible binding for global variable ‘.’
replicate_data: no visible global function definition for ‘na.omit’
replicate_data: no visible binding for global variable ‘Xa’
replicate_data: no visible binding for global variable
  ‘intercept_in_design’
replicate_data: no visible binding for global variable ‘design’
replicate_data: no visible binding for global variable
  ‘is_factor_continuous’
replicate_data: no visible binding for global variable ‘design_matrix’
replicate_data: no visible binding for global variable
  ‘X_random_intercept’
sccomp_predict.data.frame: no visible binding for global variable
  ‘count_data’
sccomp_predict.data.frame: no visible binding for global variable ‘M’
sccomp_predict.data.frame: no visible binding for global variable ‘N’
sccomp_predict.data.frame: no visible binding for global variable
  ‘2.5%’
sccomp_predict.data.frame: no visible binding for global variable
  ‘97.5%’
sccomp_replicate.data.frame: no visible binding for global variable ‘N’
sccomp_replicate.data.frame: no visible binding for global variable ‘M’
simulate_data.data.frame: no visible binding for global variable
  ‘data___’
simulate_data.data.frame: no visible binding for global variable
  ‘.exposure’
simulate_data.data.frame: no visible binding for global variable ‘N’
simulate_data.data.frame: no visible binding for global variable ‘M’
simulate_multinomial_logit_linear: no visible global function
  definition for ‘rnorm’
summary_to_tibble: no visible binding for global variable ‘.’
summary_to_tibble: no visible binding for global variable ‘.variable’
test_contrasts.data.frame: no visible binding for global variable
  ‘design_matrix_col’
test_contrasts.data.frame: no visible binding for global variable
  ‘parameter’
test_contrasts.data.frame: no visible binding for global variable ‘M’
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 R_k_hat S X XA X_random_intercept Xa
  additional_parameters_to_save adjusted_counts adjusted_proportion
  as.formula beta_1 beta_2 bigger_zero c_FDR c_effect c_lower c_upper
  cell_type cell_type_label censoring_iteration chains cores count_data
  data___ design design_matrix design_matrix_col detect_cores draw
  dummy effect estimate exposure factor_1 factors fit_list
  generated_counts generated_proportions generated_quantity
  glm_dirichlet_multinomial
  glm_dirichlet_multinomial_generate_quantities
  glm_dirichlet_multinomial_imputation group___label group___numeric
  groupings idx intercept_in_design is_factor_continuous is_group_right
  iteration logit_residuals lower mat max_factor_numeric
  max_group_numeric max_mean_idx max_minus_sum mean_idx min_mean_idx
  min_minus_sum minus_sum n_eff na.omit name observed_proportion
  outlier outlier_above outlier_below pH0 parameter pass_fit ppc
  precision proportion proportion_mean rnorm sd se_mean slope
  smaller_zero stats_name stats_value tail terms tol_rel_obj
  truncation_down truncation_up upper v_FDR v_effect v_lower v_upper
  value variable y
Consider adding
  importFrom("stats", "as.formula", "na.omit", "rnorm", "sd", "terms")
  importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
test_contrasts            53.986  0.152  54.226
sccomp_glm                52.906  0.192  53.174
remove_unwanted_variation 38.953  0.551  39.566
simulate_data             36.465  0.355  36.871
sccomp_predict            32.267  0.471  32.781
plot_summary              30.586  0.587  31.223
sccomp_replicate          26.778  0.340  27.148
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘introduction.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/sccomp.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL sccomp
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘sccomp’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++17


g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.0/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/R/R-4.3.0/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o


g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.0/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/R/R-4.3.0/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -c stanExports_glm_multi_beta_binomial.cc -o stanExports_glm_multi_beta_binomial.o
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/bessel.hpp:20,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:217:20:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:252:31:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:314:68:   required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:1176:44:   required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:2128:35:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55:   required from here
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  299 |    result_type operator()()
      |                ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:240,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:874:46:   required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:979:36:   required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38:   required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77:   required from here
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  543 |          std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol)
      |                          ^~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/binomial.hpp:15,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t<T>::result_type boost::math::detail::ibeta_fraction2_t<T>::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:123:20:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:156:31:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:729:54:   required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:1367:36:   required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:1404:20:   required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:1543:93:   required from ‘typename boost::math::tools::promote_args<RT1, RT2, A>::type boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2, A>::type = double]’
/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:28:56:   required from here
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:692:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  692 |    result_type operator()()
      |                ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:18,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/bessel.hpp:20,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial.h:20,
                 from stanExports_glm_multi_beta_binomial.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  217 |    value_type v = g();
      |               ^


g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.0/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/R/R-4.3.0/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -c stanExports_glm_multi_beta_binomial_generate_date.cc -o stanExports_glm_multi_beta_binomial_generate_date.o
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/bessel.hpp:20,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:217:20:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:252:31:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:314:68:   required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:1176:44:   required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:2128:35:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55:   required from here
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  299 |    result_type operator()()
      |                ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:240,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:874:46:   required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:979:36:   required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38:   required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77:   required from here
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  543 |          std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol)
      |                          ^~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/binomial.hpp:15,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t<T>::result_type boost::math::detail::ibeta_fraction2_t<T>::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:123:20:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:156:31:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:729:54:   required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:1367:36:   required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:1404:20:   required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:1543:93:   required from ‘typename boost::math::tools::promote_args<RT1, RT2, A>::type boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2, A>::type = double]’
/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:28:56:   required from here
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:692:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  692 |    result_type operator()()
      |                ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:18,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/bessel.hpp:20,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  217 |    value_type v = g();
      |               ^


g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.0/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/R/R-4.3.0/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -c stanExports_glm_multi_beta_binomial_simulate_data.cc -o stanExports_glm_multi_beta_binomial_simulate_data.o
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/bessel.hpp:20,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:217:20:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:252:31:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:314:68:   required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:1176:44:   required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:2128:35:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55:   required from here
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  299 |    result_type operator()()
      |                ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:240,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:874:46:   required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:979:36:   required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38:   required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77:   required from here
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  543 |          std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol)
      |                          ^~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/binomial.hpp:15,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t<T>::result_type boost::math::detail::ibeta_fraction2_t<T>::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:123:20:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:156:31:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:729:54:   required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:1367:36:   required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:1404:20:   required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:1543:93:   required from ‘typename boost::math::tools::promote_args<RT1, RT2, A>::type boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2, A>::type = double]’
/home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:28:56:   required from here
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/beta.hpp:692:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  692 |    result_type operator()()
      |                ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/gamma.hpp:18,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/special_functions/bessel.hpp:20,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev/fun.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.0/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/R/R-4.3.0/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  217 |    value_type v = g();
      |               ^
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o sccomp.so RcppExports.o stanExports_glm_multi_beta_binomial.o stanExports_glm_multi_beta_binomial_generate_date.o stanExports_glm_multi_beta_binomial_simulate_data.o -L/home/biocbuild/R/R-4.3.0/library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/R/R-4.3.0/library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/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)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(sccomp)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0 
> 
> test_check("sccomp")

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation
sccomp says: the composition design matrix has columns: typecancer, typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation
sccomp says: the composition design matrix has columns: typecancer, typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), continuous_covariate
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation
sccomp says: the composition design matrix has columns: typecancer, typehealthy, continuous_covariate
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation
sccomp says: the composition design matrix has columns: typecancer, typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation
sccomp says: the composition design matrix has columns: typecancer, typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
Loading required package: ttservice

Attaching package: 'ttservice'

The following objects are masked from 'package:dplyr':

    bind_cols, bind_rows

Loading required package: SeuratObject
Loading required package: sp
========================================
tidyseurat version 0.5.9
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 objects are masked from 'package:ttservice':

    bind_cols, bind_rows

The following objects are masked from 'package:dplyr':

    bind_cols, bind_rows

The following object is masked from 'package:stats':

    filter

sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typehealthy, batch
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: calculating residuals
sccomp says: regressing out unwanted factors
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept), typehealthy
Joining with `by = join_by(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 280 | SKIP 3 | PASS 17 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 280 | SKIP 3 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
433.888   5.439 440.101