Build/check report for BioC 3.17 - CHECK results for sccomp on kunpeng1

Hostname	OS	Arch (*)	R version	Installed pkgs
kunpeng1	Linux (Ubuntu 22.04.1 LTS)	aarch64	R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"	4266
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:sccomp.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings sccomp_1.3.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/sccomp.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘sccomp/DESCRIPTION’ ... OK
* this is package ‘sccomp’ version ‘1.3.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sccomp’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is 90.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  87.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alpha_to_CI: no visible binding for global variable ‘M’
alpha_to_CI: no visible binding for global variable ‘C_name’
alpha_to_CI: no visible binding for global variable ‘.lower’
alpha_to_CI: no visible binding for global variable ‘.median’
alpha_to_CI: no visible binding for global variable ‘.upper’
as_matrix: no visible binding for global variable ‘variable’
beta_to_CI: no visible binding for global variable ‘M’
beta_to_CI: no visible binding for global variable ‘C_name’
beta_to_CI: no visible binding for global variable ‘.lower’
beta_to_CI: no visible binding for global variable ‘.median’
beta_to_CI: no visible binding for global variable ‘.upper’
check_if_within_posterior: no visible binding for global variable
  ‘.lower’
check_if_within_posterior: no visible binding for global variable
  ‘.upper’
check_if_within_posterior: no visible binding for global variable ‘ppc’
check_random_intercept_design: no visible binding for global variable
  ‘factors’
check_random_intercept_design: no visible binding for global variable
  ‘groupings’
contrasts_to_enquos: no visible binding for global variable ‘.’
data_simulation_to_model_input: no visible binding for global variable
  ‘.’
data_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            73.006  0.424  73.433
sccomp_glm                70.141  0.216  70.360
remove_unwanted_variation 42.365  0.852  43.221
simulate_data             38.662  0.816  39.481
sccomp_predict            35.144  0.784  35.937
plot_summary              32.215  1.064  33.288
sccomp_replicate          29.786  0.612  30.403
* 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 ...

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL sccomp
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘sccomp’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++14


g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o


g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -Wall -c stanExports_glm_multi_beta_binomial.cc -o stanExports_glm_multi_beta_binomial.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-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++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-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++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_args.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:20,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:278,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpmf(const T_prob&, const T_prior_size&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_prob, T_prior_size>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
   60 |   using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
      |         ^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:328,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T4>::value, Eigen::Array<typename stan::partials_return_type<T_alpha>::type, -1, 1>, typename stan::partials_return_type<T_alpha>::type>’ locally defined but not used [-Wunused-local-typedefs]
   52 |   using T_alpha_val = typename std::conditional_t<
      |         ^~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:51,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vv_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<stan::math::var, R2, C2, (Eigen::AutoAlign | (((R2 == 1) && (C2 != 1)) ? Eigen::RowMajor : (((C2 == 1) && (R2 != 1)) ? Eigen::ColMajor :  Eigen::ColMajor))), R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<stan::math::var, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
   27 |     using idx_t = typename index_type<matrix_v>::type;
      |           ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vd_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<double, R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<double, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
   64 |     using idx_t = typename index_type<matrix_d>::type;
      |           ^~~~~
In file included from stanExports_glm_multi_beta_binomial.cc:5:
stanExports_glm_multi_beta_binomial.h: In member function ‘virtual void model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial::transform_inits(const stan::io::var_context&, std::vector<int>&, std::vector<double>&, std::ostream*) const’:
stanExports_glm_multi_beta_binomial.h:828:24: warning: typedef ‘local_scalar_t__’ locally defined but not used [-Wunused-local-typedefs]
  828 |         typedef double local_scalar_t__;
      |                        ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:48:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   74 |     for (int i = 0; i < dims.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’:
stanExports_glm_multi_beta_binomial.cc:30:89:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1238:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
 1238 |     int ret = stan::services::error_codes::CONFIG;
      |         ^~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_glm_multi_beta_binomial.cc:30:89:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:91:22: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
   91 |   if (p_names.size() != draws.cols()) {
      |       ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:109:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  109 |   for (size_t i = 0; i < draws.rows(); ++i) {
      |                      ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/err/check_cholesky_factor.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:9,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp: In instantiation of ‘static void stan::math::internal::less_or_equal<T_y, T_high, is_vec>::check(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int; bool is_vec = false]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:64:74:   required from ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int]’
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36:   required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:19:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘long int’ [-Wsign-compare]
   19 |       if (!(y <= high_vec[n])) {
      |            ~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘void stan::services::get_model_parameters(const Model&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::vector<long unsigned int> >&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:105:23:   required from ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_namespace::model_glm_multi_beta_binomial; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_glm_multi_beta_binomial.cc:30:89:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:41:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   41 |     for (int j = 0; j < dimss[i].size(); ++j)
      |                     ~~^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:46,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
   14 | static void set_zero_all_adjoints() {
      |             ^~~~~~~~~~~~~~~~~~~~~


g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -Wall -c stanExports_glm_multi_beta_binomial_generate_date.cc -o stanExports_glm_multi_beta_binomial_generate_date.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-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++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-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++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_args.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:20,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:278,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpmf(const T_prob&, const T_prior_size&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_prob, T_prior_size>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
   60 |   using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
      |         ^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:328,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T4>::value, Eigen::Array<typename stan::partials_return_type<T_alpha>::type, -1, 1>, typename stan::partials_return_type<T_alpha>::type>’ locally defined but not used [-Wunused-local-typedefs]
   52 |   using T_alpha_val = typename std::conditional_t<
      |         ^~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:51,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vv_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<stan::math::var, R2, C2, (Eigen::AutoAlign | (((R2 == 1) && (C2 != 1)) ? Eigen::RowMajor : (((C2 == 1) && (R2 != 1)) ? Eigen::ColMajor :  Eigen::ColMajor))), R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<stan::math::var, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
   27 |     using idx_t = typename index_type<matrix_v>::type;
      |           ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vd_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<double, R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<double, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
   64 |     using idx_t = typename index_type<matrix_d>::type;
      |           ^~~~~
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
stanExports_glm_multi_beta_binomial_generate_date.h: In member function ‘virtual void model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date::transform_inits(const stan::io::var_context&, std::vector<int>&, std::vector<double>&, std::ostream*) const’:
stanExports_glm_multi_beta_binomial_generate_date.h:317:24: warning: typedef ‘local_scalar_t__’ locally defined but not used [-Wunused-local-typedefs]
  317 |         typedef double local_scalar_t__;
      |                        ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:48:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   74 |     for (int i = 0; i < dims.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’:
stanExports_glm_multi_beta_binomial_generate_date.cc:30:89:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1238:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
 1238 |     int ret = stan::services::error_codes::CONFIG;
      |         ^~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_glm_multi_beta_binomial_generate_date.cc:30:89:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:91:22: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
   91 |   if (p_names.size() != draws.cols()) {
      |       ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:109:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  109 |   for (size_t i = 0; i < draws.rows(); ++i) {
      |                      ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/err/check_cholesky_factor.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:9,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp: In instantiation of ‘static void stan::math::internal::less_or_equal<T_y, T_high, is_vec>::check(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int; bool is_vec = false]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:64:74:   required from ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int]’
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36:   required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:19:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘long int’ [-Wsign-compare]
   19 |       if (!(y <= high_vec[n])) {
      |            ~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘void stan::services::get_model_parameters(const Model&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::vector<long unsigned int> >&) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:105:23:   required from ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_generate_date_namespace::model_glm_multi_beta_binomial_generate_date; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_glm_multi_beta_binomial_generate_date.cc:30:89:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:41:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   41 |     for (int j = 0; j < dimss[i].size(); ++j)
      |                     ~~^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:46,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
   14 | static void set_zero_all_adjoints() {
      |             ^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Core:503,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stanExports_glm_multi_beta_binomial_generate_date.h:20,
                 from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function ‘static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, false>; Lhs = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, -1, 1> >, const Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true>, -1, 1, false> >]’:
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:227:7: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
  225 |     internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  226 |                                                 int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  227 |       (
      |       ^
  228 |         lhs.rows(),                             // size
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  229 |         &lhs.coeffRef(0,0),  lhs.outerStride(), // lhs info
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  230 |         actualRhsPtr,                           // rhs info
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  231 |         actualDestPtr,                          // result info
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  232 |         actualAlpha                             // scale factor
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  233 |       );
      |       ~
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:39:24: note: by argument 4 of type ‘const double*’ to ‘static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]’ declared here
   39 | EIGEN_DONT_INLINE void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -Wall -c stanExports_glm_multi_beta_binomial_simulate_data.cc -o stanExports_glm_multi_beta_binomial_simulate_data.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-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++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-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++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_args.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:20,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:278,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpmf(const T_prob&, const T_prior_size&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_prob, T_prior_size>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
   60 |   using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
      |         ^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:328,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T4>::value, Eigen::Array<typename stan::partials_return_type<T_alpha>::type, -1, 1>, typename stan::partials_return_type<T_alpha>::type>’ locally defined but not used [-Wunused-local-typedefs]
   52 |   using T_alpha_val = typename std::conditional_t<
      |         ^~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
                 from /usr/include/c++/11/locale:43,
                 from /usr/include/c++/11/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:51,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vv_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<stan::math::var, R2, C2, (Eigen::AutoAlign | (((R2 == 1) && (C2 != 1)) ? Eigen::RowMajor : (((C2 == 1) && (R2 != 1)) ? Eigen::ColMajor :  Eigen::ColMajor))), R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<stan::math::var, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
   27 |     using idx_t = typename index_type<matrix_v>::type;
      |           ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vd_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<double, R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<double, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
   64 |     using idx_t = typename index_type<matrix_d>::type;
      |           ^~~~~
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
stanExports_glm_multi_beta_binomial_simulate_data.h: In member function ‘virtual void model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data::transform_inits(const stan::io::var_context&, std::vector<int>&, std::vector<double>&, std::ostream*) const’:
stanExports_glm_multi_beta_binomial_simulate_data.h:187:24: warning: typedef ‘local_scalar_t__’ locally defined but not used [-Wunused-local-typedefs]
  187 |         typedef double local_scalar_t__;
      |                        ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:48:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   74 |     for (int i = 0; i < dims.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’:
stanExports_glm_multi_beta_binomial_simulate_data.cc:30:89:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1238:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
 1238 |     int ret = stan::services::error_codes::CONFIG;
      |         ^~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_glm_multi_beta_binomial_simulate_data.cc:30:89:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:91:22: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
   91 |   if (p_names.size() != draws.cols()) {
      |       ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:109:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  109 |   for (size_t i = 0; i < draws.rows(); ++i) {
      |                      ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/err/check_cholesky_factor.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:9,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp: In instantiation of ‘static void stan::math::internal::less_or_equal<T_y, T_high, is_vec>::check(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int; bool is_vec = false]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:64:74:   required from ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int]’
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36:   required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:19:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘long int’ [-Wsign-compare]
   19 |       if (!(y <= high_vec[n])) {
      |            ~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘void stan::services::get_model_parameters(const Model&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::vector<long unsigned int> >&) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:105:23:   required from ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_glm_multi_beta_binomial_simulate_data_namespace::model_glm_multi_beta_binomial_simulate_data; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_glm_multi_beta_binomial_simulate_data.cc:30:89:   required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:41:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   41 |     for (int j = 0; j < dimss[i].size(); ++j)
      |                     ~~^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:46,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:6,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
   14 | static void set_zero_all_adjoints() {
      |             ^~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Core:503,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stanExports_glm_multi_beta_binomial_simulate_data.h:20,
                 from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function ‘static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, false>; Lhs = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, -1, 1> >, const Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true>, -1, 1, false> >]’:
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:227:7: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
  225 |     internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  226 |                                                 int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  227 |       (
      |       ^
  228 |         lhs.rows(),                             // size
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  229 |         &lhs.coeffRef(0,0),  lhs.outerStride(), // lhs info
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  230 |         actualRhsPtr,                           // rhs info
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  231 |         actualDestPtr,                          // result info
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  232 |         actualAlpha                             // scale factor
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  233 |       );
      |       ~
/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:39:24: note: by argument 4 of type ‘const double*’ to ‘static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]’ declared here
   39 | EIGEN_DONT_INLINE void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run(
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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)

CHECK results for sccomp on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
plot_summary	32.215	1.064	33.288
remove_unwanted_variation	42.365	0.852	43.221
sccomp_glm	70.141	0.216	70.360
sccomp_predict	35.144	0.784	35.937
sccomp_replicate	29.786	0.612	30.403
simulate_data	38.662	0.816	39.481
test_contrasts	73.006	0.424	73.433