##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sccomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sccomp_1.3.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/sccomp.Rcheck’
* using R Under development (unstable) (2022-12-10 r83428)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sccomp/DESCRIPTION’ ... OK
* this is package ‘sccomp’ version ‘1.3.4’
* 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
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.4Mb
* 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
  ‘covariate’
check_random_intercept_design: no visible binding for global variable
  ‘covariates’
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
  ‘covariate’
data_spread_to_model_input: no visible binding for global variable
  ‘is_covariate_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 ‘covariate_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_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_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
  ‘covariate’
get_random_intercept_design: no visible binding for global variable
  ‘is_covariate_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_covariate_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’
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_formula_random_intercept: no visible binding for global variable
  ‘covariate’
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 ‘covariate’
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 ‘covariate’
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 ‘generated_proportion_means’
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.data.frame: no visible binding for global variable
  ‘count_data’
replicate_data.data.frame: no visible global function definition for
  ‘as.formula’
replicate_data.data.frame: no visible binding for global variable ‘X’
replicate_data.data.frame: no visible binding for global variable ‘Xa’
replicate_data.data.frame: no visible binding for global variable
  ‘intercept_in_design’
replicate_data.data.frame: no visible binding for global variable
  ‘design’
replicate_data.data.frame: no visible binding for global variable
  ‘covariate’
replicate_data.data.frame: no visible binding for global variable
  ‘is_covariate_continuous’
replicate_data.data.frame: no visible binding for global variable
  ‘design_matrix’
replicate_data.data.frame: no visible binding for global variable ‘.’
replicate_data.data.frame: no visible binding for global variable
  ‘X_random_intercept’
replicate_data.data.frame: no visible binding for global variable ‘M’
replicate_data.data.frame: no visible binding for global variable ‘N’
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
  ‘covariate’
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 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 covariate covariate_1
  covariates data___ design design_matrix design_matrix_col
  detect_cores draw dummy effect estimate exposure fit_list
  generated_counts generated_proportion_means 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_covariate_continuous
  is_group_right iteration logit_residuals lower mat
  max_covariate_numeric max_group_numeric max_mean_idx max_minus_sum
  mean_idx min_mean_idx min_minus_sum minus_sum n_eff name
  observed_proportion outlier outlier_above outlier_below pH0 parameter
  pass_fit ppc precision proportion rnorm sd se_mean slope smaller_zero
  stats_name stats_value 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", "rnorm", "sd", "terms")
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 ... ERROR
Running examples in ‘sccomp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_summary
> ### Title: plot_summary
> ### Aliases: plot_summary
> 
> ### ** Examples
> 
> 
> data("counts_obj")
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> 
> estimate =
+   sccomp_glm(
+   counts_obj ,
+    ~ type, ~1, sample, cell_group, count,
+     approximate_posterior_inference = "all",
+     check_outliers = FALSE,
+     cores = 1
+   )
sccomp says: estimation [ETA: ~20s]
sccomp says: the composition design matrix has columns: (Intercept), typecancer
sccomp says: the variability design matrix has columns: (Intercept)
> 
> estimate |> plot_summary()
Exception: Variable beta_random_intercept missing  (in 'model_glm_multi_beta_binomial_generate_date' at line 45)

Joining, by = c("sample", "cell_group")
Joining, by = c("cell_group", "type")
$boxplot
$boxplot[[1]]
Warning: Removed 72000 rows containing non-finite values (`stat_summary()`).
Warning in max(f) : no non-missing arguments to max; returning -Inf
Error in `stat_summary()`:
! Problem while computing stat.
ℹ Error occurred in the 1st layer.
Caused by error in `seq_len()`:
! argument must be coercible to non-negative integer
Backtrace:
     ▆
  1. ├─base (local) `<fn>`(x)
  2. ├─ggplot2:::print.ggplot(x)
  3. │ ├─ggplot2::ggplot_build(x)
  4. │ └─ggplot2:::ggplot_build.ggplot(x)
  5. │   └─ggplot2:::by_layer(...)
  6. │     ├─rlang::try_fetch(...)
  7. │     │ ├─base::tryCatch(...)
  8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 11. │     │ └─base::withCallingHandlers(...)
 12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
 13. │       └─l$compute_statistic(d, layout)
 14. │         └─ggplot2 (local) compute_statistic(..., self = self)
 15. │           └─self$stat$compute_layer(data, self$computed_stat_params, layout)
 16. │             └─ggplot2 (local) compute_layer(..., self = self)
 17. │               └─ggplot2:::dapply(...)
 18. │                 └─ggplot2:::split_with_index(seq_len(nrow(df)), ids)
 19. └─base::.handleSimpleError(...)
 20.   └─rlang (local) h(simpleError(msg, call))
 21.     └─handlers[[1L]](cnd)
 22.       └─cli::cli_abort(...)
 23.         └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ! Can't recycle `string` (size 2) to match `pattern` (size 6).
  ── Error ('test-sccomp_.R:237'): multi beta binomial contrasts from Seurat ─────
  Error in `filter(expand_grid(distinct(data_for_model$covariate_parameter_dictionary), 
      parameter = contrasts), str_detect(contrasts, design_matrix_col))`: Problem while computing `..1 = str_detect(contrasts, design_matrix_col)`.
  Caused by error in `str_detect()`:
  ! Can't recycle `string` (size 2) to match `pattern` (size 4).
  ── Error ('test-sccomp_.R:258'): multi beta binomial contrasts from Seurat ─────
  Error in `filter(expand_grid(distinct(data_for_model$covariate_parameter_dictionary), 
      parameter = contrasts), str_detect(contrasts, design_matrix_col))`: Problem while computing `..1 = str_detect(contrasts, design_matrix_col)`.
  Caused by error in `str_detect()`:
  ! Can't recycle `string` (size 2) to match `pattern` (size 4).
  
  [ FAIL 5 | WARN 297 | SKIP 4 | PASS 5 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/sccomp.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sccomp
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘sccomp’ ...
** using staged installation
** libs


clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include' -I/usr/local/include    -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
18 warnings generated.


clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include' -I/usr/local/include    -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -Wall -g -O2  -c stanExports_glm_multi_beta_binomial.cc -o stanExports_glm_multi_beta_binomial.o
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:283:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable]
  int n = G.rows();  // number of states
      ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion]
  inline static double square(double x) { return square(x); }
                                        ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:70:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable]
    const size_t coupled_size = cvodes_data.coupled_ode_.size();
                 ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:46:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function]
static void set_zero_all_adjoints() {
            ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:47:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration]
static void set_zero_all_adjoints_nested() {
            ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:278:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef]
  using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
        ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:328:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef]
  using T_alpha_val = typename std::conditional_t<
        ^
In file included from stanExports_glm_multi_beta_binomial.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:51:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
    using idx_t = typename index_type<matrix_v>::type;
          ^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
    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:806:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef]
        typedef double local_scalar_t__;
                       ^
28 warnings generated.


clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include' -I/usr/local/include    -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -Wall -g -O2  -c stanExports_glm_multi_beta_binomial_generate_date.cc -o stanExports_glm_multi_beta_binomial_generate_date.o
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:283:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable]
  int n = G.rows();  // number of states
      ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion]
  inline static double square(double x) { return square(x); }
                                        ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:70:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable]
    const size_t coupled_size = cvodes_data.coupled_ode_.size();
                 ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:46:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function]
static void set_zero_all_adjoints() {
            ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:47:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration]
static void set_zero_all_adjoints_nested() {
            ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:278:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef]
  using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
        ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:328:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef]
  using T_alpha_val = typename std::conditional_t<
        ^
In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:51:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
    using idx_t = typename index_type<matrix_v>::type;
          ^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
    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:312:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef]
        typedef double local_scalar_t__;
                       ^
28 warnings generated.


clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include' -I/usr/local/include    -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -Wall -g -O2  -c stanExports_glm_multi_beta_binomial_simulate_data.cc -o stanExports_glm_multi_beta_binomial_simulate_data.o
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:283:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable]
  int n = G.rows();  // number of states
      ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion]
  inline static double square(double x) { return square(x); }
                                        ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:70:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable]
    const size_t coupled_size = cvodes_data.coupled_ode_.size();
                 ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:46:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function]
static void set_zero_all_adjoints() {
            ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:47:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration]
static void set_zero_all_adjoints_nested() {
            ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:278:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef]
  using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
        ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:328:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef]
  using T_alpha_val = typename std::conditional_t<
        ^
In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5:
In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:51:
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
    using idx_t = typename index_type<matrix_v>::type;
          ^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
    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:187:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef]
        typedef double local_scalar_t__;
                       ^
28 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.3/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-sccomp/00new/sccomp/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sccomp)

R Under development (unstable) (2022-12-10 r83428) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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

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

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

> library(testthat)
> library(sccomp)
> 
> test_check("sccomp")

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

sccomp says: estimation [ETA: ~20s]
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
Exception: Variable beta_random_intercept missing  (in 'model_glm_multi_beta_binomial_generate_date' at line 45)

sccomp says: estimation [ETA: ~20s]
sccomp says: estimation [ETA: ~20s]
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation [ETA: ~20s]
sccomp says: estimation [ETA: ~20s]
sccomp says: the composition design matrix has columns: (Intercept), continuous_covariate
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation [ETA: ~20s]
sccomp says: estimation [ETA: ~20s]
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation [ETA: ~20s]
sccomp says: estimation [ETA: ~20s]
Loading required package: ttservice

Attaching package: 'ttservice'

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

    bind_cols, bind_rows

Loading required package: SeuratObject
Loading required package: sp
========================================
tidyseurat version 0.5.3
If you use TIDYSEURAT in published research, please cite:

Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.

This message can be suppressed by:
  suppressPackageStartupMessages(library(tidyseurat))
  
To restore the Seurat default display use options("restore_Seurat_show" = TRUE) 
========================================


Attaching package: 'tidyseurat'

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

    bind_cols, bind_rows

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

    add_count, bind_cols, bind_rows, count

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

    filter

sccomp says: estimation [ETA: ~20s]
sccomp says: the composition design matrix has columns: (Intercept), typehealthy, batch
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: calculating residuals
Exception: Variable beta_random_intercept missing  (in 'model_glm_multi_beta_binomial_generate_date' at line 45)

sccomp says: regressing out unwanted covariates
Exception: Variable beta_random_intercept missing  (in 'model_glm_multi_beta_binomial_generate_date' at line 45)

sccomp says: estimation [ETA: ~20s]
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation [ETA: ~20s]
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept)
sccomp says: estimation [ETA: ~20s]
sccomp says: the composition design matrix has columns: (Intercept), typehealthy
sccomp says: the variability design matrix has columns: (Intercept), typehealthy
Exception: Variable beta_random_intercept missing  (in 'model_glm_multi_beta_binomial_generate_date' at line 45)

Joining, by = c("sample", "cell_group")
Joining, by = c("cell_group", "type")
Exception: Variable beta_random_intercept missing  (in 'model_glm_multi_beta_binomial_generate_date' at line 45)

Joining, by = c("sample", "cell_group")
Joining, by = c("cell_group", "type")
[ FAIL 5 | WARN 297 | SKIP 4 | PASS 5 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (4)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-sccomp_.R:68'): Generate data ──────────────────────────────────
Error in `filter(expand_grid(distinct(data_for_model$covariate_parameter_dictionary), 
    parameter = contrasts), str_detect(contrasts, design_matrix_col))`: Problem while computing `..1 = str_detect(contrasts, design_matrix_col)`.
Caused by error in `str_detect()`:
! Can't recycle `string` (size 2) to match `pattern` (size 4).
── Error ('test-sccomp_.R:109'): multilevel multi beta binomial from Seurat ────
Error in `filter(expand_grid(distinct(data_for_model$covariate_parameter_dictionary), 
    parameter = contrasts), str_detect(contrasts, design_matrix_col))`: Problem while computing `..1 = str_detect(contrasts, design_matrix_col)`.
Caused by error in `str_detect()`:
! Can't recycle `string` (size 2) to match `pattern` (size 4).
── Error ('test-sccomp_.R:168'): multilevel continuous ─────────────────────────
Error in `filter(expand_grid(distinct(data_for_model$covariate_parameter_dictionary), 
    parameter = contrasts), str_detect(contrasts, design_matrix_col))`: Problem while computing `..1 = str_detect(contrasts, design_matrix_col)`.
Caused by error in `str_detect()`:
! Can't recycle `string` (size 2) to match `pattern` (size 6).
── Error ('test-sccomp_.R:237'): multi beta binomial contrasts from Seurat ─────
Error in `filter(expand_grid(distinct(data_for_model$covariate_parameter_dictionary), 
    parameter = contrasts), str_detect(contrasts, design_matrix_col))`: Problem while computing `..1 = str_detect(contrasts, design_matrix_col)`.
Caused by error in `str_detect()`:
! Can't recycle `string` (size 2) to match `pattern` (size 4).
── Error ('test-sccomp_.R:258'): multi beta binomial contrasts from Seurat ─────
Error in `filter(expand_grid(distinct(data_for_model$covariate_parameter_dictionary), 
    parameter = contrasts), str_detect(contrasts, design_matrix_col))`: Problem while computing `..1 = str_detect(contrasts, design_matrix_col)`.
Caused by error in `str_detect()`:
! Can't recycle `string` (size 2) to match `pattern` (size 4).

[ FAIL 5 | WARN 297 | SKIP 4 | PASS 5 ]
Error: Test failures
Execution halted