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### Running command:
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###   /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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/sccomp.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sccomp’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’
A package should be listed in only one of these fields.
* 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
design_matrix_and_coefficients_to_simulation: warning in
  simulate_data(.data = input_data, .estimate_object =
  .estimate_object, formula = ~covariate_1, .sample = sample,
  .cell_group = cell_type, .coefficients = c(beta_1, beta_2), mcmc_seed
  = sample(1e+05, 1)): partial argument match of 'formula' to
  'formula_composition'
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’
data_simulation_to_model_input: no visible binding for global variable
  ‘.’
data_spread_to_model_input : get_design_matrix: no visible binding for
  global variable ‘.’
data_spread_to_model_input: no visible binding for global variable
  ‘exposure’
data_spread_to_model_input: no visible binding for global variable
  ‘covariate’
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_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 ‘.’
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_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_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’
glm_multi_beta: no visible binding for global variable ‘.’
hypothesis_test_multi_beta_binomial_glm: no visible binding for global
  variable ‘c_lower’
hypothesis_test_multi_beta_binomial_glm: no visible binding for global
  variable ‘c_effect’
hypothesis_test_multi_beta_binomial_glm: no visible binding for global
  variable ‘c_upper’
hypothesis_test_multi_beta_binomial_glm: no visible binding for global
  variable ‘.variable’
hypothesis_test_multi_beta_binomial_glm: no visible binding for global
  variable ‘v_lower’
hypothesis_test_multi_beta_binomial_glm: no visible binding for global
  variable ‘v_effect’
hypothesis_test_multi_beta_binomial_glm: no visible binding for global
  variable ‘v_upper’
hypothesis_test_multi_beta_binomial_glm: no visible binding for global
  variable ‘covariate’
hypothesis_test_multi_beta_binomial_glm: no visible binding for global
  variable ‘design_matrix_col’
hypothesis_test_multi_beta_binomial_glm: no visible binding for global
  variable ‘C_name’
inits_fx: no visible binding for global variable ‘res_discovery’
inits_fx: no visible binding for global variable ‘.variable’
inits_fx: no visible global function definition for ‘%do%’
inits_fx: no visible global function definition for ‘foreach’
inits_fx: no visible binding for global variable ‘par’
inits_fx: no visible binding for global variable ‘S’
inits_fx: no visible binding for global variable ‘G’
inits_fx: no visible binding for global variable ‘init’
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_binomial_glm: no visible binding for global variable ‘M’
multi_beta_glm: no visible global function definition for
  ‘detect_cores’
parse_fit: no visible binding for global variable ‘M’
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
  ‘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’
replicate_data.data.frame: no visible binding for global variable ‘N’
replicate_data.data.frame: no visible binding for global variable ‘M’
simulate_data.data.frame: no visible binding for global variable
  ‘data___’
simulate_data.data.frame: no visible binding for global variable
  ‘.exposure’
simulate_data.data.frame: no visible binding for global variable ‘N’
simulate_data.data.frame: no visible binding for global variable ‘M’
summary_to_tibble: no visible binding for global variable ‘.’
summary_to_tibble: no visible binding for global variable ‘.variable’
Undefined global functions or variables:
  %do% . .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 additional_parameters_to_save 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
  data___ design_matrix_col detect_cores draw dummy estimate exposure
  fit_list foreach generated_counts generated_proportions
  generated_quantity glm_dirichlet_multinomial
  glm_dirichlet_multinomial_generate_quantities
  glm_dirichlet_multinomial_imputation init is_group_right iteration
  n_eff name outlier outlier_above outlier_below par parameter pass_fit
  ppc precision proportion res_discovery se_mean slope smaller_zero
  stats_name stats_value tol_rel_obj truncation_down truncation_up
  v_FDR v_effect v_lower v_upper value variable
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
simulate_data  44.870  0.737  46.231
plot_summary   26.497  0.741  27.318
replicate_data 13.802  0.484  14.338
sccomp_glm     11.583  0.433  12.122
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/sccomp.Rcheck/00check.log’
for details.