############################################################################## ############################################################################## ### ### 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_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/sccomp.Rcheck’ * using R version 4.2.3 (2023-03-15) * 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 ‘1.2.1’ * 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 6.8Mb sub-directories of 1Mb or more: data 1.1Mb libs 4.2Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE alpha_to_CI: no visible binding for global variable ‘M’ alpha_to_CI: no visible binding for global variable ‘C_name’ alpha_to_CI: no visible binding for global variable ‘.lower’ alpha_to_CI: no visible binding for global variable ‘.median’ alpha_to_CI: no visible binding for global variable ‘.upper’ as_matrix: no visible binding for global variable ‘variable’ beta_to_CI: no visible binding for global variable ‘M’ beta_to_CI: no visible binding for global variable ‘C_name’ beta_to_CI: no visible binding for global variable ‘.lower’ beta_to_CI: no visible binding for global variable ‘.median’ beta_to_CI: no visible binding for global variable ‘.upper’ check_if_within_posterior: no visible binding for global variable ‘.lower’ check_if_within_posterior: no visible binding for global variable ‘.upper’ check_if_within_posterior: no visible binding for global variable ‘ppc’ check_random_intercept_design: no visible binding for global variable ‘factors’ check_random_intercept_design: no visible binding for global variable ‘groupings’ contrasts_to_enquos: no visible binding for global variable ‘.’ data_simulation_to_model_input: no visible binding for global variable ‘.’ data_spread_to_model_input: no visible global function definition for ‘as.formula’ data_spread_to_model_input: no visible binding for global variable ‘exposure’ data_spread_to_model_input: no visible binding for global variable ‘design’ data_spread_to_model_input: no visible binding for global variable ‘mat’ data_spread_to_model_input: no visible binding for global variable ‘is_factor_continuous’ data_spread_to_model_input: no visible binding for global variable ‘design_matrix’ data_spread_to_model_input: no visible binding for global variable ‘.’ data_spread_to_model_input: no visible binding for global variable ‘minus_sum’ data_spread_to_model_input: no visible binding for global variable ‘mean_idx’ data_spread_to_model_input: no visible binding for global variable ‘group___numeric’ data_spread_to_model_input: no visible binding for global variable ‘idx’ data_spread_to_model_input: no visible binding for global variable ‘group___label’ data_spread_to_model_input: no visible binding for global variable ‘parameter’ data_spread_to_model_input: no visible binding for global variable ‘design_matrix_col’ data_to_spread: no visible binding for global variable ‘exposure’ design_matrix_and_coefficients_to_dir_mult_simulation: no visible binding for global variable ‘cell_type’ design_matrix_and_coefficients_to_dir_mult_simulation: no visible binding for global variable ‘generated_counts’ design_matrix_and_coefficients_to_dir_mult_simulation: no visible binding for global variable ‘factor_1’ design_matrix_and_coefficients_to_simulation: no visible binding for global variable ‘cell_type’ design_matrix_and_coefficients_to_simulation: no visible binding for global variable ‘beta_1’ design_matrix_and_coefficients_to_simulation: no visible binding for global variable ‘beta_2’ dirichlet_multinomial_glm: no visible global function definition for ‘detect_cores’ dirichlet_multinomial_glm: no visible binding for global variable ‘glm_dirichlet_multinomial’ dirichlet_multinomial_glm: no visible binding for global variable ‘censoring_iteration’ dirichlet_multinomial_glm: no visible binding for global variable ‘.’ dirichlet_multinomial_glm: no visible binding for global variable ‘chains’ dirichlet_multinomial_glm: no visible binding for global variable ‘precision’ dirichlet_multinomial_glm: no visible binding for global variable ‘M’ do_inference_imputation: no visible binding for global variable ‘glm_dirichlet_multinomial_imputation’ draws_to_statistics: no visible binding for global variable ‘M’ draws_to_statistics: no visible binding for global variable ‘parameter’ draws_to_statistics: no visible binding for global variable ‘bigger_zero’ draws_to_statistics: no visible binding for global variable ‘smaller_zero’ draws_to_statistics: no visible binding for global variable ‘lower’ draws_to_statistics: no visible binding for global variable ‘effect’ draws_to_statistics: no visible binding for global variable ‘upper’ draws_to_statistics: no visible binding for global variable ‘pH0’ draws_to_statistics: no visible binding for global variable ‘FDR’ draws_to_statistics: no visible binding for global variable ‘n_eff’ draws_to_statistics: no visible binding for global variable ‘R_k_hat’ draws_to_tibble_x: no visible binding for global variable ‘.’ draws_to_tibble_x: no visible binding for global variable ‘dummy’ draws_to_tibble_x: no visible binding for global variable ‘.variable’ draws_to_tibble_x: no visible binding for global variable ‘.chain’ draws_to_tibble_x: no visible binding for global variable ‘.iteration’ draws_to_tibble_x: no visible binding for global variable ‘.draw’ draws_to_tibble_x: no visible binding for global variable ‘.value’ draws_to_tibble_x_y: no visible binding for global variable ‘.’ draws_to_tibble_x_y: no visible binding for global variable ‘dummy’ draws_to_tibble_x_y: no visible binding for global variable ‘.variable’ draws_to_tibble_x_y: no visible binding for global variable ‘.chain’ draws_to_tibble_x_y: no visible binding for global variable ‘.iteration’ draws_to_tibble_x_y: no visible binding for global variable ‘.draw’ draws_to_tibble_x_y: no visible binding for global variable ‘.value’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘N’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘M’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘5%’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘95%’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘truncation_up’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘truncation_down’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘.lower’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘.’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘50%’ estimate_multi_beta_binomial_glm: no visible binding for global variable ‘.upper’ find_optimal_number_of_chains: no visible binding for global variable ‘chains’ find_optimal_number_of_chains: no visible binding for global variable ‘.’ fit_and_generate_quantities: no visible binding for global variable ‘N’ fit_and_generate_quantities: no visible binding for global variable ‘M’ fit_and_generate_quantities: no visible binding for global variable ‘precision’ fit_model: no visible binding for global variable ‘.’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘N’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘M’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘cores’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘additional_parameters_to_save’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘pass_fit’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘tol_rel_obj’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘glm_dirichlet_multinomial_generate_quantities’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.draw’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.chain’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.iteration’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.draw_imputation’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.variable’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘fit_list’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘n_eff’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘se_mean’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘sd’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘C_name’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.lower’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.median’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘.upper’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘5%’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘95%’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘50%’ fit_model_and_parse_out_missing_data: no visible binding for global variable ‘precision’ fit_model_and_parse_out_no_missing_data: no visible binding for global variable ‘glm_dirichlet_multinomial_generate_quantities’ fit_to_counts_rng: no visible binding for global variable ‘.variable’ fit_to_counts_rng: no visible binding for global variable ‘S’ fit_to_counts_rng: no visible binding for global variable ‘G’ fit_to_counts_rng: no visible binding for global variable ‘.’ generate_quantities: no visible binding for global variable ‘N_M’ generate_quantities: no visible binding for global variable ‘generated_quantity’ generate_quantities: no visible binding for global variable ‘draw’ generate_quantities: no visible binding for global variable ‘N’ generate_quantities: no visible binding for global variable ‘M’ get_FDR: no visible binding for global variable ‘value’ get_FDR: no visible binding for global variable ‘name’ get_FDR: no visible binding for global variable ‘FDR’ get_abundance_contrast_draws: no visible binding for global variable ‘X’ get_abundance_contrast_draws: no visible binding for global variable ‘.value’ get_abundance_contrast_draws: no visible binding for global variable ‘.’ get_abundance_contrast_draws: no visible binding for global variable ‘X_random_intercept’ get_abundance_contrast_draws: no visible binding for global variable ‘.variable’ get_abundance_contrast_draws: no visible binding for global variable ‘y’ get_abundance_contrast_draws: no visible binding for global variable ‘M’ get_abundance_contrast_draws: no visible binding for global variable ‘parameter’ get_abundance_contrast_draws: no visible binding for global variable ‘n_eff’ get_abundance_contrast_draws: no visible binding for global variable ‘R_k_hat’ get_design_matrix: no visible binding for global variable ‘.’ get_mean_precision: no visible binding for global variable ‘M’ get_mean_precision: no visible binding for global variable ‘2.5%’ get_mean_precision: no visible binding for global variable ‘97.5%’ get_mean_precision_association: no visible binding for global variable ‘.’ get_probability_non_zero: no visible binding for global variable ‘M’ get_probability_non_zero: no visible binding for global variable ‘C_name’ get_probability_non_zero: no visible binding for global variable ‘bigger_zero’ get_probability_non_zero: no visible binding for global variable ‘smaller_zero’ get_probability_non_zero_OLD: no visible binding for global variable ‘.’ get_probability_non_zero_OLD: no visible binding for global variable ‘.draw’ get_probability_non_zero_OLD: no visible binding for global variable ‘M’ get_probability_non_zero_OLD: no visible binding for global variable ‘C_name’ get_probability_non_zero_OLD: no visible binding for global variable ‘bigger_zero’ get_probability_non_zero_OLD: no visible binding for global variable ‘smaller_zero’ get_random_intercept_design: no visible binding for global variable ‘is_factor_continuous’ get_random_intercept_design: no visible binding for global variable ‘design’ get_random_intercept_design: no visible binding for global variable ‘max_mean_idx’ get_random_intercept_design: no visible binding for global variable ‘max_minus_sum’ get_random_intercept_design: no visible binding for global variable ‘max_factor_numeric’ get_random_intercept_design: no visible binding for global variable ‘max_group_numeric’ get_random_intercept_design: no visible binding for global variable ‘min_mean_idx’ get_random_intercept_design: no visible binding for global variable ‘min_minus_sum’ get_variability_contrast_draws: no visible binding for global variable ‘XA’ get_variability_contrast_draws: no visible binding for global variable ‘.value’ get_variability_contrast_draws: no visible binding for global variable ‘.’ get_variability_contrast_draws: no visible binding for global variable ‘.variable’ get_variability_contrast_draws: no visible binding for global variable ‘y’ get_variability_contrast_draws: no visible binding for global variable ‘M’ get_variability_contrast_draws: no visible binding for global variable ‘parameter’ get_variability_contrast_draws: no visible binding for global variable ‘n_eff’ get_variability_contrast_draws: no visible binding for global variable ‘R_k_hat’ glm_multi_beta: no visible binding for global variable ‘.’ label_deleterious_outliers: no visible binding for global variable ‘.count’ label_deleterious_outliers: no visible binding for global variable ‘95%’ label_deleterious_outliers: no visible binding for global variable ‘5%’ label_deleterious_outliers: no visible binding for global variable ‘X’ label_deleterious_outliers: no visible binding for global variable ‘iteration’ label_deleterious_outliers: no visible binding for global variable ‘outlier_above’ label_deleterious_outliers: no visible binding for global variable ‘slope’ label_deleterious_outliers: no visible binding for global variable ‘is_group_right’ label_deleterious_outliers: no visible binding for global variable ‘outlier_below’ multi_beta_glm: no visible global function definition for ‘detect_cores’ parse_fit: no visible binding for global variable ‘M’ parse_formula: no visible global function definition for ‘terms’ parse_formula: no visible binding for global variable ‘.’ parse_formula_random_intercept: no visible global function definition for ‘terms’ parse_generated_quantities: no visible binding for global variable ‘.draw’ parse_generated_quantities: no visible binding for global variable ‘N’ parse_generated_quantities: no visible binding for global variable ‘.value’ parse_generated_quantities: no visible binding for global variable ‘generated_counts’ parse_generated_quantities: no visible binding for global variable ‘M’ parse_generated_quantities: no visible binding for global variable ‘generated_proportions’ plot_1d_intervals: no visible binding for global variable ‘parameter’ plot_1d_intervals: no visible binding for global variable ‘estimate’ plot_1d_intervals: no visible binding for global variable ‘value’ plot_2d_intervals: no visible binding for global variable ‘v_effect’ plot_2d_intervals: no visible binding for global variable ‘parameter’ plot_2d_intervals: no visible binding for global variable ‘.’ plot_2d_intervals: no visible binding for global variable ‘c_effect’ plot_2d_intervals: no visible binding for global variable ‘c_lower’ plot_2d_intervals: no visible binding for global variable ‘c_upper’ plot_2d_intervals: no visible binding for global variable ‘c_FDR’ plot_2d_intervals: no visible binding for global variable ‘v_lower’ plot_2d_intervals: no visible binding for global variable ‘v_upper’ plot_2d_intervals: no visible binding for global variable ‘v_FDR’ plot_2d_intervals: no visible binding for global variable ‘cell_type_label’ plot_boxplot: no visible binding for global variable ‘stats_name’ plot_boxplot: no visible binding for global variable ‘parameter’ plot_boxplot: no visible binding for global variable ‘stats_value’ plot_boxplot: no visible binding for global variable ‘count_data’ plot_boxplot: no visible binding for global variable ‘generated_proportions’ plot_boxplot: no visible binding for global variable ‘proportion’ plot_boxplot: no visible binding for global variable ‘name’ plot_boxplot: no visible binding for global variable ‘outlier’ plot_summary: no visible binding for global variable ‘parameter’ plot_summary: no visible binding for global variable ‘count_data’ plot_summary: no visible binding for global variable ‘v_effect’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘proportion_mean’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘y’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘observed_proportion’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘logit_residuals’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘exposure’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘adjusted_proportion’ remove_unwanted_variation.data.frame: no visible binding for global variable ‘adjusted_counts’ replicate_data: no visible binding for global variable ‘count_data’ replicate_data: no visible binding for global variable ‘exposure’ replicate_data: no visible global function definition for ‘tail’ replicate_data: no visible global function definition for ‘as.formula’ replicate_data: no visible binding for global variable ‘.’ replicate_data: no visible global function definition for ‘na.omit’ replicate_data: no visible binding for global variable ‘Xa’ replicate_data: no visible binding for global variable ‘intercept_in_design’ replicate_data: no visible binding for global variable ‘design’ replicate_data: no visible binding for global variable ‘is_factor_continuous’ replicate_data: no visible binding for global variable ‘design_matrix’ replicate_data: no visible binding for global variable ‘X_random_intercept’ sccomp_predict.data.frame: no visible binding for global variable ‘count_data’ sccomp_predict.data.frame: no visible binding for global variable ‘M’ sccomp_predict.data.frame: no visible binding for global variable ‘N’ sccomp_predict.data.frame: no visible binding for global variable ‘2.5%’ sccomp_predict.data.frame: no visible binding for global variable ‘97.5%’ sccomp_replicate.data.frame: no visible binding for global variable ‘N’ sccomp_replicate.data.frame: no visible binding for global variable ‘M’ simulate_data.data.frame: no visible binding for global variable ‘data___’ simulate_data.data.frame: no visible binding for global variable ‘.exposure’ simulate_data.data.frame: no visible binding for global variable ‘N’ simulate_data.data.frame: no visible binding for global variable ‘M’ simulate_multinomial_logit_linear: no visible global function definition for ‘rnorm’ summary_to_tibble: no visible binding for global variable ‘.’ summary_to_tibble: no visible binding for global variable ‘.variable’ test_contrasts.data.frame: no visible binding for global variable ‘design_matrix_col’ test_contrasts.data.frame: no visible binding for global variable ‘parameter’ test_contrasts.data.frame: no visible binding for global variable ‘M’ Undefined global functions or variables: . .chain .count .draw .draw_imputation .exposure .iteration .lower .median .upper .value .variable 2.5% 5% 50% 95% 97.5% C_name FDR G M N N_M R_k_hat S X XA X_random_intercept Xa additional_parameters_to_save adjusted_counts adjusted_proportion as.formula beta_1 beta_2 bigger_zero c_FDR c_effect c_lower c_upper cell_type cell_type_label censoring_iteration chains cores count_data data___ design design_matrix design_matrix_col detect_cores draw dummy effect estimate exposure factor_1 factors fit_list generated_counts generated_proportions generated_quantity glm_dirichlet_multinomial glm_dirichlet_multinomial_generate_quantities glm_dirichlet_multinomial_imputation group___label group___numeric groupings idx intercept_in_design is_factor_continuous is_group_right iteration logit_residuals lower mat max_factor_numeric max_group_numeric max_mean_idx max_minus_sum mean_idx min_mean_idx min_minus_sum minus_sum n_eff na.omit name observed_proportion outlier outlier_above outlier_below pH0 parameter pass_fit ppc precision proportion proportion_mean rnorm sd se_mean slope smaller_zero stats_name stats_value tail terms tol_rel_obj truncation_down truncation_up upper v_FDR v_effect v_lower v_upper value variable y Consider adding importFrom("stats", "as.formula", "na.omit", "rnorm", "sd", "terms") importFrom("utils", "tail") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sccomp_glm 41.685 0.798 42.564 test_contrasts 41.399 1.039 42.662 remove_unwanted_variation 24.416 1.330 25.955 simulate_data 20.457 1.118 21.686 plot_summary 19.500 1.215 20.849 sccomp_predict 17.891 1.031 19.076 sccomp_replicate 15.092 0.929 16.128 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/sccomp.Rcheck/00check.log’ for details.