############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sccomp.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sccomp_2.1.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sccomp.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘sccomp/DESCRIPTION’ ... OK * this is package ‘sccomp’ version ‘2.1.8’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... INFO installed size is 6.6Mb sub-directories of 1Mb or more: data 3.9Mb figures 1.9Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE as_matrix: no visible binding for global variable ‘.’ check_if_any_NA: no visible binding for global variable ‘columns’ check_if_columns_right_class: no visible global function definition for ‘is’ check_if_count_integer: no visible global function definition for ‘is’ check_if_sample_is_a_unique_identifier: no visible binding for global variable ‘n___’ check_sample_consistency_of_factors: no visible binding for global variable ‘name’ check_sample_consistency_of_factors: no visible binding for global variable ‘correct_size’ data_to_spread: no visible binding for global variable ‘exposure’ draws_to_statistics: no visible binding for global variable ‘rhat’ draws_to_statistics: no visible binding for global variable ‘ess_bulk’ draws_to_statistics: no visible binding for global variable ‘ess_tail’ draws_to_statistics: no visible binding for global variable ‘.value’ draws_to_statistics: no visible global function definition for ‘setNames’ draws_to_tibble_x_y: no visible binding for global variable ‘parameter’ find_optimal_number_of_chains: no visible binding for global variable ‘.’ fit_model: no visible global function definition for ‘setNames’ fit_model: no visible binding for global variable ‘pf’ get_abundance_contrast_draws: no visible global function definition for ‘setNames’ get_abundance_contrast_draws: no visible binding for global variable ‘.’ get_abundance_contrast_draws: no visible binding for global variable ‘parameters_name’ get_abundance_contrast_draws: no visible binding for global variable ‘n_random_eff’ get_abundance_contrast_draws: no visible binding for global variable ‘.chain’ get_abundance_contrast_draws: no visible binding for global variable ‘.iteration’ get_abundance_contrast_draws: no visible binding for global variable ‘.draw’ get_abundance_contrast_draws: no visible global function definition for ‘sd’ get_abundance_contrast_draws: no visible binding for global variable ‘point_estimate’ get_abundance_contrast_draws: no visible binding for global variable ‘sd_of_point_estimates’ get_abundance_contrast_draws: no visible binding for global variable ‘X_random_effect_2’ get_model_from_data: no visible global function definition for ‘stan_model’ get_random_effect_design3: no visible binding for global variable ‘value’ get_random_effect_design3: no visible binding for global variable ‘group___label’ get_random_effect_design3: no visible binding for global variable ‘group___numeric’ get_variability_contrast_draws: no visible binding for global variable ‘parameters_name’ get_variability_contrast_draws: no visible binding for global variable ‘.variable’ get_variability_contrast_draws: no visible global function definition for ‘setNames’ get_variability_contrast_draws: no visible binding for global variable ‘.’ mutate_from_expr_list: no visible binding for global variable ‘M’ mutate_from_expr_list: no visible binding for global variable ‘.chain’ mutate_from_expr_list: no visible binding for global variable ‘.iteration’ mutate_from_expr_list: no visible binding for global variable ‘.draw’ parse_formula: no visible binding for global variable ‘.’ pillar___format_comment: no visible global function definition for ‘map_chr’ pillar___wrap: no visible global function definition for ‘get_extent’ plot_2D_intervals: no visible binding for global variable ‘.’ plot_2D_intervals: no visible binding for global variable ‘multipanel_theme’ plot_boxplot: no visible binding for global variable ‘factor_values’ plot_boxplot: no visible binding for global variable ‘is_zero’ plot_scatterplot: no visible binding for global variable ‘factor_values’ prepare_replicate_data: no visible global function definition for ‘is’ prepare_replicate_data: no visible binding for global variable ‘exposure’ prepare_replicate_data: no visible binding for global variable ‘dummy’ prepare_replicate_data: no visible global function definition for ‘tail’ prepare_replicate_data: no visible binding for global variable ‘.’ prepare_replicate_data: no visible global function definition for ‘na.omit’ prepare_replicate_data: no visible binding for global variable ‘formula’ prepare_replicate_data: no visible binding for global variable ‘design’ prepare_replicate_data: no visible binding for global variable ‘design_matrix’ print.sccomp_tbl: no visible binding for global variable ‘N’ print.sccomp_tbl: no visible binding for global variable ‘M’ print_red_tibble: no visible global function definition for ‘capture.output’ sccomp_boxplot: no visible binding for global variable ‘parameter’ sccomp_boxplot: no visible binding for global variable ‘proportion’ sccomp_boxplot: no visible binding for global variable ‘adjusted_proportion’ sccomp_boxplot: no visible binding for global variable ‘multipanel_theme’ sccomp_calculate_residuals.sccomp_tbl: no visible binding for global variable ‘proportion_mean’ sccomp_calculate_residuals.sccomp_tbl: no visible binding for global variable ‘is_proportion’ sccomp_calculate_residuals.sccomp_tbl: no visible binding for global variable ‘y_proportion’ sccomp_calculate_residuals.sccomp_tbl: no visible binding for global variable ‘observed_proportion’ sccomp_calculate_residuals.sccomp_tbl: no visible binding for global variable ‘residuals’ sccomp_calculate_residuals.sccomp_tbl: no visible binding for global variable ‘exposure’ sccomp_glm_data_frame_counts: no visible global function definition for ‘is’ sccomp_glm_data_frame_counts: no visible binding for global variable ‘N’ sccomp_glm_data_frame_counts: no visible binding for global variable ‘M’ sccomp_glm_data_frame_counts: no visible global function definition for ‘na.omit’ sccomp_predict.sccomp_tbl: no visible global function definition for ‘is’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘M’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘N’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘2.5%’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘97.5%’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘.value’ sccomp_predict.sccomp_tbl: no visible binding for global variable ‘.draw’ sccomp_proportional_fold_change.sccomp_tbl: no visible binding for global variable ‘ratio_mean’ sccomp_proportional_fold_change.sccomp_tbl: no visible binding for global variable ‘ratio_upper’ sccomp_proportional_fold_change.sccomp_tbl: no visible binding for global variable ‘proportion_fold_change’ sccomp_proportional_fold_change.sccomp_tbl: no visible binding for global variable ‘ratio_lower’ sccomp_proportional_fold_change.sccomp_tbl: no visible binding for global variable ‘difference_proportion_upper_fold_change’ sccomp_proportional_fold_change.sccomp_tbl: no visible binding for global variable ‘difference_proportion_lower_fold_change’ sccomp_proportional_fold_change.sccomp_tbl: no visible binding for global variable ‘average_uncertainty’ sccomp_proportional_fold_change.sccomp_tbl: no visible binding for global variable ‘statement’ sccomp_remove_outliers.sccomp_tbl: no visible global function definition for ‘is’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘N’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘M’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘5%’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘95%’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘truncation_up’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘truncation_down’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘value’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘columns’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘.lower’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘50%’ sccomp_remove_outliers.sccomp_tbl: no visible binding for global variable ‘.upper’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘proportion_mean’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘adjusted_proportion’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘exposure’ sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for global variable ‘adjusted_counts’ sccomp_replicate.sccomp_tbl: no visible binding for global variable ‘N’ sccomp_replicate.sccomp_tbl: no visible binding for global variable ‘M’ sccomp_test.sccomp_tbl: no visible binding for global variable ‘design_matrix_col’ sccomp_test.sccomp_tbl: no visible binding for global variable ‘parameter’ sccomp_test.sccomp_tbl: no visible binding for global variable ‘M’ simulate_data.tbl: no visible binding for global variable ‘data___’ simulate_data.tbl: no visible binding for global variable ‘.exposure’ simulate_data.tbl: no visible binding for global variable ‘N’ simulate_data.tbl: 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 ‘variable’ vb_iterative : : no visible binding for global variable ‘model_name’ Undefined global functions or variables: . .chain .draw .exposure .iteration .lower .upper .value .variable 2.5% 5% 50% 95% 97.5% M N X_random_effect_2 adjusted_counts adjusted_proportion average_uncertainty capture.output columns correct_size data___ design design_matrix design_matrix_col difference_proportion_lower_fold_change difference_proportion_upper_fold_change dummy ess_bulk ess_tail exposure factor_values formula get_extent group___label group___numeric is is_proportion is_zero map_chr model_name multipanel_theme n___ n_random_eff na.omit name observed_proportion parameter parameters_name pf point_estimate proportion proportion_fold_change proportion_mean ratio_lower ratio_mean ratio_upper residuals rhat rnorm sd sd_of_point_estimates setNames stan_model statement tail truncation_down truncation_up value variable y_proportion Consider adding importFrom("methods", "is") importFrom("stats", "formula", "na.omit", "pf", "residuals", "rnorm", "sd", "setNames") importFrom("utils", "capture.output", "tail") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... INFO Package unavailable to check Rd xrefs: ‘cmdstanr’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/sccomp.Rcheck/00check.log’ for details.