############################################################################## ############################################################################## ### ### 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_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sccomp.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sccomp/DESCRIPTION’ ... OK * this is package ‘sccomp’ version ‘1.10.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 6.0Mb sub-directories of 1Mb or more: data 4.0Mb figures 1.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘stats’ ‘knitr’ 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 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 dependencies in R code ... WARNING 'loadNamespace' or 'requireNamespace' call not declared from: ‘cmdstanr’ Namespaces in Imports field not imported from: ‘SeuratObject’ ‘callr’ ‘digest’ ‘fs’ ‘withr’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE check_if_columns_right_class: no visible global function definition for ‘is’ check_if_count_integer: no visible global function definition for ‘is’ data_to_spread: no visible binding for global variable ‘exposure’ draws_to_tibble_x_y: no visible binding for global variable ‘.’ 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 binding for global variable ‘pf’ get_abundance_contrast_draws: no visible binding for global variable ‘.’ 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 binding for global variable ‘X_random_effect_2’ get_abundance_contrast_draws: no visible binding for global variable ‘Rhat’ get_model_from_data: no visible global function definition for ‘stan_model’ 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_: no visible binding for global variable ‘name’ get_probability_non_zero_: no visible binding for global variable ‘value’ get_probability_non_zero_OLD: no visible binding for global variable ‘.’ 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 ‘Rhat’ parse_formula: no visible binding for global variable ‘.’ plot_2D_intervals: no visible binding for global variable ‘.’ replicate_data: no visible binding for global variable ‘count_data’ replicate_data: no visible global function definition for ‘is’ replicate_data: no visible binding for global variable ‘exposure’ replicate_data: no visible binding for global variable ‘dummy’ replicate_data: no visible global function definition for ‘tail’ 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 ‘design_matrix’ replicate_data: no visible binding for global variable ‘X_random_effect’ replicate_data: no visible binding for global variable ‘X_random_effect_2’ sccomp_boxplot: no visible binding for global variable ‘parameter’ sccomp_boxplot: no visible binding for global variable ‘count_data’ 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 binding for global variable ‘count_data’ 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 binding for global variable ‘count_data’ 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 ‘count_data’ 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 ‘.’ summary_to_tibble: no visible binding for global variable ‘variable’ Undefined global functions or variables: . .chain .draw .exposure .iteration .lower .upper .value .variable 2.5% 5% 50% 95% 97.5% C_name M N Rhat X_random_effect X_random_effect_2 Xa adjusted_counts adjusted_proportion average_uncertainty bigger_zero columns count_data data___ design design_matrix design_matrix_col difference_proportion_lower_fold_change difference_proportion_upper_fold_change dummy exposure intercept_in_design is is_proportion multipanel_theme n_random_eff na.omit name observed_proportion parameter pf proportion_fold_change proportion_mean ratio_lower ratio_mean ratio_upper residuals rnorm smaller_zero stan_model statement tail truncation_down truncation_up value variable y_proportion Consider adding importFrom("methods", "is") importFrom("stats", "na.omit", "pf", "residuals", "rnorm") importFrom("utils", "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 ... 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 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/sccomp.Rcheck/00check.log’ for details.