* using log directory ‘/srv/hornik/tmp/CRAN/explainer.Rcheck’ * using R Under development (unstable) (2023-11-20 r85569) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.5 (1) Debian flang-new version 17.0.5 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘explainer/DESCRIPTION’ ... OK * this is package ‘explainer’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Ramtin Zargari Marandi ’ New submission Possibly misspelled words in DESCRIPTION: Explainer (2:31) Shapley (7:172) The Description field should not start with the package name, 'This package' or similar. * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'cowplot', 'data.table', 'dplyr', 'ggplot2', 'mlr3', 'mlr3learners', 'knitr', 'broom', 'cvms', 'iml', 'tidyverse' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘explainer’ can be installed ... [6s/6s] WARNING Found the following significant warnings: Note: possible error in 'layout(title = "ROC plots on the development set")': unused argument (title = "ROC plots on the development set") Note: possible error in 'layout(title = "ROC plots on the test set")': unused argument (title = "ROC plots on the test set") See ‘/srv/hornik/tmp/CRAN/explainer.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘broom’ ‘cowplot’ ‘cvms’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘iml’ ‘knitr’ ‘mlr3’ ‘mlr3learners’ ‘tidyverse’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [3s/3s] NOTE PP_vs_FVAL_plt: no visible global function definition for ‘ggplot’ PP_vs_FVAL_plt: no visible global function definition for ‘aes’ PP_vs_FVAL_plt: no visible binding for global variable ‘f_val’ PP_vs_FVAL_plt: no visible binding for global variable ‘pred_prob’ PP_vs_FVAL_plt: no visible global function definition for ‘geom_point’ PP_vs_FVAL_plt: no visible binding for global variable ‘correct_prediction’ PP_vs_FVAL_plt: no visible global function definition for ‘xlab’ PP_vs_FVAL_plt: no visible global function definition for ‘ylab’ PP_vs_FVAL_plt: no visible global function definition for ‘facet_wrap’ PP_vs_FVAL_plt: no visible global function definition for ‘ggplotly’ SHAP_vs_FVAL_plt: no visible global function definition for ‘ggplot’ SHAP_vs_FVAL_plt: no visible global function definition for ‘aes’ SHAP_vs_FVAL_plt: no visible binding for global variable ‘f_val’ SHAP_vs_FVAL_plt: no visible binding for global variable ‘Phi’ SHAP_vs_FVAL_plt: no visible global function definition for ‘geom_point’ SHAP_vs_FVAL_plt: no visible binding for global variable ‘correct_prediction’ SHAP_vs_FVAL_plt: no visible global function definition for ‘xlab’ SHAP_vs_FVAL_plt: no visible global function definition for ‘ylab’ SHAP_vs_FVAL_plt: no visible global function definition for ‘facet_wrap’ SHAP_vs_FVAL_plt: no visible global function definition for ‘ggplotly’ SHAPclust: no visible global function definition for ‘kmeans’ SHAPclust: no visible global function definition for ‘capture.output’ SHAPclust: no visible global function definition for ‘%>%’ SHAPclust: no visible global function definition for ‘mutate’ SHAPclust: no visible global function definition for ‘:=’ SHAPclust: no visible binding for global variable ‘prediction_correctness’ SHAPclust: no visible binding for global variable ‘truth’ SHAPclust: no visible binding for global variable ‘response’ SHAPclust: no visible binding for global variable ‘fval’ SHAPclust: no visible binding for global variable ‘.SD’ SHAPclust: no visible binding for global variable ‘variable’ SHAPclust: no visible binding for global variable ‘mean_absolute_shap’ SHAPclust: no visible global function definition for ‘ggplot’ SHAPclust: no visible global function definition for ‘aes’ SHAPclust: no visible binding for global variable ‘feature’ SHAPclust: no visible binding for global variable ‘value’ SHAPclust: no visible global function definition for ‘geom_violin’ SHAPclust: no visible global function definition for ‘geom_line’ SHAPclust: no visible binding for global variable ‘sample_num’ SHAPclust: no visible global function definition for ‘coord_flip’ SHAPclust: no visible global function definition for ‘geom_jitter’ SHAPclust: no visible global function definition for ‘position_jitter’ SHAPclust: no visible global function definition for ‘scale_shape_manual’ SHAPclust: no visible global function definition for ‘labs’ SHAPclust: no visible global function definition for ‘scale_colour_gradient2’ SHAPclust: no visible global function definition for ‘geom_text’ SHAPclust: no visible global function definition for ‘theme’ SHAPclust: no visible global function definition for ‘element_blank’ SHAPclust: no visible global function definition for ‘geom_hline’ SHAPclust: no visible global function definition for ‘element_text’ SHAPclust: no visible global function definition for ‘element_line’ SHAPclust: no visible global function definition for ‘ylim’ SHAPclust: no visible global function definition for ‘facet_wrap’ SHAPclust: no visible global function definition for ‘ggsave’ SHAPclust: no visible global function definition for ‘ggplotly’ SHAPclust: no visible global function definition for ‘tibble’ SHAPclust: no visible global function definition for ‘as_tibble’ SHAPclust: no visible global function definition for ‘ggtitle’ eCM_plot: no visible global function definition for ‘tibble’ eDecisionCurve: no visible global function definition for ‘ggplot’ eDecisionCurve: no visible global function definition for ‘aes’ eDecisionCurve: no visible binding for global variable ‘threshold’ eDecisionCurve: no visible binding for global variable ‘value’ eDecisionCurve: no visible binding for global variable ‘variable’ eDecisionCurve: no visible global function definition for ‘geom_point’ eDecisionCurve: no visible global function definition for ‘geom_line’ eDecisionCurve: no visible global function definition for ‘scale_color_manual’ eDecisionCurve: no visible global function definition for ‘geom_vline’ eDecisionCurve: no visible global function definition for ‘ylim’ eDecisionCurve: no visible global function definition for ‘labs’ eDecisionCurve: no visible global function definition for ‘theme’ eDecisionCurve: no visible global function definition for ‘element_blank’ eDecisionCurve: no visible global function definition for ‘ggplotly’ eFairness: no visible global function definition for ‘as.data.table’ eFairness: no visible global function definition for ‘set’ eFairness: no visible global function definition for ‘ggplot’ eFairness: no visible global function definition for ‘aes’ eFairness: no visible binding for global variable ‘truth’ eFairness: no visible binding for global variable ‘pos_class_prob’ eFairness: no visible binding for global variable ‘subgroups’ eFairness: no visible global function definition for ‘labs’ eROC_plot: no visible global function definition for ‘labs’ eROC_plot: no visible global function definition for ‘theme’ eROC_plot: no visible global function definition for ‘element_blank’ eROC_plot: no visible global function definition for ‘guides’ eSHAP_plot: no visible global function definition for ‘%>%’ eSHAP_plot: no visible global function definition for ‘mutate’ eSHAP_plot: no visible binding for global variable ‘feature’ eSHAP_plot: no visible global function definition for ‘ggplot’ eSHAP_plot: no visible global function definition for ‘aes’ eSHAP_plot: no visible global function definition for ‘geom_violin’ eSHAP_plot: no visible global function definition for ‘geom_line’ eSHAP_plot: no visible binding for global variable ‘sample_num’ eSHAP_plot: no visible global function definition for ‘coord_flip’ eSHAP_plot: no visible global function definition for ‘geom_jitter’ eSHAP_plot: no visible global function definition for ‘position_jitter’ eSHAP_plot: no visible binding for global variable ‘correct_prediction’ eSHAP_plot: no visible global function definition for ‘scale_shape_manual’ eSHAP_plot: no visible global function definition for ‘labs’ eSHAP_plot: no visible global function definition for ‘scale_colour_gradient2’ eSHAP_plot: no visible global function definition for ‘geom_text’ eSHAP_plot: no visible global function definition for ‘theme’ eSHAP_plot: no visible global function definition for ‘element_blank’ eSHAP_plot: no visible global function definition for ‘geom_hline’ eSHAP_plot: no visible global function definition for ‘element_text’ eSHAP_plot: no visible global function definition for ‘element_line’ eSHAP_plot: no visible global function definition for ‘ylim’ eSHAP_plot: no visible global function definition for ‘ggplotly’ eSHAP_plot_reg: no visible global function definition for ‘%>%’ eSHAP_plot_reg: no visible global function definition for ‘mutate’ eSHAP_plot_reg: no visible binding for global variable ‘feature’ eSHAP_plot_reg: no visible global function definition for ‘ggplot’ eSHAP_plot_reg: no visible global function definition for ‘aes’ eSHAP_plot_reg: no visible global function definition for ‘geom_violin’ eSHAP_plot_reg: no visible global function definition for ‘geom_line’ eSHAP_plot_reg: no visible binding for global variable ‘sample_num’ eSHAP_plot_reg: no visible global function definition for ‘coord_flip’ eSHAP_plot_reg: no visible global function definition for ‘geom_jitter’ eSHAP_plot_reg: no visible global function definition for ‘position_jitter’ eSHAP_plot_reg: no visible global function definition for ‘scale_colour_gradient2’ eSHAP_plot_reg: no visible global function definition for ‘geom_text’ eSHAP_plot_reg: no visible global function definition for ‘theme’ eSHAP_plot_reg: no visible global function definition for ‘element_blank’ eSHAP_plot_reg: no visible global function definition for ‘geom_hline’ eSHAP_plot_reg: no visible global function definition for ‘labs’ eSHAP_plot_reg: no visible global function definition for ‘element_text’ eSHAP_plot_reg: no visible global function definition for ‘element_line’ eSHAP_plot_reg: no visible global function definition for ‘ylim’ eSHAP_plot_reg: no visible global function definition for ‘ggplotly’ eperformance: no visible global function definition for ‘complete.cases’ eperformance: no visible global function definition for ‘ggplot’ eperformance: no visible global function definition for ‘aes’ eperformance: no visible binding for global variable ‘fpr’ eperformance: no visible binding for global variable ‘tpr’ eperformance: no visible global function definition for ‘geom_point’ eperformance: no visible binding for global variable ‘threshold’ eperformance: no visible global function definition for ‘geom_line’ eperformance: no visible global function definition for ‘scale_colour_gradient2’ eperformance: no visible binding for global variable ‘x’ eperformance: no visible binding for global variable ‘y’ eperformance: no visible global function definition for ‘labs’ eperformance: no visible global function definition for ‘scale_x_continuous’ eperformance: no visible global function definition for ‘scale_y_continuous’ eperformance: no visible global function definition for ‘theme’ eperformance: no visible binding for global variable ‘ppv’ eperformance: no visible global function definition for ‘ggplotly’ eperformance: no visible global function definition for ‘%>%’ eperformance: no visible global function definition for ‘subplot’ eperformance: no visible global function definition for ‘layout’ range01: no visible global function definition for ‘median’ range01: no visible global function definition for ‘mad’ regressmdl_eval: no visible global function definition for ‘cor’ Undefined global functions or variables: %>% .SD := Phi aes as.data.table as_tibble capture.output complete.cases coord_flip cor correct_prediction element_blank element_line element_text f_val facet_wrap feature fpr fval geom_hline geom_jitter geom_line geom_point geom_text geom_violin geom_vline ggplot ggplotly ggsave ggtitle guides kmeans labs layout mad mean_absolute_shap median mutate pos_class_prob position_jitter ppv pred_prob prediction_correctness response sample_num scale_color_manual scale_colour_gradient2 scale_shape_manual scale_x_continuous scale_y_continuous set subgroups subplot theme threshold tibble tpr truth value variable x xlab y ylab ylim Consider adding importFrom("graphics", "layout") importFrom("stats", "complete.cases", "cor", "kmeans", "mad", "median") importFrom("utils", "capture.output") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 examples ... [3s/3s] OK * checking PDF version of manual ... [3s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 5 NOTEs