* using log directory 'd:/RCompile/CRANincoming/R-devel/explainer.Rcheck' * using R Under development (unstable) (2023-11-20 r85569 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * 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 ... NOTE Maintainer: 'Ramtin Zargari Marandi ' New submission Possibly misspelled words in DESCRIPTION: Explainer (2:31) Shapley (7:155) serveral (7:58) Unknown, possibly misspelled, fields in DESCRIPTION: 'VignetteIndexEntry' Package has a VignetteBuilder field but no prebuilt vignette index. The Description field should not start with the package name, 'This package' or similar. Size of tarball: 8053842 bytes * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'cowplot', 'data.table', 'dplyr', 'ggplot2', 'ggpmisc', 'ggpubr', 'mlr3', 'mlr3learners', 'knitr', 'broom', 'cvms', 'egg', 'forcats', 'iml', 'mlr3viz', 'plotROC', 'psych', 'reshape2', 'writexl', 'magrittr', 'tidyverse', 'plotly' 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 hidden files and directories ... OK * checking for portable file names ... NOTE Found the following non-portable file paths: explainer/vignettes/rsconnect/documents/explainer_tutorial.Rmd/plnxpersimcn01.unix.regionh.top.local/RZAR0002/explainer_tutorial.dcf explainer/vignettes/rsconnect/documents/explainer_tutorial.Rmd/plnxpersimcn01.unix.regionh.top.local/RZAR0002 Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section 'Package structure' in the 'Writing R Extensions' manual. * checking serialization versions ... OK * checking whether package 'explainer' can be installed ... OK * checking installed package size ... OK * 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 ... NOTE Non-standard file/directory found at top level: 'docs' * 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 loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to 'ggplot2' which was already attached by Depends. Please remove these calls from your code. Packages in Depends field not imported from: 'broom' 'cowplot' 'cvms' 'data.table' 'dplyr' 'egg' 'forcats' 'ggplot2' 'ggpmisc' 'ggpubr' 'iml' 'knitr' 'magrittr' 'mlr3' 'mlr3learners' 'mlr3viz' 'plotROC' 'plotly' 'psych' 'reshape2' 'tidyverse' 'writexl' 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 ... 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 ... 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 ... WARNING Undocumented arguments in Rd file 'eSHAP_plot_reg.Rd' 'sample.size' 'seed' 'subset' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': 'SHAP_clusters_kmeans246.pdf' 'confusion_matrices.pdf' 'confusion_matrices.png' 'explainer_tutorial.Rmd' 'explainer_tutorial.nb.html' 'explainer_tutorial_regression.Rmd' 'kmeans_info246.txt' 'pandoc7df041c51b07.nb.html' 'rsconnect/documents/explainer_tutorial.Rmd/plnxpersimcn01.unix.regionh.top.local/RZAR0002/explainer_tutorial.dcf' 'sessioninfo246.xlsx' 'shap_PL_kmeans_clusters246.xlsx' 'shap_PL_kmeans_clusters_detailed246.xlsx' Files named as vignettes but with no recognized vignette engine: 'vignettes/explainer_tutorial.Rmd' 'vignettes/explainer_tutorial_regression.Rmd' (Is a VignetteBuilder field missing?) * checking examples ... OK * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 2 WARNINGs, 7 NOTEs