* using log directory ‘/srv/hornik/tmp/CRAN/MantaID.Rcheck’ * using R Under development (unstable) (2024-08-16 r87026) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘MantaID/DESCRIPTION’ ... OK * this is package ‘MantaID’ version ‘1.0.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Zhengpeng Zeng ’ New submission Package was archived on CRAN CRAN repository db overrides: X-CRAN-Comment: Archived on 2024-07-16 as issues were not corrected in time. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Size of tarball: 21441980 bytes * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'biomaRt', 'xgboost', 'caret', 'data.table', 'dplyr', 'ggplot2', 'keras', 'magrittr', 'mlr3tuning', 'mlr3', 'mlr3learners', 'purrr', 'reshape2', 'scutr', 'stringr', 'tibble', 'tidyr', 'tidyselect', 'paradox', 'RColorBrewer', 'ggcorrplot', 'ranger', 'rpart', 'mlr3hyperband' 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 whether package ‘MantaID’ can be installed ... [16s/16s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘Graph’ ‘MantaID_mouse_tutorial.Rmd’ ‘MantaID_tutorial.html’ ‘bacteria’ ‘logo.svg’ * 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 ... [5s/5s] OK * checking whether the package can be loaded with stated dependencies ... [5s/5s] OK * checking whether the package can be unloaded cleanly ... [5s/5s] OK * checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK * checking whether the namespace can be unloaded cleanly ... [5s/5s] OK * checking loading without being on the library search path ... [5s/5s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘mlr3hyperband’ ‘mlr3learners’ ‘ranger’ ‘rpart’ ‘xgboost’ 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 ... [21s/21s] NOTE mi_clean_data: no visible global function definition for ‘all_of’ mi_filter_feat: no visible binding for global variable ‘Var1’ mi_filter_feat: no visible binding for global variable ‘Var2’ mi_filter_feat: no visible binding for global variable ‘value’ mi_filter_feat: no visible global function definition for ‘pmap’ mi_filter_feat: no visible global function definition for ‘add_column’ mi_filter_feat: no visible global function definition for ‘distinct’ mi_filter_feat: no visible binding for global variable ‘Key’ mi_filter_feat: no visible global function definition for ‘starts_with’ mi_filter_feat: no visible binding for global variable ‘var’ mi_get_ID : to_2col: no visible global function definition for ‘str_detect’ mi_get_ID : to_2col: no visible binding for global variable ‘ID’ mi_get_ID : to_2col: no visible global function definition for ‘tibble’ mi_get_ID: no visible global function definition for ‘drop_na’ mi_get_importance: no visible global function definition for ‘tibble’ mi_get_importance: no visible global function definition for ‘scale_y_discrete’ mi_get_importance: no visible global function definition for ‘geom_bar’ mi_get_importance: no visible binding for global variable ‘importance’ mi_get_importance: no visible binding for global variable ‘feature’ mi_unify_mod : prd_new: no visible binding for global variable ‘truth’ mi_unify_mod : prd_new: no visible binding for global variable ‘row_ids’ mi_unify_mod : major: no visible global function definition for ‘tibble’ mi_unify_mod : major: no visible binding for global variable ‘weight’ mi_unify_mod: no visible global function definition for ‘pmap’ Undefined global functions or variables: ID Key Var1 Var2 add_column all_of distinct drop_na feature geom_bar importance pmap row_ids scale_y_discrete starts_with str_detect tibble truth value var weight Consider adding importFrom("stats", "var") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [8s/8s] OK * checking PDF version of manual ... [3s/3s] 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: 5 NOTEs