* using log directory ‘/srv/hornik/tmp/CRAN_pretest/thresholdanalysis.Rcheck’ * using R Under development (unstable) (2025-11-11 r89006) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (7) Debian flang-new version 19.1.7 (7) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘thresholdanalysis/DESCRIPTION’ ... OK * this is package ‘thresholdanalysis’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Song Sheng <747367050@qq.com>’ New submission Possibly misspelled words in DESCRIPTION: Confounder (19:7) RCS (15:74) * checking package namespace information ... OK * checking package dependencies ... OK * 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 ... NOTE Found the following hidden files and directories: R/inst/extdata/.RData These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. CRAN-pack does not know about R/inst/extdata/.RData * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘thresholdanalysis’ can be installed ... [1s/1s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘1.R’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... WARNING Found the following file with non-ASCII characters: R/linear_threshold.R Portable packages must use only ASCII characters in their R code and NAMESPACE directives, except perhaps in comments. Use \uxxxx escapes for other characters. Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII characters in files. * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] 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 ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘scales’ 'library' or 'require' calls not declared from: ‘broom’ ‘dplyr’ ‘ggplot2’ ‘lmtest’ ‘mgcv’ ‘openxlsx’ ‘purrr’ ‘readr’ ‘rms’ ‘splines’ ‘survival’ 'library' or 'require' calls in package code: ‘broom’ ‘dplyr’ ‘ggplot2’ ‘lmtest’ ‘mgcv’ ‘openxlsx’ ‘purrr’ ‘readr’ ‘rms’ ‘splines’ ‘survival’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [3s/3s] NOTE cox_threshold: no visible global function definition for ‘reformulate’ cox_threshold: no visible binding for '<<-' assignment to ‘dd’ cox_threshold: no visible global function definition for ‘terms’ cox_threshold : : no visible global function definition for ‘coxph’ cox_threshold: no visible binding for global variable ‘dd’ cox_threshold: no visible global function definition for ‘qnorm’ cox_threshold: no visible global function definition for ‘median’ cox_threshold: no visible global function definition for ‘predict’ cox_threshold : find_threshold: no visible global function definition for ‘quantile’ cox_threshold : find_threshold: no visible global function definition for ‘coxph’ cox_threshold: no visible global function definition for ‘%>%’ cox_threshold: no visible global function definition for ‘mutate’ cox_threshold: no visible binding for global variable ‘.data’ cox_threshold: no visible global function definition for ‘coxph’ cox_threshold: no visible global function definition for ‘as.formula’ cox_threshold: no visible global function definition for ‘createWorkbook’ cox_threshold: no visible global function definition for ‘addWorksheet’ cox_threshold: no visible global function definition for ‘writeData’ cox_threshold : extract_results: no visible global function definition for ‘tidy’ cox_threshold: no visible global function definition for ‘lrtest’ cox_threshold: no visible global function definition for ‘saveWorkbook’ cox_threshold: no visible global function definition for ‘ggplot’ cox_threshold: no visible global function definition for ‘aes’ cox_threshold: no visible global function definition for ‘geom_line’ cox_threshold: no visible global function definition for ‘geom_ribbon’ cox_threshold: no visible binding for global variable ‘low’ cox_threshold: no visible binding for global variable ‘up’ cox_threshold: no visible global function definition for ‘geom_vline’ cox_threshold: no visible global function definition for ‘geom_rug’ cox_threshold: no visible global function definition for ‘labs’ cox_threshold: no visible global function definition for ‘theme_minimal’ cox_threshold: no visible global function definition for ‘theme’ cox_threshold: no visible global function definition for ‘element_blank’ cox_threshold: no visible global function definition for ‘element_line’ cox_threshold: no visible global function definition for ‘element_text’ cox_threshold: no visible global function definition for ‘scale_y_continuous’ cox_threshold: no visible global function definition for ‘expansion’ linear_threshold: no visible global function definition for ‘update’ linear_threshold: no visible global function definition for ‘as.formula’ linear_threshold: no visible global function definition for ‘gam’ linear_threshold: no visible global function definition for ‘gaussian’ linear_threshold : search_threshold: no visible global function definition for ‘quantile’ linear_threshold : search_threshold: no visible global function definition for ‘update’ linear_threshold : search_threshold: no visible global function definition for ‘glm’ linear_threshold : search_threshold: no visible binding for global variable ‘gaussian’ linear_threshold : search_threshold: no visible global function definition for ‘logLik’ linear_threshold: no visible global function definition for ‘%>%’ linear_threshold: no visible global function definition for ‘mutate’ linear_threshold: no visible binding for global variable ‘.data’ linear_threshold: no visible global function definition for ‘glm’ linear_threshold: no visible binding for global variable ‘gaussian’ linear_threshold : : no visible global function definition for ‘median’ linear_threshold: no visible global function definition for ‘predict’ linear_threshold: no visible global function definition for ‘lm’ linear_threshold: no visible global function definition for ‘ggplot’ linear_threshold: no visible global function definition for ‘aes’ linear_threshold: no visible binding for global variable ‘x’ linear_threshold: no visible global function definition for ‘geom_line’ linear_threshold: no visible global function definition for ‘geom_ribbon’ linear_threshold: no visible binding for global variable ‘low’ linear_threshold: no visible binding for global variable ‘up’ linear_threshold: no visible global function definition for ‘geom_vline’ linear_threshold: no visible global function definition for ‘geom_rug’ linear_threshold: no visible global function definition for ‘labs’ linear_threshold: no visible global function definition for ‘theme_minimal’ linear_threshold: no visible global function definition for ‘theme’ linear_threshold: no visible global function definition for ‘element_blank’ linear_threshold: no visible global function definition for ‘element_line’ linear_threshold: no visible global function definition for ‘element_text’ linear_threshold: no visible global function definition for ‘scale_y_continuous’ linear_threshold: no visible global function definition for ‘expansion’ linear_threshold: no visible global function definition for ‘lrtest’ linear_threshold : extract_var_results: no visible global function definition for ‘tidy’ linear_threshold : extract_var_results: no visible global function definition for ‘%>%’ linear_threshold : extract_var_results: no visible global function definition for ‘rename’ linear_threshold : extract_var_results: no visible binding for global variable ‘term’ linear_threshold : extract_var_results: no visible binding for global variable ‘estimate’ linear_threshold : extract_var_results: no visible binding for global variable ‘conf.low’ linear_threshold : extract_var_results: no visible binding for global variable ‘conf.high’ linear_threshold : extract_var_results: no visible binding for global variable ‘p.value’ linear_threshold: no visible global function definition for ‘createWorkbook’ linear_threshold: no visible global function definition for ‘addWorksheet’ linear_threshold: no visible global function definition for ‘writeData’ linear_threshold: no visible global function definition for ‘saveWorkbook’ logistic_threshold: no visible global function definition for ‘as.formula’ logistic_threshold: no visible global function definition for ‘gam’ logistic_threshold: no visible binding for global variable ‘binomial’ logistic_threshold: no visible global function definition for ‘predict’ logistic_threshold: no visible global function definition for ‘%>%’ logistic_threshold: no visible global function definition for ‘mutate’ logistic_threshold: no visible global function definition for ‘:=’ logistic_threshold: no visible global function definition for ‘plogis’ logistic_threshold: no visible global function definition for ‘coef’ logistic_threshold : search_threshold: no visible global function definition for ‘%>%’ logistic_threshold : search_threshold: no visible global function definition for ‘filter’ logistic_threshold : search_threshold: no visible binding for global variable ‘.data’ logistic_threshold : search_threshold: no visible global function definition for ‘quantile’ logistic_threshold : search_threshold: no visible global function definition for ‘as.formula’ logistic_threshold : search_threshold: no visible global function definition for ‘glm’ logistic_threshold : search_threshold: no visible binding for global variable ‘binomial’ logistic_threshold : search_threshold: no visible global function definition for ‘logLik’ logistic_threshold : : no visible global function definition for ‘median’ logistic_threshold: no visible global function definition for ‘glm’ logistic_threshold: no visible global function definition for ‘ggplot’ logistic_threshold: no visible global function definition for ‘aes’ logistic_threshold: no visible binding for global variable ‘x’ logistic_threshold: no visible global function definition for ‘geom_line’ logistic_threshold: no visible binding for global variable ‘fit’ logistic_threshold: no visible global function definition for ‘geom_ribbon’ logistic_threshold: no visible binding for global variable ‘low’ logistic_threshold: no visible binding for global variable ‘up’ logistic_threshold: no visible global function definition for ‘geom_vline’ logistic_threshold: no visible global function definition for ‘geom_rug’ logistic_threshold: no visible binding for global variable ‘.data’ logistic_threshold: no visible global function definition for ‘labs’ logistic_threshold: no visible global function definition for ‘theme_minimal’ logistic_threshold: no visible global function definition for ‘theme’ logistic_threshold: no visible global function definition for ‘element_blank’ logistic_threshold: no visible global function definition for ‘element_line’ logistic_threshold: no visible global function definition for ‘element_text’ logistic_threshold: no visible global function definition for ‘scale_y_continuous’ logistic_threshold: no visible global function definition for ‘expansion’ logistic_threshold: no visible global function definition for ‘lrtest’ logistic_threshold : extract_var_results: no visible global function definition for ‘tidy’ logistic_threshold : extract_var_results: no visible global function definition for ‘rename’ logistic_threshold : extract_var_results: no visible binding for global variable ‘term’ logistic_threshold : extract_var_results: no visible binding for global variable ‘estimate’ logistic_threshold : extract_var_results: no visible binding for global variable ‘conf.low’ logistic_threshold : extract_var_results: no visible binding for global variable ‘conf.high’ logistic_threshold : extract_var_results: no visible binding for global variable ‘p.value’ logistic_threshold: no visible global function definition for ‘createWorkbook’ logistic_threshold: no visible global function definition for ‘addWorksheet’ logistic_threshold: no visible global function definition for ‘writeData’ logistic_threshold: no visible global function definition for ‘saveWorkbook’ Undefined global functions or variables: %>% .data := addWorksheet aes as.formula binomial coef conf.high conf.low coxph createWorkbook dd element_blank element_line element_text estimate expansion filter fit gam gaussian geom_line geom_ribbon geom_rug geom_vline ggplot glm labs lm logLik low lrtest median mutate p.value plogis predict qnorm quantile reformulate rename saveWorkbook scale_y_continuous term terms theme theme_minimal tidy up update writeData x Consider adding importFrom("stats", "as.formula", "binomial", "coef", "filter", "gaussian", "glm", "lm", "logLik", "median", "plogis", "predict", "qnorm", "quantile", "reformulate", "terms", "update") 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 ... NONE * checking PDF version of manual ... [4s/4s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Unicode character β (U+03B2) not set up for use with LaTeX. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [0s/0s] OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘thresholdanalysis-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 4 WARNINGs, 6 NOTEs