* using log directory 'd:/RCompile/CRANincoming/R-devel/mt.surv.Rcheck' * using R Under development (unstable) (2025-05-04 r88189 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'mt.surv/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'mt.surv' version '1.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Alexander Loncar ' New submission Possibly misspelled words in DESCRIPTION: perfrom (28:31) Package has a VignetteBuilder field but no prebuilt vignette index. The Title field should be in title case. Current version is: 'Multi-threshold survival analysis' In title case that is: 'Multi-Threshold Survival Analysis' The Description field should not start with the package name, 'This package' or similar. The Date field is over a month old. * checking package namespace information ... OK * checking package dependencies ... INFO Vignette dependency required without any vignettes: 'knitr' * 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 serialization versions ... OK * checking whether package 'mt.surv' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Maintainer field differs from that derived from Authors@R Maintainer: 'Alexander Loncar ' Authors@R: 'Daniel Spakowicz ' * 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 loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE StackBarinput: no visible global function definition for '%>%' StackBarinput: no visible binding for global variable 'ID' StackBarinput: no visible binding for global variable '.' StackBarinput: no visible binding for global variable 'phylum' StackBarinput: no visible binding for global variable 'exo.ra' StackBarinput: no visible binding for global variable 'diagnosis' StackBarinput: no visible binding for global variable 'vitalstatus' StackBarinput: no visible binding for global variable 'days' StackBarinput: no visible binding for global variable 'AgeCollect' StackBarinput: no visible binding for global variable 'AvatarKey' StackBarinput: no visible binding for global variable 'AgeAtLastContact' StackBarinput: no visible binding for global variable 'Primary/Met' StackBarinput: no visible binding for global variable 'ra' StackBarinput: no visible binding for global variable 'sum.ra' StackBarinput: no visible binding for global variable 'type' ToWide : exoRAtowide: no visible global function definition for '%>%' ToWide : exoRAtowide: no visible binding for global variable 'ID' ToWide : exoRAtowide: no visible binding for global variable 'exo.ra' ToWide : exoRAtowide: no visible binding for global variable 'Taxa' butterfly_input: no visible global function definition for '%>%' butterfly_input: no visible binding for global variable 'type' butterfly_input: no visible binding for global variable 'area' butterfly_input: no visible binding for global variable 'species' butterfly_input: no visible binding for global variable 'T.area' butterfly_input: no visible binding for global variable 'O.area' butterfly_input: no visible binding for global variable 'sum.area' butterfly_input: no visible binding for global variable 'Taxa' butterfly_input: no visible global function definition for 'tail' butterfly_input: no visible global function definition for 'ggplot' butterfly_input: no visible global function definition for 'aes' butterfly_input: no visible global function definition for 'geom_col' butterfly_input: no visible global function definition for 'ylab' butterfly_input: no visible global function definition for 'xlab' butterfly_input: no visible global function definition for 'theme' butterfly_input: no visible global function definition for 'element_blank' calculateArea: no visible global function definition for '%>%' calculateArea: no visible binding for global variable 'pval' calculateArea: no visible binding for global variable 'hazard.direction' calculateArea: no visible binding for global variable 'survival.effect' calculateArea: no visible binding for global variable 'sig.dif' generate_surv_input: no visible binding for global variable 'subgroup' generate_surv_input: no visible global function definition for 'exoToDF' generate_surv_input: no visible global function definition for '%>%' generate_surv_input : : no visible global function definition for 'left_join' generate_surv_input: no visible binding for global variable 'ID' generate_surv_input: no visible binding for global variable 'type' generate_surv_input: no visible binding for global variable 'species' plot_emp: no visible global function definition for '%>%' plot_emp: no visible global function definition for 'mutate' plot_emp: no visible binding for global variable 'seeds' plot_emp: no visible binding for global variable 'area' plot_emp: no visible binding for global variable '.' plot_emp: no visible global function definition for 'group_by' plot_emp: no visible binding for global variable 'Taxa' plot_emp: no visible global function definition for 'summarise' plot_emp: no visible global function definition for 'sd' plot_emp: no visible global function definition for 'pnorm' plot_emp: no visible binding for global variable 'o.area' plot_emp: no visible binding for global variable 'ave' plot_emp: no visible binding for global variable 'sd' plot_emp: no visible global function definition for 'filter' plot_emp: no visible global function definition for 'ggplot' plot_emp: no visible global function definition for 'aes' plot_emp: no visible global function definition for 'geom_histogram' plot_emp: no visible binding for global variable '..density..' plot_emp: no visible global function definition for 'geom_density' plot_emp: no visible global function definition for 'facet_wrap' plot_emp: no visible global function definition for 'geom_vline' plot_emp: no visible global function definition for 'geom_text' plot_emp: no visible binding for global variable 'pval' plot_emp: no visible global function definition for 'theme_classic' plot_emp: no visible global function definition for 'theme' plot_emp: no visible global function definition for 'element_text' plot_emp: no visible global function definition for 'scale_x_continuous' plot_emp: no visible global function definition for 'scale_y_continuous' plot_emp: no visible global function definition for 'ggtitle' survivalByQuantile : aa: no visible global function definition for 'quantile' survivalByQuantile : aa: no visible global function definition for '%>%' survivalByQuantile : aa: no visible binding for global variable 'term' survivalByQuantile : aa: no visible binding for global variable 'estimate' survivalByQuantile : aa: no visible binding for global variable 'conf.low' survivalByQuantile : aa: no visible binding for global variable 'conf.high' survivalByQuantile : aa: no visible binding for global variable 'percentile' survivalByQuantile : aa: no visible binding for global variable 'cutoff.value' survivalByQuantile : aa: no visible binding for global variable 'p.value' survivalByQuantile : aa: no visible binding for global variable 'hazard.direction' survival_plot: no visible global function definition for '%>%' survival_plot: no visible binding for global variable 'pval' survival_plot: no visible binding for global variable 'percentile' survival_plot: no visible binding for global variable 'Taxa' survival_plot: no visible global function definition for 'ggsurvplot' Undefined global functions or variables: %>% . ..density.. AgeAtLastContact AgeCollect AvatarKey ID O.area Primary/Met T.area Taxa aes area ave conf.high conf.low cutoff.value days diagnosis element_blank element_text estimate exo.ra exoToDF facet_wrap filter geom_col geom_density geom_histogram geom_text geom_vline ggplot ggsurvplot ggtitle group_by hazard.direction left_join mutate o.area p.value percentile phylum pnorm pval quantile ra scale_x_continuous scale_y_continuous sd seeds sig.dif species subgroup sum.area sum.ra summarise survival.effect tail term theme theme_classic type vitalstatus xlab ylab Consider adding importFrom("stats", "ave", "filter", "pnorm", "quantile", "sd") importFrom("utils", "tail") 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... NONE * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * checking for code which exercises the package ... WARNING No examples, no tests, no vignettes * DONE Status: 1 WARNING, 3 NOTEs