* using log directory 'd:/RCompile/CRANincoming/R-devel/epiworldRShiny.Rcheck' * using R Under development (unstable) (2024-02-05 r85863 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 'epiworldRShiny/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'epiworldRShiny' version '0.0-3.9000' * package encoding: UTF-8 * checking CRAN incoming feasibility ... WARNING Maintainer: 'Derek Meyer ' New submission Version contains large components (0.0-3.9000) Non-FOSS package license (file LICENSE) Possibly misspelled words in DESCRIPTION: Epi (3:25) RShiny (3:38) SEIR (13:386) backend (13:183) Strong dependencies not in mainstream repositories: epiworldR Package has a VignetteBuilder field but no prebuilt vignette index. Found the following (possibly) invalid URLs: URL: https://uofuepibio.github.io/epiworldRShiny/ From: DESCRIPTION Status: 404 Message: Not Found * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'epiworldRShiny' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'epiworldRShiny' Warning: replacing previous import 'shiny::renderDataTable' by 'DT::renderDataTable' when loading 'epiworldRShiny' See 'd:/RCompile/CRANincoming/R-devel/epiworldRShiny.Rcheck/00install.out' for details. * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE 'LinkingTo' field is unused: package has no 'src' directory * checking top-level files ... NOTE Non-standard file/directory found at top level: 'Makefile' * 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 ... WARNING Missing or unexported objects: 'epiworldR::add_globalevent' 'epiworldR::globalevent_tool' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE epiworldRShiny: no visible binding for global variable 'epiworldR_env' epiworldRShiny : server: no visible binding for global variable 'epiworldR_env' epiworldRShiny : server : : no visible global function definition for 'write.csv' plot_epi: no visible global function definition for 'reshape' plot_epi: no visible global function definition for 'as.formula' plot_reproductive_epi: no visible global function definition for 'aggregate' Undefined global functions or variables: aggregate as.formula epiworldR_env reshape write.csv Consider adding importFrom("stats", "aggregate", "as.formula", "reshape") importFrom("utils", "write.csv") to your NAMESPACE file. Found the following assignments to the global environment: File 'epiworldRShiny/R/app.R': assign("epiworldR_env", new.env(parent = .GlobalEnv), envir = .GlobalEnv) File 'epiworldRShiny/R/functions-ui.R': assign(paste0(id, "_panel"), pfun(nam), envir = .GlobalEnv) * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: 'epiworldRShiny' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'network_input.Rd' 'model_name' Undocumented arguments in Rd file 'npi_add_all.Rd' 'input' Undocumented arguments in Rd file 'npis_input.Rd' 'model_name' Undocumented arguments in Rd file 'numeric_input_ndays.Rd' 'model_name' Undocumented arguments in Rd file 'population_input.Rd' 'model_name' Undocumented arguments in Rd file 'seed_input.Rd' 'model_name' Undocumented arguments in Rd file 'simulate_button.Rd' 'model_name' Undocumented arguments in Rd file 'slider_input_rate.Rd' 'model_name' 'rate_name' 'value' 'maxval' 'input_label' Undocumented arguments in Rd file 'slider_prevalence.Rd' 'model_name' Undocumented arguments in Rd file 'text_input_disease_name.Rd' 'model_name' 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking examples ... ERROR Running examples in 'epiworldRShiny-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: pop_generator > ### Title: pop_generator Function > ### Aliases: pop_generator > > ### ** Examples > > pop_generator(100) 0-19 20-59 60+ NotHispanic Female [1,] 0 0 1 0 1 [2,] 0 0 1 1 1 [3,] 0 1 0 1 0 [4,] 1 0 0 0 1 [5,] 0 0 1 0 1 [6,] 1 0 0 1 0 [7,] 1 0 0 1 0 [8,] 0 1 0 1 1 [9,] 0 1 0 0 1 [10,] 0 0 1 0 0 [11,] 0 0 1 0 0 [12,] 0 0 1 0 1 [13,] 0 1 0 1 0 [14,] 0 0 1 1 0 [15,] 1 0 0 1 0 [16,] 0 1 0 1 1 [17,] 1 0 0 0 0 [18,] 1 0 0 1 0 [19,] 0 0 1 1 0 [20,] 1 0 0 0 1 [21,] 1 0 0 0 1 [22,] 0 0 1 1 1 [23,] 0 1 0 1 1 [24,] 0 0 1 1 0 [25,] 0 0 1 0 0 [26,] 0 0 1 1 0 [27,] 0 0 1 0 1 [28,] 0 0 1 1 1 [29,] 1 0 0 1 1 [30,] 0 0 1 0 0 [31,] 0 1 0 0 1 [32,] 0 1 0 1 1 [33,] 0 1 0 1 1 [34,] 0 0 1 0 0 [35,] 1 0 0 0 1 [36,] 0 1 0 0 0 [37,] 1 0 0 0 0 [38,] 0 0 1 0 0 [39,] 1 0 0 0 1 [40,] 0 1 0 0 1 [41,] 1 0 0 0 1 [42,] 0 1 0 0 0 [43,] 1 0 0 1 0 [44,] 0 1 0 1 1 [45,] 0 1 0 0 1 [46,] 1 0 0 1 1 [47,] 0 0 1 1 1 [48,] 0 1 0 0 1 [49,] 1 0 0 1 1 [50,] 0 1 0 0 0 [51,] 0 1 0 0 0 [52,] 1 0 0 0 0 [53,] 0 1 0 1 1 [54,] 0 0 1 1 0 [55,] 0 0 1 0 1 [56,] 0 0 1 1 1 [57,] 0 0 1 0 1 [58,] 0 1 0 1 1 [59,] 0 1 0 1 1 [60,] 0 1 0 1 0 [61,] 1 0 0 1 0 [62,] 0 0 1 0 1 [63,] 0 1 0 1 1 [64,] 0 0 1 0 0 [65,] 0 1 0 0 0 [66,] 0 0 1 1 1 [67,] 0 1 0 1 1 [68,] 1 0 0 1 0 [69,] 0 0 1 0 0 [70,] 1 0 0 1 1 [71,] 0 0 1 0 1 [72,] 1 0 0 0 1 [73,] 0 0 1 0 1 [74,] 0 0 1 1 1 [75,] 0 1 0 1 1 [76,] 1 0 0 0 1 [77,] 1 0 0 0 1 [78,] 0 0 1 0 1 [79,] 1 0 0 0 1 [80,] 1 0 0 0 0 [81,] 0 1 0 1 1 [82,] 1 0 0 1 0 [83,] 0 0 1 0 0 [84,] 0 0 1 0 1 [85,] 1 0 0 0 1 [86,] 0 0 1 1 1 [87,] 1 0 0 0 1 [88,] 0 0 1 0 1 [89,] 0 0 1 0 1 [90,] 0 0 1 0 1 [91,] 0 0 1 0 1 [92,] 0 0 1 1 1 [93,] 0 1 0 1 0 [94,] 1 0 0 0 1 [95,] 1 0 0 1 0 [96,] 1 0 0 0 0 [97,] 0 1 0 1 1 [98,] 0 1 0 0 1 [99,] 1 0 0 1 1 [100,] 0 1 0 0 0 > pop_generator(100, prop_hispanic = 0.3, prop_female = 0.6, prop_19_59_60plus = c(0.4, 0.4, 0.2)) Error in sample.int(3, size = n, replace = TRUE, prob = prop_19_59_60plus) : incorrect number of probabilities Calls: pop_generator -> sample.int Execution halted * checking PDF version of manual ... [13s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 5 WARNINGs, 3 NOTEs