* using log directory 'd:/RCompile/CRANincoming/R-devel/doublIn.Rcheck' * using R version 4.4.0 alpha (2024-04-08 r86370 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'doublIn/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'doublIn' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Vera Arntzen ' New submission Possibly misspelled words in DESCRIPTION: Weibull (8:487) Found the following \keyword or \concept entries which likely give several index terms: File 'Estimate_doublIn.Rd': \keyword{censoring,} File 'Plot_doublIn.Rd': \keyword{function,} \keyword{visualization,} File 'Visualize_contact_tracing_data.Rd': \keyword{data,} * 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 whether package 'doublIn' can be installed ... WARNING Found the following significant warnings: Note: break used in wrong context: no loop is visible Warning: replacing previous import 'coda::thin' by 'epicontacts::thin' when loading 'doublIn' Warning: replacing previous import 'DT::formatDate' by 'mStats::formatDate' when loading 'doublIn' Warning: replacing previous import 'lubridate::day' by 'mStats::day' when loading 'doublIn' Warning: replacing previous import 'dplyr::recode' by 'mStats::recode' when loading 'doublIn' Warning: replacing previous import 'lubridate::month' by 'mStats::month' when loading 'doublIn' Warning: replacing previous import 'lubridate::is.Date' by 'mStats::is.Date' when loading 'doublIn' Warning: replacing previous import 'lubridate::year' by 'mStats::year' when loading 'doublIn' Warning: replacing previous import 'ggplot2::last_plot' by 'plotly::last_plot' when loading 'doublIn' Warning: replacing previous import 'DT::dataTableOutput' by 'shiny::dataTableOutput' when loading 'doublIn' Warning: replacing previous import 'DT::renderDataTable' by 'shiny::renderDataTable' when loading 'doublIn' Warning: replacing previous import 'mStats::label' by 'xtable::label' when loading 'doublIn' See 'd:/RCompile/CRANincoming/R-devel/doublIn.Rcheck/00install.out' for details. Information on the location(s) of code generating the 'Note's can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to 'yes'. * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Subdirectory 'data' contains no data sets. * 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 ... [12s] NOTE Estimate_doublIn: no visible global function definition for 'error' Estimate_doublIn: no visible binding for global variable 'L0' Estimate_doublIn: no visible binding for global variable 'L1' Estimate_doublIn: no visible binding for global variable 'R0' Estimate_doublIn: no visible binding for global variable 'R1' Estimate_doublIn : gg_running: no visible binding for global variable 'chain' Estimate_doublIn : gg_running: no visible binding for global variable 'values' Estimate_doublIn : gg_running: no visible binding for global variable 'iter' Estimate_doublIn : gg_running: no visible binding for global variable 'median' Estimate_doublIn : gg_running: no visible binding for global variable 'lower' Estimate_doublIn : gg_running: no visible binding for global variable 'upper' Estimate_doublIn : qggamma: no visible global function definition for 'qgamma' Estimate_doublIn: no visible global function definition for 'runif' Estimate_doublIn : jags_inits: no visible global function definition for 'runif' Estimate_doublIn: no visible global function definition for 'quantile' Estimate_doublIn: no visible global function definition for 'median' Estimate_doublIn: no visible binding for global variable 'par' Estimate_doublIn: no visible binding for global variable 'est' Estimate_doublIn: no visible binding for global variable 'lower_CI' Estimate_doublIn: no visible binding for global variable 'upper_CI' Estimate_doublIn: no visible binding for global variable 'f' Estimate_doublIn: no visible binding for global variable 'g' Estimate_doublIn: no visible binding for global variable 'thinning' Plot_doublIn: no visible binding for global variable 'par' Plot_doublIn: no visible binding for global variable 'est' Plot_doublIn: no visible binding for global variable 'lower_CI' Plot_doublIn: no visible binding for global variable 'upper_CI' Visualize_contact_tracing_data : : no visible binding for global variable 'row_nr' Visualize_contact_tracing_data : : no visible binding for global variable 'Case_ID' Visualize_contact_tracing_data : : no visible binding for global variable 'infector' Visualize_contact_tracing_data : : no visible binding for global variable '.' Visualize_contact_tracing_data : : no visible binding for global variable 'start_of_exposure' Visualize_contact_tracing_data : : no visible binding for global variable 'new_row_nr' Visualize_contact_tracing_data : : no visible binding for global variable 'end_of_exposure' Visualize_contact_tracing_data : : no visible binding for global variable 'last_negative' Visualize_contact_tracing_data : : no visible binding for global variable 'first_positive' Visualize_contact_tracing_data : : no visible binding for global variable 'symptom_onset' Visualize_contact_tracing_data : : no visible binding for global variable 'xloc' Visualize_contact_tracing_data : : no visible binding for global variable 'case_var' Undefined global functions or variables: . Case_ID L0 L1 R0 R1 case_var chain end_of_exposure error est f first_positive g infector iter last_negative lower lower_CI median new_row_nr par qgamma quantile row_nr runif start_of_exposure symptom_onset thinning upper upper_CI values xloc Consider adding importFrom("graphics", "par") importFrom("stats", "median", "qgamma", "quantile", "runif") to your NAMESPACE file. Found if() conditions comparing class() to string: File 'doublIn/R/fun_Estimate_doublIn.R': if (class(dat) != "data.frame") ... Use inherits() (or maybe is()) instead. * 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 'Estimate_doublIn.Rd' 'burnin_period' Documented arguments not in \usage in Rd file 'Estimate_doublIn.Rd': 'burnin_period:' 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 contents of 'data' directory ... WARNING Files not of a type allowed in a 'data' directory: 'df2.rds' Please use e.g. 'inst/extdata' for non-R data files * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [27s] NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed Estimate_doublIn 24.22 0.11 24.33 * checking for unstated dependencies in 'tests' ... OK * checking tests ... OK Running 'testthat.R' * checking PDF version of manual ... [12s] OK * checking HTML version of manual ... OK * DONE Status: 4 WARNINGs, 4 NOTEs