* using log directory ‘/srv/hornik/tmp/CRAN_pretest/RwPFS.Rcheck’ * using R Under development (unstable) (2024-11-25 r87381) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘RwPFS/DESCRIPTION’ ... OK * this is package ‘RwPFS’ version ‘0.0.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Michael Bretscher ’ New submission Possibly misspelled words in DESCRIPTION: PFS (9:41, 9:124, 9:245) RwPFS (9:173) rwPFS (3:19, 9:161) * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘RwPFS’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 ... [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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [3s/3s] NOTE compare_rwPFS: no visible binding for global variable ‘.’ compare_rwPFS: no visible binding for global variable ‘patientid’ compare_rwPFS: no visible binding for global variable ‘rwPFS_definition’ compare_rwPFS : f: no visible binding for global variable ‘rwPFS_definition’ compare_rwPFS : f: no visible binding for global variable ‘median’ compare_rwPFS : f: no visible binding for global variable ‘lower’ compare_rwPFS : f: no visible binding for global variable ‘upper’ compare_rwPFS : f: no visible binding for global variable ‘estimate’ compare_rwPFS : f: no visible binding for global variable ‘conf.low’ compare_rwPFS : f: no visible binding for global variable ‘conf.high’ compare_rwPFS: no visible binding for global variable ‘grouping_var’ compare_rwPFS: no visible binding for global variable ‘data’ compare_rwPFS: no visible binding for global variable ‘rwPFS_event_type’ compare_rwPFS: no visible binding for global variable ‘KM_median’ compare_rwPFS: no visible binding for global variable ‘hazard_ratio’ compare_rwPFS: no visible binding for global variable ‘Death’ compare_rwPFS: no visible binding for global variable ‘Censoring’ compare_rwPFS: no visible binding for global variable ‘Progression’ compare_rwPFS: no visible binding for global variable ‘Incremental_deaths’ compare_rwPFS: no visible binding for global variable ‘Percent_death’ Undefined global functions or variables: . Censoring Death Incremental_deaths KM_median Percent_death Progression conf.high conf.low data estimate grouping_var hazard_ratio lower median patientid rwPFS_definition rwPFS_event_type upper Consider adding importFrom("stats", "median") importFrom("utils", "data") to your NAMESPACE file. Found if() conditions comparing class() to string: File ‘RwPFS/R/calc_rwPFS.R’: if (is.null(.death_window_days) | class(.death_window_days) != "numeric" | .death_window_days < 0) ... File ‘RwPFS/R/compare_rwPFS.R’: if (is.null(.labels) | class(.labels) != "character" | length(.labels) < 2) ... File ‘RwPFS/R/compare_rwPFS.R’: if (is.null(.reference) | class(.reference) != "character") ... File ‘RwPFS/R/compare_rwPFS.R’: if (is.null(.incremental_deaths_column) | class(.incremental_deaths_column) != "logical") ... Use inherits() (or maybe is()) instead. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'calc_rwPFS.Rd': \examples lines wider than 100 characters: .death_window_days = 30, #include death events <30d after progression EOF .label = "_all_events" #Label for this rwPFS endpoint (for comparisons) Rd file 'compare_rwPFS.Rd': \examples lines wider than 100 characters: .death_window_days = 30, #include death events <30d after progression EOF .label = "_all_events" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 30, #include death events <30d after progression EOF .label = "_discard_le_14d" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 30, #include death events <30d after progression EOF .label = "_radiographic_only" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 30, #include death events <30d after progression EOF .label = "_no_pseudoprogression" #Label for this rwPFS endpoint (for comparisons) #On a side note, supplying a custom date column as .visit_gap_start_date can e.g. be used to trick calc_rwPFS into censoring observatio ... [TRUNCATED] #Similarly, progression events can be imputed (e.g. at a line of therapy change) by creating a custom .progression_date column. .death_window_days = 30, #include death events <30d after progression EOF .label = "_ignore_visit_gaps" #Label for this rwPFS endpoint (for comparisons) .labels = c( #Specify the rwPFS labels to be tabulated (in the desired order) .death_window_days = 0, #include death events <30d after progression EOF .label = "_0d_window" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 10, #include death events <30d after progression EOF .label = "_10d_window" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 20, #include death events <30d after progression EOF .label = "_20d_window" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 30, #include death events <30d after progression EOF .label = "_30d_window" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 40, #include death events <30d after progression EOF .label = "_40d_window" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 50, #include death events <30d after progression EOF .label = "_50d_window" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 60, #include death events <30d after progression EOF .label = "_60d_window" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 70, #include death events <30d after progression EOF .label = "_70d_window" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 80, #include death events <30d after progression EOF .label = "_80d_window" #Label for this rwPFS endpoint (for comparisons) .death_window_days = 90, #include death events <30d after progression EOF .label = "_90d_window" #Label for this rwPFS endpoint (for comparisons) .labels = paste0("_", 0:9*10, "d_window"),#Specify the rwPFS labels to be tabulated (in the desired order) These lines will be truncated in the PDF manual. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... WARNING '::' or ':::' import not declared from: ‘tibble’ * checking tests ... [2s/2s] OK Running ‘testthat.R’ [2s/2s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [5s/5s] OK * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] NOTE Found the following HTML validation problems: calc_rwPFS.html:109:10 (calc_rwPFS.Rd:59): Warning: missing before calc_rwPFS.html:109:35 (calc_rwPFS.Rd:59): Warning: inserting implicit before

calc_rwPFS.html:109:38 (calc_rwPFS.Rd:59): Warning: inserting implicit

calc_rwPFS.html:112:40 (calc_rwPFS.Rd:62): Warning: inserting implicit

calc_rwPFS.html:114:34 (calc_rwPFS.Rd:64): Warning: inserting implicit

calc_rwPFS.html:116:34 (calc_rwPFS.Rd:66): Warning: inserting implicit

calc_rwPFS.html:118:35 (calc_rwPFS.Rd:68): Warning: inserting implicit

calc_rwPFS.html:120:36 (calc_rwPFS.Rd:70): Warning: inserting implicit

calc_rwPFS.html:130:5 (calc_rwPFS.Rd:81): Warning: inserting implicit