* using log directory ‘/srv/hornik/tmp/CRAN_pretest/starling.Rcheck’ * using R Under development (unstable) (2025-11-11 r88995) * 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 ‘starling/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘starling’ version ‘0.5.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘The package maintainer ’ New submission Possibly misspelled words in DESCRIPTION: Murmuration (12:22, 13:5, 14:5) analses (14:172) attendences (13:119) linelist (10:81) murmuration (11:130) The Description field should not start with the package name, 'This package' or similar. DESCRIPTION fields with placeholder content: Maintainer: The package maintainer * checking package namespace information ... OK * checking package dependencies ... INFO Depends: includes the non-default packages: 'dplyr', 'lubridate', 'janitor', 'stringr', 'tidyr', 'reclin2', 'datawizard', 'tinylabels' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 whether package ‘starling’ can be installed ... [4s/4s] 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: ‘The package maintainer ’ Authors@R: ‘Nicolas Smoll ’ * 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 ... WARNING Found the following file with non-ASCII characters: R/tweet.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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] 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 ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘digest’ ‘rlang’ Packages in Depends field not imported from: ‘datawizard’ ‘dplyr’ ‘janitor’ ‘lubridate’ ‘reclin2’ ‘tidyr’ ‘tinylabels’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [4s/4s] NOTE calculate_age_if_missing: no visible global function definition for ‘%>%’ calculate_age_if_missing: no visible binding for global variable ‘.data’ clean_the_nest: no visible global function definition for ‘data_rename’ clean_the_nest: no visible global function definition for ‘%>%’ clean_the_nest: no visible global function definition for ‘str_replace_all’ clean_the_nest: no visible global function definition for ‘case_when’ clean_the_nest: no visible global function definition for ‘mutate’ clean_the_nest: no visible binding for global variable ‘dob_yr’ clean_the_nest: no visible global function definition for ‘n’ clean_the_nest: no visible global function definition for ‘group_by’ clean_the_nest: no visible global function definition for ‘fill’ clean_the_nest: no visible binding for global variable ‘last_vax_type’ clean_the_nest: no visible global function definition for ‘pivot_wider’ clean_the_nest: no visible global function definition for ‘clean_names’ clean_the_nest: no visible global function definition for ‘filter’ clean_the_nest: no visible global function definition for ‘row_number’ clean_the_nest: no visible global function definition for ‘select’ clean_the_nest: no visible global function definition for ‘starts_with’ clean_the_nest: no visible global function definition for ‘left_join’ clean_the_nest: no visible global function definition for ‘ungroup’ clean_the_nest: no visible global function definition for ‘any_of’ clean_the_nest: no visible global function definition for ‘contains’ create_age_variables: no visible global function definition for ‘%>%’ create_age_variables: no visible binding for global variable ‘.data’ create_comprehensive_age_categories: no visible global function definition for ‘%>%’ homing: no visible global function definition for ‘%>%’ identify_ucodes: no visible global function definition for ‘%>%’ identify_ucodes: no visible global function definition for ‘mutate’ identify_ucodes: no visible global function definition for ‘across’ identify_ucodes: no visible global function definition for ‘all_of’ identify_ucodes: no visible global function definition for ‘:=’ identify_ucodes: no visible global function definition for ‘sym’ identify_ucodes: no visible global function definition for ‘select’ identify_ucodes: no visible binding for global variable ‘.’ identify_ucodes: no visible global function definition for ‘case_when’ molting: no visible global function definition for ‘%>%’ molting: no visible global function definition for ‘:=’ murmuration: no visible global function definition for ‘%>%’ murmuration: no visible global function definition for ‘select’ murmuration: no visible binding for global variable ‘weights’ murmuration: no visible binding for global variable ‘threshold’ murmuration: no visible global function definition for ‘pair_blocking’ murmuration: no visible global function definition for ‘compare_pairs’ murmuration: no visible global function definition for ‘jaro_winkler’ murmuration: no visible global function definition for ‘problink_em’ murmuration: no visible global function definition for ‘reformulate’ murmuration: no visible global function definition for ‘predict’ murmuration: no visible global function definition for ‘select_threshold’ murmuration: no visible global function definition for ‘link’ murmuration: no visible global function definition for ‘mutate’ murmuration: no visible binding for global variable ‘admission_date’ murmuration: no visible global function definition for ‘case_when’ murmuration: no visible global function definition for ‘across’ murmuration: no visible global function definition for ‘ends_with’ murmuration: no visible global function definition for ‘starts_with’ murmuration: no visible global function definition for ‘any_of’ murmuration: no visible global function definition for ‘group_by’ murmuration: no visible binding for global variable ‘id_var.x’ murmuration: no visible global function definition for ‘arrange’ murmuration: no visible global function definition for ‘desc’ murmuration: no visible global function definition for ‘slice’ murmuration: no visible global function definition for ‘ungroup’ murmuration: no visible global function definition for ‘rename’ murmuration: no visible binding for global variable ‘id_var.y’ murmuration: no visible global function definition for ‘if_else’ murmuration: no visible binding for global variable ‘total_admissions’ murmuration: no visible binding for global variable ‘onset_adm_diff’ murmuration: no visible binding for global variable ‘discharge_date’ murmuration: no visible binding for global variable ‘icu_date’ murmuration: no visible binding for global variable ‘icu_hours’ murmuration: no visible binding for global variable ‘los’ murmuration: no visible binding for global variable ‘hospital’ murmuration: no visible binding for global variable ‘icd_code’ murmuration: no visible binding for global variable ‘drg’ murmuration: no visible binding for global variable ‘diagnosis_description’ murmuration: no visible binding for global variable ‘dialysis’ murmuration: no visible binding for global variable ‘first_admission_date’ murmuration: no visible global function definition for ‘rowwise’ murmuration: no visible global function definition for ‘c_across’ murmuration: no visible global function definition for ‘replace_nan_inf’ murmuration: no visible binding for global variable ‘first_vax’ murmuration: no visible binding for global variable ‘last_vax’ murmuration: no visible global function definition for ‘na.omit’ murmuration: no visible binding for global variable ‘vaccination_status’ murmuration: no visible global function definition for ‘rename_with’ murmuration: no visible global function definition for ‘everything’ preening: no visible global function definition for ‘%>%’ preening: no visible binding for global variable ‘onset_date’ preening: no visible binding for global variable ‘admission_date’ preening: no visible binding for global variable ‘event_date’ tweet: no visible global function definition for ‘median’ tweet: no visible global function definition for ‘quantile’ tweet: no visible global function definition for ‘na.omit’ Undefined global functions or variables: %>% . .data := across admission_date all_of any_of arrange c_across case_when clean_names compare_pairs contains data_rename desc diagnosis_description dialysis discharge_date dob_yr drg ends_with event_date everything fill filter first_admission_date first_vax group_by hospital icd_code icu_date icu_hours id_var.x id_var.y if_else jaro_winkler last_vax last_vax_type left_join link los median mutate n na.omit onset_adm_diff onset_date pair_blocking pivot_wider predict problink_em quantile reformulate rename rename_with replace_nan_inf row_number rowwise select select_threshold slice starts_with str_replace_all sym threshold total_admissions ungroup vaccination_status weights Consider adding importFrom("stats", "filter", "median", "na.omit", "predict", "quantile", "reformulate", "weights") to your NAMESPACE file. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'clean_the_nest.Rd': \examples lines wider than 100 characters: # basic usage of clean_the_nest. Use this to set up for datalinkage using the murmuration command and then cleaning with preening Rd file 'murmuration.Rd': \examples lines wider than 100 characters: # basic usage of murmuration to link cases to vaccination history. The df_diag and df_vax object/dataframe was created using clean_the_ ... [TRUNCATED] # basic usage of murmuration to link cases (previously linked to vaccination history) to hospitalization outcomes. The df_hosp object/d ... [TRUNCATED] These lines will be truncated in the PDF manual. * checking Rd cross-references ... WARNING Missing link(s) in Rd file 'clean_the_nest.Rd': ‘gtsummary::tbl_summary’ Missing link(s) in Rd file 'murmuration.Rd': ‘gtsummary::tbl_summary’ Missing link(s) in Rd file 'preening.Rd': ‘gtsummary::tbl_summary’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: clean_the_nest.Rd: gtsummary::tbl_summary murmuration.Rd: gtsummary::tbl_summary preening.Rd: gtsummary::tbl_summary Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘dx_data’ ‘hosp_data’ ‘vax_data’ Undocumented data sets: ‘dx_data’ ‘hosp_data’ ‘vax_data’ 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 'clean_the_nest.Rd' ‘latitude’ ‘hospital’ ‘icu_hours’ ‘dialysis’ Documented arguments not in \usage in Rd file 'clean_the_nest.Rd': ‘lattitude’ 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 ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [1s/1s] ERROR Running examples in ‘starling-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: identify_ucodes > ### Title: Identify Chronic Conditions Using ICD-10-AM U-Codes > ### Aliases: identify_ucodes > > ### ** Examples > > # Create sample hospitalization data > hospital_data <- data.frame( + patient_id = 1:3, + icd_codes = c( + "K29.70", "U78.1, U83.2, U82.3", + "U79.3, U83.3", + "U80.1, U86.2" + ) + ) Error in data.frame(patient_id = 1:3, icd_codes = c("K29.70", "U78.1, U83.2, U82.3", : arguments imply differing number of rows: 3, 4 Execution halted * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 5 WARNINGs, 4 NOTEs