* using log directory ‘/srv/hornik/tmp/CRAN_pretest/hybridEHR.Rcheck’ * using R Under development (unstable) (2026-04-04 r89791) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (3+b1) Debian flang version 21.1.8 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-04-05 20:27:06 UTC * checking for file ‘hybridEHR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘hybridEHR’ version ‘0.2.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Dennis Opoku Boadu ’ Size of tarball: 27442041 bytes * 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 whether package ‘hybridEHR’ can be installed ... [4s/4s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘SARS_ct_dataset_export’ * 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 ... [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 ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] NOTE generate_hybrid_ehr_dataset: no visible binding for global variable ‘hx_cancer’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘hx_stroke’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘hx_liver_disease’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘hx_dementia’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘comorbidity_index’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘SARS_vaccinated’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘vaccine_doses’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘is_sars_suspected’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘p_emergency’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘p_inpatient’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘SARS_test_result’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘severity_num’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘acuity_score’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘los_mu’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘los_days’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘labs_mu’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘meds_mu’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘proc_nonzero_prob’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘proc_nonzero’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘procs_mu’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘encounter_sequence’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘discharge_datetime’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘outcome’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘SARS_severity’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘days_from_symptom_onset’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘o2_support_binary’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘n_vitals_enc’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘n_labs_enc’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘n_meds_enc’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘n_procs_enc’ generate_hybrid_ehr_dataset: no visible global function definition for ‘ave’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘vital_sequence’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘charttime’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘pain_score’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘collection_time’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘test_name’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘unit’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘normal_low’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘normal_high’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘start_time’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘med_name’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘med_class’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘end_time’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘procedure_name’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘procedure_group’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘procedure_time’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘had_ct’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘medication_count’ generate_hybrid_ehr_dataset: no visible binding for global variable ‘procedure_count’ Undefined global functions or variables: SARS_severity SARS_test_result SARS_vaccinated acuity_score ave charttime collection_time comorbidity_index days_from_symptom_onset discharge_datetime encounter_sequence end_time had_ct hx_cancer hx_dementia hx_liver_disease hx_stroke is_sars_suspected labs_mu los_days los_mu med_class med_name medication_count meds_mu n_labs_enc n_meds_enc n_procs_enc n_vitals_enc normal_high normal_low o2_support_binary outcome p_emergency p_inpatient pain_score proc_nonzero proc_nonzero_prob procedure_count procedure_group procedure_name procedure_time procs_mu severity_num start_time test_name unit vaccine_doses vital_sequence Consider adding importFrom("stats", "ave") to your NAMESPACE file. * checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/1s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [0s/0s] OK * checking PDF version of manual ... [2s/2s] 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: 3 NOTEs