* using log directory ‘/srv/hornik/tmp/CRAN_pretest/LABTNSCPSS.Rcheck’
* using R Under development (unstable) (2025-09-03 r88788)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘LABTNSCPSS/DESCRIPTION’ ... OK
* this is package ‘LABTNSCPSS’ version ‘1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Azadeh Bayani <azadeh.bayani@umontreal.ca>’

New submission

Possibly misspelled words in DESCRIPTION:
  ICD (4:89, 4:104, 4:115, 4:130)

Size of tarball: 53280822 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 ... NOTE
Found the following hidden files and directories:
  .RDataTmp
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

CRAN-pack does not know about
  .RDataTmp
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘LABTNSCPSS’ can be installed ... [5s/5s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘stats::filter’ by ‘dplyr::filter’ when loading ‘LABTNSCPSS’
See ‘/srv/hornik/tmp/CRAN_pretest/LABTNSCPSS.Rcheck/00install.out’ for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  ‘Frailty_Comorbidity_Pipeline.R’ ‘LABTNSCPSS_Code’ ‘LABTNSCPSS_Data’
  ‘data-raw’ ‘my_data.xlsx’
* 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 ... WARNING
'library' or 'require' calls not declared from:
  ‘data.table’ ‘dplyr’ ‘glue’ ‘lubridate’ ‘tidyr’
'library' or 'require' calls in package code:
  ‘data.table’ ‘dplyr’ ‘glue’ ‘lubridate’ ‘tidyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/5s] NOTE
Comorbidity_Frailty_Calculation: no visible global function definition
  for ‘%>%’
Comorbidity_Frailty_Calculation: no visible global function definition
  for ‘separate_rows’
Comorbidity_Frailty_Calculation: no visible binding for global variable
  ‘coding_system’
Comorbidity_Frailty_Calculation: no visible binding for global variable
  ‘.’
Comorbidity_Frailty_Calculation: no visible binding for global variable
  ‘id’
Comorbidity_Frailty_Calculation: no visible global function definition
  for ‘separate’
Comorbidity_Frailty_Calculation: no visible binding for global variable
  ‘Charlson_score’
Comorbidity_Frailty_Calculation: no visible global function definition
  for ‘across’
Comorbidity_Frailty_Calculation: no visible global function definition
  for ‘left_join’
Create_data: no visible binding for global variable ‘col_mapping’
Create_data: no visible global function definition for ‘%>%’
Create_data: no visible global function definition for
  ‘parse_date_time’
Frailty_Calculation: no visible binding for global variable
  ‘coding_system’
Frailty_Calculation: no visible binding for global variable
  ‘Frailty_mapping’
Frailty_Calculation: no visible binding for global variable
  ‘Frailty_ICD10CM’
Frailty_Calculation: no visible binding for global variable
  ‘Frailty_ICD11’
Frailty_Calculation: no visible binding for global variable
  ‘Frailty_Comorbidity_Mapping’
Frailty_Calculation: no visible global function definition for ‘%>%’
Frailty_Calculation: no visible global function definition for
  ‘arrange’
Frailty_Calculation: no visible binding for global variable ‘.’
Frailty_Calculation: no visible global function definition for ‘all_of’
Frailty_Calculation: no visible global function definition for ‘across’
Frailty_Calculation: no visible global function definition for ‘where’
chronic_pathologies: no visible binding for global variable
  ‘coding_system’
chronic_pathologies: no visible global function definition for ‘%>%’
chronic_pathologies: no visible global function definition for
  ‘group_by’
chronic_pathologies: no visible global function definition for
  ‘summarise’
chronic_pathologies: no visible binding for global variable
  ‘category_codes’
chronic_pathologies : <anonymous>: no visible global function
  definition for ‘ymd’
chronic_pathologies: no visible global function definition for
  ‘arrange’
chronic_pathologies: no visible global function definition for
  ‘ungroup’
chronic_pathologies: no visible global function definition for ‘across’
chronic_pathologies: no visible global function definition for ‘where’
chronic_pathologies: no visible global function definition for ‘.’
chronic_pathologies: no visible global function definition for ‘unnest’
chronic_pathologies_v2: no visible binding for global variable
  ‘coding_system’
chronic_pathologies_v2: no visible global function definition for ‘%>%’
chronic_pathologies_v2: no visible global function definition for
  ‘arrange’
chronic_pathologies_v2: no visible global function definition for
  ‘group_by’
chronic_pathologies_v2: no visible global function definition for
  ‘summarise’
chronic_pathologies_v2: no visible global function definition for
  ‘rowwise’
chronic_pathologies_v2: no visible global function definition for
  ‘ungroup’
chronic_pathologies_v2: no visible binding for global variable
  ‘category_codes’
chronic_pathologies_v2: no visible global function definition for ‘ymd’
chronic_pathologies_v2: no visible global function definition for
  ‘unnest’
Undefined global functions or variables:
  %>% . Charlson_score Frailty_Comorbidity_Mapping Frailty_ICD10CM
  Frailty_ICD11 Frailty_mapping across all_of arrange category_codes
  coding_system col_mapping group_by id left_join parse_date_time
  rowwise separate separate_rows summarise ungroup unnest where ymd

Found the following calls to data() loading into the global environment:
File ‘LABTNSCPSS/R/Chronic_Pathologies.R’:
  data("ICD10CA_categorisation")
  data("ICD10CM_categorisation")
  data("ICD11_categorisation")
  data("Basal_Codes")
  data("ICD10CM_Basal_Codes")
  data("ICD11_Basal_Codes")
File ‘LABTNSCPSS/R/Chronic_Pathologies_v2.R’:
  data("ICD10CA_categorisation")
  data("ICD10CM_categorisation")
  data("ICD11_categorisation")
  data("Basal_Codes")
  data("ICD10CM_Basal_Codes")
  data("ICD11_Basal_Codes")
File ‘LABTNSCPSS/R/Frailty_Calculation.R’:
  data("Frailty_mapping")
  data("Frailty_ICD10CM")
  data("Frailty_ICD11")
  data("Frailty_Comorbidity_Mapping")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... NOTE
Rd files without \alias:
  ‘Chronic_Pathologies.Rd’ ‘Pathologie_chronic.Rd’
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Data codoc mismatches from Rd file 'Basal_Codes.Rd':
Variables in data frame 'Basal_Codes'
  Code: B_ICD10CAcodesBasale Comp_ICD10CAcodes code_category
        complication_category
  Docs: category code description

* 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 ... [1s/1s] WARNING
  Warning: found non-ASCII strings
  'Fracture et ost<c3><a9>oporose' in object 'Frailty_Comorbidity_Mapping'
  'Ulc<c3><a9>re et affection des tissus mous' in object 'Frailty_Comorbidity_Mapping'
  'Maladie h<c3><a9>patique' in object 'Frailty_Comorbidity_Mapping'
  'D<c3><a9>pendance envers machine' in object 'Frailty_Comorbidity_Mapping'
  'D<c3><a9>pendance fonctionnelle' in object 'Frailty_Comorbidity_Mapping'
  'Activit<c3><a9>s de la vie quotidienne et activit<c3><a9>s instrumentales de la vie quotidienne' in object 'Frailty_Comorbidity_Mapping'
  'Diab<c3><a8>te avec complications' in object 'Frailty_Comorbidity_Mapping'
  'Immobilit<c3><a9>' in object 'Frailty_Comorbidity_Mapping'
  'Usage chronique de m<c3><a9>dicaments' in object 'Frailty_Comorbidity_Mapping'
  'An<c3><a9>mie' in object 'Frailty_Comorbidity_Mapping'
  'D<c3><a9>s<c3><a9>quilibre hydro-<c3><a9>lectrolytique' in object 'Frailty_Comorbidity_Mapping'
  'Maladie h<c3><a9>patique s<c3><a9>v<c3><a9>re' in object 'Frailty_Comorbidity_Mapping'
  'Maladie c<c3><a9>r<c3><a9>brovasculaire' in object 'Frailty_Comorbidity_Mapping'
  'D<c3><a9>pression et anxi<c3><a9>t<c3><a9>' in object 'Frailty_Comorbidity_Mapping'
  'D<c3><a9>mence et maladie d'Alzheimer' in object 'Frailty_Comorbidity_Mapping'
  'Ob<c3><a9>sit<c3><a9>' in object 'Frailty_Comorbidity_Mapping'
  'Diab<c3><a8>te sans complications' in object 'Frailty_Comorbidity_Mapping'
  '<c3><a9>pilepsie' in object 'Frailty_Comorbidity_Mapping'
  'Blessures et l<c3><a9>sion' in object 'Frailty_Comorbidity_Mapping'
  'Tumeur solide sans m<c3><a9>tastases' in object 'Frailty_Comorbidity_Mapping'
  'Maladie r<c3><a9>nale et urinaire' in object 'Frailty_Comorbidity_Mapping'
  'Troubles de la vision et de l'ou<c3><af>e' in object 'Frailty_Comorbidity_Mapping'
  'Cancer m<c3><a9>tastatique' in object 'Frailty_Comorbidity_Mapping'
  'Maladie vasculaire p<c3><a9>riph<c3><a9>rique' in object 'Frailty_Comorbidity_Mapping'
  'Hypothyro<c3><af>die' in object 'Frailty_Comorbidity_Mapping'
  'Cancer h<c3><a9>matologique' in object 'Frailty_Comorbidity_Mapping'
  'Maladie cardiaque ath<c3><a9>roscl<c3><a9>rotique' in object 'Frailty_Comorbidity_Mapping'
  'D<c3><a9>conditionnement' in object 'Frailty_Comorbidity_Mapping'
  'Affection et <c3><a9>tat associ<c3><a9> <c3><a0> la fragilit<c3><a9>' in object 'Frailty_Comorbidity_Mapping'
  'Beh<ef><bf><bd>et's disease' in object 'Frailty_Comorbidity_Mapping'
  'Sicca syndrome [Sj<ef><bf><bd>gren]' in object 'Frailty_Comorbidity_Mapping'
  'Concentric sclerosis [Bal<ef><bf><bd>]' in object 'Frailty_Comorbidity_Mapping'
  'Waldenstr<ef><bf><bd>m macroglobulinaemia' in object 'Frailty_Comorbidity_Mapping'
  'S<ef><bf><bd>zary disease' in object 'Frailty_Comorbidity_Mapping'
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking examples ... [1s/1s] ERROR
Running examples in ‘LABTNSCPSS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: comorbidity
> ### Title: Comorbidity mapping.
> ### Aliases: comorbidity
> 
> ### ** Examples
> 
> set.seed(1)
> x <- data.frame(
+   id = sample(1:15, size = 200, replace = TRUE),
+   code = sample_diag(200),
+   stringsAsFactors = FALSE
+ )
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘comorbidity’
Calls: data.frame -> sample_diag -> <Anonymous> -> find.package
Execution halted
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 4 WARNINGs, 5 NOTEs