* using log directory 'd:/RCompile/CRANincoming/R-devel/aNCA.Rcheck'
* using R Under development (unstable) (2025-11-06 r88990 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'aNCA/DESCRIPTION' ... OK
* this is package 'aNCA' version '0.0.0.9179'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Valentin Legras <anca.pharmaverse@gmail.com>'

New submission

Version contains large components (0.0.0.9179)

Possibly misspelled words in DESCRIPTION:
  NCA (2:23, 18:65)
  Pre (2:9)
  pre (18:73)

Found the following (possibly) invalid URLs:
  URL: https://opensource.org/licenses/Apache-2.0 (moved to https://opensource.org/license/apache-2-0)
    From: README.md
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.

Found the following (possibly) invalid file URIs:
  URI: inst/shiny/tlg.yaml
    From: inst/doc/adding_tlg.html
  URI: /DESCRIPTION
    From: inst/doc/contributing.html
  URI: .github/PULL_REQUEST_TEMPLATE.md
    From: inst/doc/contributing.html
  URI: CONTRIBUTING.md
    From: README.md
* 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 'aNCA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'PKNCA.R' 'apply_mapping.R' 'calculate_summary_stats.R'
    'export_cdisc.R' 'filter_breaks.R' 'flexible_violinboxplot.R'
    'g_pkcg.R' 'intervals_helpers.R' 'l_pkcl01.R' 'label_operators.R'
    'officer-utils.R' 'read_pk.R' 'run_app.R' 'utils-slope_selector.R'
    'utils.R'
* 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 ... 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 whether startup messages can be suppressed ... 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 ... [17s] OK
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [38s] ERROR
  Running 'testthat.R' [38s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(shinytest2)
  > library(aNCA)
  > 
  > test_check("aNCA")
  Joining with `by = join_by(ATPTREF)`
  * USUBJID -> id
  * PARAM -> analyte
  * DOSETRT -> drug
  * AVAL -> CONC
  * AVALU -> CONC_unit
  * DOSE -> dose
  * ADOSEDUR -> dosedur
  * AFRLT -> TIME
  * ATPTREF -> DOSNO
  Row 1: Converted volume from 1 L to 1000 mL based on concentration unit ug/mL
  Row 1: Converted volume from 2 mL to 2 g based on concentration unit mg/g
  Row 1: Converted volume from 1 L to 1000 mL based on concentration unit ug/mL
  Row 2: Converted volume from 0.5 mL to 0.5 g based on concentration unit mg/g
  Loading required namespace: ggh4x
  Failed with error:  'unused argument (silently = TRUE)'
  Failed with error:  'unused argument (silently = TRUE)'
  Failed with error:  'unused argument (silently = TRUE)'
  Failed with error:  'unused argument (silently = TRUE)'
  [ FAIL 4 | WARN 0 | SKIP 13 | PASS 746 ]
  
  ══ Skipped tests (13) ══════════════════════════════════════════════════════════
  • On CRAN (12): 'test-g_pkcg.R:14:5', 'test-g_pkcg.R:29:5',
    'test-g_pkcg.R:44:5', 'test-g_pkcg.R:88:5', 'test-g_pkcg.R:127:5',
    'test-g_pkcg.R:135:5', 'test-g_pkcg.R:149:5', 'test-g_pkcg.R:170:5',
    'test-g_pkcg.R:183:5', 'test-g_pkcg.R:229:5', 'test-g_pkcg.R:274:5',
    'test-g_pkcg.R:285:5'
  • Skipping (1): 'test-e2e-runner.R:5:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-read_pk.R:27:5'): read_pk: reads excel data correctly ──────────
  Error in `readers[[format]](path)`: Handling .xlsx files requires `openxlsx2` package, please install it with `install.packages('openxlsx2')`
  Backtrace:
      ▆
   1. └─aNCA::read_pk(tmp_xlsx) at test-read_pk.R:27:5
   2.   ├─aNCA:::validate_pk(readers[[format]](path))
   3.   └─readers[[format]](path)
  ── Error ('test-read_pk.R:39:5'): read_pk: reads sas data correctly ────────────
  Error in `readers[[format]](path)`: Handling .sas7bdat files requires `haven` package, please install it with `install.packages('haven')`
  Backtrace:
      ▆
   1. └─aNCA::read_pk(tmp_sas) at test-read_pk.R:39:5
   2.   ├─aNCA:::validate_pk(readers[[format]](path))
   3.   └─readers[[format]](path)
  ── Error ('test-read_pk.R:51:5'): read_pk: reads xpt files correctly ───────────
  Error in `readers[[format]](path)`: Handling .xpt files requires `haven` package, please install it with `install.packages('haven')`
  Backtrace:
      ▆
   1. └─aNCA::read_pk(tmp_xpt) at test-read_pk.R:51:5
   2.   ├─aNCA:::validate_pk(readers[[format]](path))
   3.   └─readers[[format]](path)
  ── Error ('test-read_pk.R:63:5'): read_pk: reads parquet files correctly ───────
  Error in `readers[[format]](path)`: Handling .parquet files requires `arrow` package, please install it with `install.packages('arrow')`
  Backtrace:
      ▆
   1. └─aNCA::read_pk(tmp_parquet) at test-read_pk.R:63:5
   2.   ├─aNCA:::validate_pk(readers[[format]](path))
   3.   └─readers[[format]](path)
  
  [ FAIL 4 | WARN 0 | SKIP 13 | PASS 746 ]
  Deleting unused snapshots:
  • g_pkcg/combined-lin-plot2.svg
  • g_pkcg/combined-log-plot2.svg
  • g_pkcg/combined-sbs-plot2.svg
  • g_pkcg/lin-plot2.svg
  • g_pkcg/lin-plot3.svg
  • g_pkcg/log-plot2.svg
  • g_pkcg/log-plot3.svg
  • g_pkcg/sbs-plot2.svg
  • g_pkcg/sbs-plot3.svg
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... [12s] OK
* DONE
Status: 1 ERROR, 2 NOTEs