* using log directory ‘/srv/hornik/tmp/CRAN_pretest/PKbioanalysis.Rcheck’
* using R Under development (unstable) (2026-01-13 r89301)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1)
    Debian flang version 21.1.8 (1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘PKbioanalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PKbioanalysis’ version ‘0.4.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] OK
* 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 ‘PKbioanalysis’ can be installed ... [17s/17s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] NOTE
Warning in readLines(file, warn = readLines.warn) :
  incomplete final line found on '/tmp/check-CRAN-incoming-hornik/config/R/PKbioanalysis/config.yaml'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking whether startup messages can be suppressed ... [3s/3s] 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 ... [23s/23s] OK
* 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 examples ... [8s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [42s/41s] ERROR
  Running ‘testthat.R’ [42s/41s]
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(PKbioanalysis)
  
  Attaching package: 'PKbioanalysis'
  
  The following object is masked from 'package:stats':
  
      integrate
  
  Warning message:
  In readLines(file, warn = readLines.warn) :
    incomplete final line found on '/tmp/check-CRAN-incoming-hornik/config/R/PKbioanalysis/config.yaml'
  > 
  > test_check("PKbioanalysis")
  Plate not registered. To register, use register_plate()
  Plate not registered. To register, use register_plate()
  Plate not registered. To register, use register_plate()
  Plate not registered. To register, use register_plate()
  Plate not registered. To register, use register_plate()
  Plate not registered. To register, use register_plate()
  Plate not registered. To register, use register_plate()
  Plate not registered. To register, use register_plate()
  "My Plate" |> generate_96() |> add_blank(group = "A") |> fill_scheme(fill = "h") |> add_suitability() |> fill_scheme(tbound = 1, fill = "v")Saving _problems/test-pydeps-3.R
  Saving _problems/test-pydeps-4.R
  Saving _problems/test-pydeps-5.R
  Saving _problems/test-pydeps-6.R
  Saving _problems/test-pydeps-7.R
  i Created study with ID: 501517cd-130d-4c0b-a611-72087459ca02
  i Adding dosing and subjects information...
  v Dosing information added.
  i Adding subjects information...
  v Subjects information added.
  i Adding sample log information...
  v Sample log information added.
  i Created study with ID: 983dddd3-2fc0-47bc-9c92-f537b439fa0f
  v Dosing information added.
  i Adding subjects information...
  v Subjects information added.
  i Adding sample log information...
  v Sample log information added.
  i Created study with ID: df67276e-3e5e-4fcd-bcbd-cda4ebd15dde
  v Dosing information added.
  i Adding subjects information...
  v Subjects information added.
  i Adding sample log information...
  v Sample log information added.
  `geom_smooth()` using formula = 'y ~ x'
  [ FAIL 5 | WARN 0 | SKIP 15 | PASS 116 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • On CRAN (10): 'test-apps.R:1:1', 'test-injec_list.R:8:3',
    'test-injec_list.R:51:3', 'test-injec_list.R:88:3',
    'test-injec_list.R:118:3', 'test-injec_list.R:140:3',
    'test-injec_list.R:178:3', 'test-plate.R:10:3', 'test-plate.R:22:3',
    'test_methodsfile.R:1:1'
  • empty test (5): 'test-estimresiduals.R:1:1', 'test-estimresiduals.R:18:1',
    'test-plate.R:158:1', 'test-plate_expr.R:56:1', 'test-quant_parsers.R:9:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-pydeps.R:3:3'): pydeps ───────────────────────────────────────
  Expected `reticulate::py_module_available("numpy")` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-pydeps.R:4:3'): pydeps ───────────────────────────────────────
  Expected `reticulate::py_module_available("scipy")` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-pydeps.R:5:3'): pydeps ───────────────────────────────────────
  Expected `reticulate::py_module_available("pandas")` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-pydeps.R:6:3'): pydeps ───────────────────────────────────────
  Expected `reticulate::py_module_available("rainbow")` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-pydeps.R:7:3'): pydeps ───────────────────────────────────────
  Expected `reticulate::py_module_available("src")` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 5 | WARN 0 | SKIP 15 | PASS 116 ]
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE