* using log directory ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/biodosetools.Rcheck’
* using R version 4.5.1 Patched (2025-10-13 r88918)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.3.0-8) 14.3.0
    GNU Fortran (Debian 14.3.0-8) 14.3.0
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘biodosetools/DESCRIPTION’ ... OK
* this is package ‘biodosetools’ version ‘3.6.2’
* package encoding: UTF-8
* 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 ‘biodosetools’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/biodosetools-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... 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 ... [4s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
* checking whether the package can be unloaded cleanly ... [4s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
* checking loading without being on the library search path ... [4s/5s] OK
* checking whether startup messages can be suppressed ... [4s/6s] 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 ... [38s/46s] OK
* checking Rd files ... [1s/1s] 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 ... [0s/0s] 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 ... [17s/22s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [18s/28s] ERROR
  Running ‘testthat.R’ [18s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biodosetools)
  Loading required package: shiny
  Loading required package: golem
  > 
  > test_check("biodosetools")
  ! Problem with `glm()` -> constraint ML optimization will be used instead
  ! Problem with `glm()` -> constraint ML optimization will be used instead
  number of iterations= 43 
  ! Problem with `glm()` -> constraint ML optimization will be used instead
  ! Problem with `glm()` -> constraint ML optimization will be used instead
  number of iterations= 43 
  ! Problem with `glm()` -> constraint ML optimization will be used instead
  ! Problem with `glm()` -> constraint ML optimization will be used instead
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 455 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-golem-recommended.R:71:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-golem-recommended.R:2:3'): app ui ──────────────────────────────
  Error in `file(con, "w")`: cannot open the connection
  Backtrace:
       ▆
    1. └─biodosetools:::app_ui() at test-golem-recommended.R:2:3
    2.   ├─htmltools::tagList(...)
    3.   │ └─rlang::dots_list(...)
    4.   ├─shinydashboard::dashboardPage(...)
    5.   │ └─shinydashboard:::tagAssert(body, type = "div", class = "content-wrapper")
    6.   └─biodosetools:::dashboard_body()
    7.     ├─shinydashboard::dashboardBody(...)
    8.     │ ├─htmltools::div(...)
    9.     │ │ └─rlang::dots_list(...)
   10.     │ └─tags$section(class = "content", ...)
   11.     │   └─rlang::dots_list(...)
   12.     ├─shinydashboard::tabItems(...)
   13.     │ └─base::lapply(list(...), tagAssert, class = "tab-pane")
   14.     └─biodosetools:::dashboard_home()
   15.       ├─shinydashboard::tabItem(...)
   16.       │ └─htmltools::div(...)
   17.       │   └─rlang::dots_list(...)
   18.       ├─htmltools::div(...)
   19.       │ └─rlang::dots_list(...)
   20.       └─htmltools::includeMarkdown(...)
   21.         └─markdown::mark(path, output = NULL)
   22.           └─xfun::write_utf8(c("---", yaml, "---", parts$body), file)
   23.             └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
   24.               └─base::file(con, "w")
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 455 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [73s/105s] OK
* checking PDF version of manual ... [8s/11s] OK
* checking HTML version of manual ... [2s/4s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR