• using R version 4.5.0 beta (2025-03-27 r88065)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘biodosetools/DESCRIPTION’ ... OK
• this is package ‘biodosetools’ version ‘3.6.1’
• 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 the install log 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 ... [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/2s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking whether startup messages can be suppressed ... [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 ... [16s/21s] OK
• checking Rd files ... [0s/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 ... NONE
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [21s/25s] ERROR   Running ‘testthat.R’ [20s/25s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(biodosetools)   >   > 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   Loading required package: shiny      ── Dose estimation calculations ────────────────────────────────────────────────   ℹ Parsing dose-effect curve...      ── Dose estimation calculations ────────────────────────────────────────────────   ℹ Parsing dose-effect curve...      ── Dose estimation calculations ────────────────────────────────────────────────   ℹ Parsing dose-effect curve...   ! Problem with `glm()` -> constraint ML optimization will be used instead   ! Problem with `glm()` -> constraint ML optimization will be used instead   [ FAIL 1 | WARN 4 | SKIP 1 | PASS 234 ]      ══ 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 4 | SKIP 1 | PASS 234 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [20s/30s] OK
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR