• using R Under development (unstable) (2026-01-28 r89344)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.8 (1+b1)     Debian flang version 21.1.8 (1+b1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘phers/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘phers’ version ‘1.0.2’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘qs’
• 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 ‘phers’ can be installed ... OK See the install log for details.
• 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 ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
• checking loading without being on the library search path ... [2s/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 ... [11s/14s] 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 ... [2s/2s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [21s/19s] OK Examples with CPU (user + system) or elapsed time > 5s                      user system elapsed mapDiseaseToPhecode 6.624 0.02 6.875 getWeights 6.572 0.04 6.043
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [3s/4s] ERROR   Running ‘testthat.R’ [3s/3s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(phers)   >   > test_check('phers')      Attaching package: 'data.table'      The following object is masked from 'package:base':          %notin%      Error in `source_dir()`:   ! Failed to evaluate './setup.R'.   Caused by error in `library()`:   ! there is no package called 'qs'   Backtrace:        ▆     1. ├─testthat::test_check("phers")     2. │ └─testthat::test_dir(...)     3. │ └─testthat:::test_files(...)     4. │ └─testthat:::test_files_serial(...)     5. │ └─testthat:::test_files_setup_state(...)     6. │ └─testthat::source_test_setup(".", env)     7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)     8. │ └─base::lapply(...)     9. │ └─testthat (local) FUN(X[[i]], ...)    10. │ └─testthat::source_file(...)    11. │ ├─base::withCallingHandlers(...)    12. │ └─base::eval(exprs, env)    13. │ └─base::eval(exprs, env)    14. │ └─base::library("qs") at ./setup.R:3:1    15. │ └─base::stop(packageNotFoundError(package, lib.loc, sys.call()))    16. └─testthat (local) `<fn>`(`<S3: packageNotFoundError>`)    17. └─cli::cli_abort(...)    18. └─rlang::abort(...)   Execution halted
• checking PDF version of manual ... [4s/5s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR