• using R Under development (unstable) (2025-02-26 r87830)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (1+b1)     Debian flang-new version 19.1.7 (1+b1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘survHE/DESCRIPTION’ ... OK
• this is package ‘survHE’ version ‘2.0.2’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Packages suggested but not available for checking:   'survHEinla', 'survHEhmc', 'INLA'
• 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 ‘survHE’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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:     ‘make.surv.R’ ‘plot_tranformed_km.R’ ‘utils_make_surv.R’     ‘utils_plot_survHE.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 ... [4s/6s] OK
• checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
• checking whether the package can be unloaded cleanly ... [4s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/5s] 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 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 ... [30s/39s] 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 examples ... [6s/8s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [36s/44s] ERROR   Running ‘testthat.R’ [36s/44s] 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/tests.html   > # * https://testthat.r-lib.org/reference/test_package.html#special-files   >   > library(testthat)   > library(survHE)   Loading required package: flexsurv   Loading required package: survival   Loading required package: dplyr      Attaching package: 'dplyr'      The following object is masked from 'package:testthat':          matches      The following objects are masked from 'package:stats':          filter, lag      The following objects are masked from 'package:base':          intersect, setdiff, setequal, union      Loading required package: ggplot2   >   > test_check("survHE")   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-make.surv.R:13:3'): output plots don't throw an error and return ggplot2 list ──   Error in `select(., -matches("(Intercept)", everything()))`: i In argument: `matches("(Intercept)", everything())`.   Caused by error in `grep()`:   ! 'length = 3' in coercion to 'logical(1)'   Backtrace:        ▆     1. ├─testthat::expect_type(plot(mle, nsim = 10), "list") at test-make.surv.R:13:3     2. │ └─testthat::quasi_label(enquo(object), arg = "object")     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))     4. ├─base::plot(mle, nsim = 10)     5. ├─survHE::plot.survHE(mle, nsim = 10)     6. │ └─survHE:::plot_ggplot_survHE(exArgs)     7. │ ├─dplyr::ungroup(...)     8. │ ├─dplyr::mutate(...)     9. │ ├─dplyr::group_by(...)    10. │ ├─dplyr::bind_rows(...)    11. │ │ └─rlang::list2(...)    12. │ └─base::lapply(...)    13. │ └─survHE (local) FUN(X[[i]], ...)    14. │ ├─dplyr::mutate(...)    15. │ └─survHE:::make_data_surv(...)    16. │ └─base::lapply(...)    17. │ └─survHE (local) FUN(X[[i]], ...)    18. │ ├─... %>% select(strata)    19. │ └─base::lapply(...)    20. │ └─survHE (local) FUN(X[[i]], ...)    21. │ └─... %>% ...    22. ├─dplyr::select(., strata)    23. ├─dplyr::bind_rows(.)    24. │ └─rlang::list2(...)    25. ├─dplyr::mutate(., strata = paste0(names(.), "=", ., collapse = ","))    26. ├─dplyr::slice(., x)    27. ├─dplyr::select(., -matches("(Intercept)", everything()))    28. ├─dplyr:::select.data.frame(., -matches("(Intercept)", everything()))    29. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)    30. │ └─tidyselect:::eval_select_impl(...)    31. │ ├─tidyselect:::with_subscript_errors(...)    32. │ │ └─base::withCallingHandlers(...)    33. │ └─tidyselect:::vars_select_eval(...)    34. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)    35. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)    36. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)    37. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)    38. │ └─tidyselect:::eval_context(expr, context_mask, call = error_call)    39. │ ├─tidyselect:::with_chained_errors(...)    40. │ │ └─base::withCallingHandlers(...)    41. │ └─rlang::eval_tidy(as_quosure(expr, env), context_mask)    42. ├─tidyselect::matches("(Intercept)", everything())    43. │ └─tidyselect:::flat_map_int(...)    44. │ └─tidyselect:::map(unname(.x), .fn, ...)    45. │ └─base::lapply(.x, .f, ...)    46. │ └─tidyselect (local) FUN(X[[i]], ...)    47. │ └─base::grep(needle, haystack, ...)    48. └─base::.handleSimpleError(...)    49. └─tidyselect (local) h(simpleError(msg, call))    50. └─cli::cli_abort(c(i = msg), call = call, parent = cnd)    51. └─rlang::abort(...)      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]   Error: Test failures   Execution halted
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE