* using log directory ‘/Users/ripley/R/packages/tests-devel/MIC.Rcheck’
* using R Under development (unstable) (2026-09-18 r90566)
* using platform: aarch64-apple-darwin27.0.0
* R was compiled by
    Apple clang version 21.0.0 (clang-2100.3.34.2)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Golden Gate 27.0.1
* using session charset: UTF-8
* current time: 2026-10-16 12:40:52 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘MIC/DESCRIPTION’ ... OK
* this is package ‘MIC’ version ‘2.0.1’
* 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 ‘MIC’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking examples ... ERROR
Running examples in ‘MIC-Ex.R’ failed
The error most likely occurred in:

> ### Name: mic_r_breakpoint
> ### Title: R breakpoint for MIC
> ### Aliases: mic_r_breakpoint
> 
> ### ** Examples
> 
> mic_r_breakpoint("B_ESCHR_COLI", "AMK")
Error in mic_r_breakpoint("B_ESCHR_COLI", "AMK") : 
  No clinical breakpoints available for AMKB_ESCHR_COLI(consider using accept_ecoff if appropriate.
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [27s/58s]
 [28s/58s] ERROR
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(MIC)
  
  Attaching package: 'MIC'
  
  The following object is masked from 'package:base':
  
      table
  
  > 
  > test_check("MIC")
  Saving _problems/test-mic_manipulation-152.R
  Saving _problems/test-mic_manipulation-167.R
  Saving _problems/test-validation-182.R
  Saving _problems/test-validation-205.R
  Saving _problems/test-validation-217.R
  Saving _problems/test-validation-219.R
  [ FAIL 6 | WARN 7 | SKIP 0 | PASS 176 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-mic_manipulation.R:150:3'): test mic_s_breakpoint ────────────
  Expected `mic_s_breakpoint(mo = "E. coli", ab = "CHL", accept_ecoff = TRUE)` to be an S3 object.
  Actual OO type: none.
  Backtrace:
      ▆
   1. ├─base::suppressMessages(...) at test-mic_manipulation.R:150:3
   2. │ └─base::withCallingHandlers(...)
   3. └─testthat::expect_s3_class(...)
  ── Failure ('test-mic_manipulation.R:165:3'): test mic_r_breakpoint ────────────
  Expected `mic_r_breakpoint(mo = "E. coli", ab = "CHL", accept_ecoff = TRUE)` to be an S3 object.
  Actual OO type: none.
  Backtrace:
      ▆
   1. ├─base::suppressMessages(...) at test-mic_manipulation.R:165:3
   2. │ └─base::withCallingHandlers(...)
   3. └─testthat::expect_s3_class(...)
  ── Failure ('test-validation.R:182:3'): test compare_sir ───────────────────────
  Expected `sum_val$very_major_error_pcent[sum_val$ab == "GEN"]` to equal 50.
  Differences:
    `actual`:  0.0
  `expected`: 50.0
  
  ── Failure ('test-validation.R:204:3'): test fall back to ECOFFS in compare_mic ──
  Expected `val$error[val$ab == "CHL"]` to equal `factor("vM", levels = c("M", "vM", "m"))`.
  Differences:
  `actual`:   "NA"
  `expected`: "vM"
  
  ── Failure ('test-validation.R:217:3'): test fall back to ECOFFS in compare_mic ──
  Expected `sum_val$very_major_error_pcent[sum_val$ab == "CHL"]` to equal 25.
  Differences:
    `actual`:  0.0
  `expected`: 25.0
  
  ── Failure ('test-validation.R:219:3'): test fall back to ECOFFS in compare_mic ──
  Expected `sum_val$major_error_pcent[sum_val$ab == "CHL"]` to equal 25.
  Differences:
    `actual`:  0.0
  `expected`: 25.0
  
  
  [ FAIL 6 | WARN 7 | SKIP 0 | PASS 176 ]
  Error:
  ! Test failures.
  Execution halted
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs
See
  ‘/Users/ripley/R/packages/tests-devel/MIC.Rcheck/00check.log’
for details.

       99.50 real        44.64 user         6.96 sys