• using R Under development (unstable) (2026-10-16 r90678)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 23.1.3     flang version 23.1.3
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-10-16 13:44:12 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 See the install log for details.
• 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 ... [5s/14s] OK
• checking Rd files ... 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 ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking examples ... [9s/16s] 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 ... [77s/79s] ERROR   Running ‘testthat.R’ [77s/78s] 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 non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs