• using R Under development (unstable) (2026-07-23 r90295)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 22.1.8 (https://github.com/llvm/llvm-project ca7933e47d3a3451d81e72ac174dcb5aa28b59d1)     flang version 22.1.8 (https://github.com/llvm/llvm-project ca7933e47d3a3451d81e72ac174dcb5aa28b59d1)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-07-24 09:00:20 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘amregtest/DESCRIPTION’ ... OK
• this is package ‘amregtest’ version ‘1.2.0’
• 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 ‘amregtest’ 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 ... 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 examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [12m/13m] ERROR   Running ‘testthat.R’ [12m/13m] 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/testing-design.html#sec-tests-files-overview   > # * https://testthat.r-lib.org/articles/special-files.html   >   > library(testthat)   > library(amregtest)   Loading required package: allelematch   Loading required package: dynamicTreeCut   >   > test_check("amregtest")   Saving _problems/test-allelematch_3-amPairwise_negative-45.R   Cleaning up 1 leaked TEMP file(s):     /tmp/RtmpTOFCr8/working_dir/RtmpilU2wU/pdfa7dcc6219965b   Cleaning up 1 leaked TEMP file(s):     /tmp/RtmpTOFCr8/working_dir/RtmpilU2wU/pdfa7dcc388a483   Cleaning up 1 leaked TEMP file(s):     /tmp/RtmpTOFCr8/working_dir/RtmpilU2wU/pdfa7dcc3cd33918   Cleaning up 1 leaked TEMP file(s):     /tmp/RtmpTOFCr8/working_dir/RtmpilU2wU/pdfa7dcc413a2994   Cleaning up 1 leaked TEMP file(s):     /tmp/RtmpTOFCr8/working_dir/RtmpilU2wU/pdfa7dcc1645a4a3   [ FAIL 2 | WARN 0 | SKIP 24 | PASS 135 ]      ══ Skipped tests (24) ══════════════════════════════════════════════════════════   • On CRAN (24): 'test-allelematch_1-amDataset.R:47:1',     'test-allelematch_1-amDataset.R:147:1', 'test-allelematch_2-amMatrix.R:2:1',     'test-allelematch_2-amMatrix.R:90:1',     'test-allelematch_2-amMatrix_negative.R:2:1',     'test-allelematch_3-amPairwise.R:7:1',     'test-allelematch_3-amPairwise.R:74:1',     'test-allelematch_3-amPairwise_print.R:2:1',     'test-allelematch_4-amCluster-Ex1.R:2:1',     'test-allelematch_4-amCluster-Ex2.R:2:1',     'test-allelematch_4-amCluster-Ex3.R:2:1',     'test-allelematch_4-amCluster-Ex4.R:2:1',     'test-allelematch_4-amCluster-Ex5.R:2:1',     'test-allelematch_4-amCluster-amMini.R:2:1',     'test-allelematch_4-amCluster_print.R:2:1',     'test-allelematch_5-amAlleleFreq.R:2:1', 'test-allelematch_6-amUnique.R:2:1',     'test-allelematch_6-amUnique_print.R:2:1',     'test-allelematch_7-amUniqueProfile.R:2:1', 'test-amExample1.R:10:1',     'test-amExample2.R:10:1', 'test-amExample3.R:11:1', 'test-amExample4.R:15:1',     'test-ggData.R:11:1'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-allelematch_3-amPairwise_negative.R:45:5'): Validation of arguments to amPairwise() is working ──   Error: allelematch: please specify alleleMismatch OR matchThreshold   Backtrace:       ▆    1. ├─testthat::expect_error(amPairwise(amdataOdd2), "allelematch:\\s+please specify alleleMismatch OR matchThreshold.") at test-allelematch_3-amPairwise_negative.R:45:5    2. │ └─testthat:::expect_condition_matching_(...)    3. │ └─testthat:::quasi_capture(...)    4. │ ├─testthat (local) .capture(...)    5. │ │ └─base::withCallingHandlers(...)    6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))    7. └─allelematch::amPairwise(amdataOdd2)   ── Error ('test-allelematch_6-amUnique_negative.R:40:5'): Validation of arguments to amUnique() is working ──   Error: allelematch: please specify alleleMismatch OR matchThreshold OR cutHeight   Backtrace:       ▆    1. ├─testthat::expect_error(...) at test-allelematch_6-amUnique_negative.R:40:5    2. │ └─testthat:::expect_condition_matching_(...)    3. │ └─testthat:::quasi_capture(...)    4. │ ├─testthat (local) .capture(...)    5. │ │ └─base::withCallingHandlers(...)    6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))    7. └─allelematch::amUnique(amdata, multilocusMap = c(1, 1, 2, 2))      [ FAIL 2 | WARN 0 | SKIP 24 | PASS 135 ]   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: 1 ERROR