• using R Under development (unstable) (2026-07-30 r90327)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-3) 16.1.0     GNU Fortran (Debian 16.1.0-3) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-07-31 13:23:41 UTC
• checking for file ‘amregtest/DESCRIPTION’ ... OK
• this is package ‘amregtest’ version ‘1.2.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• 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 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 ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
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• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/1s] 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 ... [4s/6s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
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• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
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• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
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• checking LazyData ... OK
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• checking examples ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [263s/342s] ERROR   Running ‘testthat.R’ [262s/342s] 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):     /home/hornik/tmp/scratch/RtmpgoanAA/pdf334b57612c02d7   Cleaning up 1 leaked TEMP file(s):     /home/hornik/tmp/scratch/RtmpgoanAA/pdf334b575dfb3525   Cleaning up 1 leaked TEMP file(s):     /home/hornik/tmp/scratch/RtmpgoanAA/pdf334b575001c365   Cleaning up 1 leaked TEMP file(s):     /home/hornik/tmp/scratch/RtmpgoanAA/pdf334b5729ff9801   Cleaning up 1 leaked TEMP file(s):     /home/hornik/tmp/scratch/RtmpgoanAA/pdf334b57107f6d37   [ 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 ... [4s/6s] OK
• checking HTML version of manual ... [0s/0s] OK
• checking for non-standard things in the check directory ... OK
• checking for new files in some other directories ... NOTE Found the following files/directories:   ‘~/tmp/scratch/Rtmp05Hdrp’ ‘~/tmp/scratch/Rtmp0FsrsN’   ‘~/tmp/scratch/Rtmp0pFBPU’ ‘~/tmp/scratch/Rtmp0tvOKN’   ‘~/tmp/scratch/Rtmp1Rgeyd’ ‘~/tmp/scratch/Rtmp1iSVgM’   ‘~/tmp/scratch/Rtmp1loDdR’ ‘~/tmp/scratch/Rtmp1m6Mx6’   ‘~/tmp/scratch/Rtmp24bVVd’ ‘~/tmp/scratch/Rtmp2dmKoZ’   ‘~/tmp/scratch/Rtmp485LpO’ ‘~/tmp/scratch/Rtmp4cW4yd’   ‘~/tmp/scratch/Rtmp4kgaVb’ ‘~/tmp/scratch/Rtmp4n3Fs4’   ‘~/tmp/scratch/Rtmp50WFKM’ ‘~/tmp/scratch/Rtmp5BTisy’   ‘~/tmp/scratch/Rtmp5XOdif’ ‘~/tmp/scratch/Rtmp5qsGjw’   ‘~/tmp/scratch/Rtmp5wfWBU’ ‘~/tmp/scratch/Rtmp6GzWST’   ‘~/tmp/scratch/Rtmp6U0Ccw’ ‘~/tmp/scratch/Rtmp6cI7Zo’   ‘~/tmp/scratch/Rtmp6rTSGF’ ‘~/tmp/scratch/Rtmp732T6i’   ‘~/tmp/scratch/Rtmp77SbQb’ ‘~/tmp/scratch/Rtmp79JvZg’   ‘~/tmp/scratch/Rtmp7S7v5H’ ‘~/tmp/scratch/Rtmp7X02ve’   ‘~/tmp/scratch/Rtmp7r3Bui’ ‘~/tmp/scratch/Rtmp8iQgIU’   ‘~/tmp/scratch/Rtmp957DCt’ ‘~/tmp/scratch/Rtmp9USSr6’   ‘~/tmp/scratch/Rtmp9m5lqS’ ‘~/tmp/scratch/Rtmp9ns4ZJ’   ‘~/tmp/scratch/Rtmp9oRI97’ ‘~/tmp/scratch/RtmpANfOLm’   ‘~/tmp/scratch/RtmpAYo0FK’ ‘~/tmp/scratch/RtmpB1W4Dt’   ‘~/tmp/scratch/RtmpBNOL0H’ ‘~/tmp/scratch/RtmpBrRZYI’   ‘~/tmp/scratch/RtmpBwsDc9’ ‘~/tmp/scratch/RtmpBxpSrs’   ‘~/tmp/scratch/RtmpCRE3F2’ ‘~/tmp/scratch/RtmpCmnrxI’   ‘~/tmp/scratch/RtmpCohKzG’ ‘~/tmp/scratch/RtmpEJ992f’   ‘~/tmp/scratch/RtmpEu8VIJ’ ‘~/tmp/scratch/RtmpF9ZdxG’   ‘~/tmp/scratch/RtmpFBJirM’ ‘~/tmp/scratch/RtmpFJIT30’   ‘~/tmp/scratch/RtmpFRHC5T’ ‘~/tmp/scratch/RtmpGOZa2t’   ‘~/tmp/scratch/RtmpGTpqm3’ ‘~/tmp/scratch/RtmpGZljC7’   ‘~/tmp/scratch/RtmpGnSSqc’ ‘~/tmp/scratch/RtmpGuefKf’   ‘~/tmp/scratch/RtmpIA03Vo’ ‘~/tmp/scratch/RtmpJ5OBxK’   ‘~/tmp/scratch/RtmpJfW0ux’ ‘~/tmp/scratch/RtmpJfZBXY’   ‘~/tmp/scratch/RtmpJgxXMi’ ‘~/tmp/scratch/RtmpK0euU6’   ‘~/tmp/scratch/RtmpKL7kSt’ ‘~/tmp/scratch/RtmpKVg0Zv’   ‘~/tmp/scratch/RtmpLIYS8T’ ‘~/tmp/scratch/RtmpLeE23E’   ‘~/tmp/scratch/RtmpMHgfKi’ ‘~/tmp/scratch/RtmpMOGo5N’   ‘~/tmp/scratch/RtmpMy3Wkj’ ‘~/tmp/scratch/RtmpNosZZs’   ‘~/tmp/scratch/RtmpO26lvk’ ‘~/tmp/scratch/RtmpOmCuoL’   ‘~/tmp/scratch/RtmpOsLSU6’ ‘~/tmp/scratch/RtmpP1BRnO’   ‘~/tmp/scratch/RtmpQ5j2aI’ ‘~/tmp/scratch/RtmpQO9sSZ’   ‘~/tmp/scratch/RtmpRcisz7’ ‘~/tmp/scratch/RtmpSaB8fh’   ‘~/tmp/scratch/RtmpSbQ81O’ ‘~/tmp/scratch/RtmpTPoMUm’   ‘~/tmp/scratch/RtmpTqd9Gw’ ‘~/tmp/scratch/RtmpUFEG6x’   ‘~/tmp/scratch/RtmpUmVUsS’ ‘~/tmp/scratch/RtmpV6Ktce’   ‘~/tmp/scratch/RtmpVoE0VI’ ‘~/tmp/scratch/RtmpW3X971’   ‘~/tmp/scratch/RtmpWUEmPn’ ‘~/tmp/scratch/RtmpWgJqFY’   ‘~/tmp/scratch/RtmpWxTm0g’ ‘~/tmp/scratch/RtmpXAWL9K’   ‘~/tmp/scratch/RtmpXk9emO’ ‘~/tmp/scratch/RtmpXkGxk8’   ‘~/tmp/scratch/RtmpXlnlWk’ ‘~/tmp/scratch/RtmpXtO1rf’   ‘~/tmp/scratch/RtmpY1mFgl’ ‘~/tmp/scratch/RtmpY6b9FV’   ‘~/tmp/scratch/RtmpYvjdik’ ‘~/tmp/scratch/RtmpZ3Q2MX’   ‘~/tmp/scratch/RtmpZvN47P’ ‘~/tmp/scratch/Rtmpa61LrF’   ‘~/tmp/scratch/RtmpaDoMq0’ ‘~/tmp/scratch/Rtmpb2U3gO’   ‘~/tmp/scratch/Rtmpb8LEtP’ ‘~/tmp/scratch/RtmpbRXzwv’ 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‘~/tmp/scratch/RtmpnxAGLL’   ‘~/tmp/scratch/Rtmpo2hSV5’ ‘~/tmp/scratch/RtmpohLChR’   ‘~/tmp/scratch/Rtmpp0OI9J’ ‘~/tmp/scratch/RtmppXixls’   ‘~/tmp/scratch/Rtmppb81AY’ ‘~/tmp/scratch/RtmpqAVvFu’   ‘~/tmp/scratch/RtmpqDLndw’ ‘~/tmp/scratch/RtmpqJTsC7’   ‘~/tmp/scratch/RtmpqovsXn’ ‘~/tmp/scratch/Rtmpqu9VHe’   ‘~/tmp/scratch/Rtmpr3xnTB’ ‘~/tmp/scratch/RtmprIJY8b’   ‘~/tmp/scratch/RtmprWBcVI’ ‘~/tmp/scratch/RtmprmSPqM’   ‘~/tmp/scratch/RtmpsLfVZA’ ‘~/tmp/scratch/RtmpshQy71’   ‘~/tmp/scratch/Rtmpspx565’ ‘~/tmp/scratch/RtmptaLFrV’   ‘~/tmp/scratch/RtmptlsMvn’ ‘~/tmp/scratch/RtmptoH8WI’   ‘~/tmp/scratch/Rtmpu1VRCB’ ‘~/tmp/scratch/RtmpuFOIOa’   ‘~/tmp/scratch/RtmpuPj8rK’ ‘~/tmp/scratch/Rtmpuzdeps’   ‘~/tmp/scratch/RtmpvQb0Bv’ ‘~/tmp/scratch/RtmpvUkaou’   ‘~/tmp/scratch/RtmpvaGgM5’ ‘~/tmp/scratch/RtmpvzHma7’   ‘~/tmp/scratch/RtmpxpiqM1’ ‘~/tmp/scratch/RtmpyDsF8e’   ‘~/tmp/scratch/RtmpyWNtR5’ ‘~/tmp/scratch/RtmpyXQjO1’   ‘~/tmp/scratch/RtmpybWyfa’ ‘~/tmp/scratch/RtmpyvXqjJ’   ‘~/tmp/scratch/Rtmpz6ORaM’ ‘~/tmp/scratch/RtmpzFXv4s’   ‘~/tmp/scratch/RtmpzI2nmA’ ‘~/tmp/scratch/RtmpztQPnR’   ‘~/tmp/scratch/xvfb-run.0mv95A’ ‘~/tmp/scratch/xvfb-run.1c6XaJ’   ‘~/tmp/scratch/xvfb-run.2mS8wx’ ‘~/tmp/scratch/xvfb-run.3QG4HT’   ‘~/tmp/scratch/xvfb-run.3V34JV’ ‘~/tmp/scratch/xvfb-run.3p31Vk’   ‘~/tmp/scratch/xvfb-run.5Mhvsv’ ‘~/tmp/scratch/xvfb-run.5qT8YS’   ‘~/tmp/scratch/xvfb-run.7SeZAm’ ‘~/tmp/scratch/xvfb-run.7YDKjx’   ‘~/tmp/scratch/xvfb-run.9cv9NE’ ‘~/tmp/scratch/xvfb-run.A7yuHX’   ‘~/tmp/scratch/xvfb-run.BwgXAY’ ‘~/tmp/scratch/xvfb-run.C8B0ST’   ‘~/tmp/scratch/xvfb-run.D7kXtZ’ ‘~/tmp/scratch/xvfb-run.EpvzRq’   ‘~/tmp/scratch/xvfb-run.FBIYF5’ ‘~/tmp/scratch/xvfb-run.H7vK2d’   ‘~/tmp/scratch/xvfb-run.HDAAEE’ ‘~/tmp/scratch/xvfb-run.ItG88I’   ‘~/tmp/scratch/xvfb-run.IxEBUn’ ‘~/tmp/scratch/xvfb-run.J2hmsl’   ‘~/tmp/scratch/xvfb-run.JKESpO’ ‘~/tmp/scratch/xvfb-run.LChWNL’   ‘~/tmp/scratch/xvfb-run.MCuaO8’ ‘~/tmp/scratch/xvfb-run.MEiTrd’   ‘~/tmp/scratch/xvfb-run.MlErSN’ ‘~/tmp/scratch/xvfb-run.NBw3L2’   ‘~/tmp/scratch/xvfb-run.NXGzpv’ ‘~/tmp/scratch/xvfb-run.OReBwC’   ‘~/tmp/scratch/xvfb-run.PQ8O0d’ ‘~/tmp/scratch/xvfb-run.R3L4DC’   ‘~/tmp/scratch/xvfb-run.REUjfu’ ‘~/tmp/scratch/xvfb-run.Rydwtk’   ‘~/tmp/scratch/xvfb-run.SE7sk0’ ‘~/tmp/scratch/xvfb-run.SN4Ymn’   ‘~/tmp/scratch/xvfb-run.StYvTq’ ‘~/tmp/scratch/xvfb-run.TALACV’   ‘~/tmp/scratch/xvfb-run.TBhAiw’ ‘~/tmp/scratch/xvfb-run.Uaugvs’   ‘~/tmp/scratch/xvfb-run.V6A5IM’ ‘~/tmp/scratch/xvfb-run.VpmhMO’   ‘~/tmp/scratch/xvfb-run.WLjpHH’ ‘~/tmp/scratch/xvfb-run.YhNJdV’   ‘~/tmp/scratch/xvfb-run.Yy2idq’ ‘~/tmp/scratch/xvfb-run.YyE5ch’   ‘~/tmp/scratch/xvfb-run.aVUof4’ ‘~/tmp/scratch/xvfb-run.av9Q6d’   ‘~/tmp/scratch/xvfb-run.dhobxk’ ‘~/tmp/scratch/xvfb-run.e8bp7j’   ‘~/tmp/scratch/xvfb-run.ehPILO’ ‘~/tmp/scratch/xvfb-run.fBCLyP’   ‘~/tmp/scratch/xvfb-run.fEv6fM’ ‘~/tmp/scratch/xvfb-run.fSRZ9I’   ‘~/tmp/scratch/xvfb-run.fYwqZo’ ‘~/tmp/scratch/xvfb-run.fxiSJL’   ‘~/tmp/scratch/xvfb-run.iSzRwO’ ‘~/tmp/scratch/xvfb-run.iptWpP’   ‘~/tmp/scratch/xvfb-run.jSpfj2’ ‘~/tmp/scratch/xvfb-run.jtY6jd’   ‘~/tmp/scratch/xvfb-run.kpNQoV’ ‘~/tmp/scratch/xvfb-run.kxT5qM’   ‘~/tmp/scratch/xvfb-run.lhXV2D’ ‘~/tmp/scratch/xvfb-run.nbrkXf’   ‘~/tmp/scratch/xvfb-run.pj4pii’ ‘~/tmp/scratch/xvfb-run.qiBEQS’   ‘~/tmp/scratch/xvfb-run.quluor’ ‘~/tmp/scratch/xvfb-run.qzz9e5’   ‘~/tmp/scratch/xvfb-run.rE0fk3’ ‘~/tmp/scratch/xvfb-run.rduK8v’   ‘~/tmp/scratch/xvfb-run.sVI4pv’ ‘~/tmp/scratch/xvfb-run.sxj4pH’   ‘~/tmp/scratch/xvfb-run.uIoIQp’ ‘~/tmp/scratch/xvfb-run.uYs0mv’   ‘~/tmp/scratch/xvfb-run.v7ULrc’ ‘~/tmp/scratch/xvfb-run.wK27fl’   ‘~/tmp/scratch/xvfb-run.x4j1ON’ ‘~/tmp/scratch/xvfb-run.xd14q4’   ‘~/tmp/scratch/xvfb-run.yy8hws’ ‘~/tmp/scratch/xvfb-run.z2Lhx9’   ‘~/tmp/scratch/xvfb-run.zU4OLp’
• DONE

Status: 1 ERROR, 1 NOTE