• using R version 4.6.1 Patched (2026-06-28 r90209)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.3.0-1) 15.3.0     GNU Fortran (Debian 15.3.0-1) 15.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-07-08 08:39:36 UTC
• checking for file ‘amregtest/DESCRIPTION’ ... OK
• this is package ‘amregtest’ version ‘1.1.0’
• 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 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 ... [1s/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
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/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
• 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/1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [433s/586s] ERROR   Running ‘testthat.R’ [433s/586s] 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")             Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=1)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=2)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=4)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=1)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=2)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=4)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=2)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=1, consensusMethod=2)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=1, consensusMethod=2)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.7, missingMethod=2, consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=4)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=1, consensusMethod=4)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=2, consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=1, consensusMethod=4)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_4-amCluster     Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=2, consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=1)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=2)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=4)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=1)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=2)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=4)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=1)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=2)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=4)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=1)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=2)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=4)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample4, cutHeight=0.7, doPsib="missing", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample4, cutHeight=0.7, doPsib="all", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample4, cutHeight=0.9, doPsib="missing", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample4, cutHeight=0.9, doPsib="all", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample4, cutHeight=0.95, doPsib="missing", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample4, cutHeight=0.95, doPsib="all", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample4, cutHeight=0.99, doPsib="missing", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample4, cutHeight=0.99, doPsib="all", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample4, cutHeight=1, doPsib="missing", consensusMethod=3)                Error : allelematch: amCluster: no clusters formed.     Test : test-allelematch_6-amUnique     Rejected : amUnique(amdataExample4, cutHeight=1, doPsib="all", consensusMethod=3)      Cleaning up 1 leaked TEMP file(s):     /home/hornik/tmp/scratch/RtmpB2zqc6/pdfa1066636166b6   Cleaning up 1 leaked TEMP file(s):     /home/hornik/tmp/scratch/RtmpB2zqc6/pdfa106665b5a723   Cleaning up 1 leaked TEMP file(s):     /home/hornik/tmp/scratch/RtmpB2zqc6/pdfa10666bd826fb   Cleaning up 1 leaked TEMP file(s):     /home/hornik/tmp/scratch/RtmpB2zqc6/pdfa10662e5284e2   Cleaning up 1 leaked TEMP file(s):     /home/hornik/tmp/scratch/RtmpB2zqc6/pdfa10665c6afd8b   [ FAIL 9 | WARN 0 | SKIP 20 | PASS 146 ]      ══ Skipped tests (20) ══════════════════════════════════════════════════════════   • On CRAN (20): '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:2:1',     'test-allelematch_3-amPairwise.R:68:1',     'test-allelematch_3-amPairwise_negative.R:2:1',     'test-allelematch_3-amPairwise_print.R:2:1',     'test-allelematch_4-amCluster.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:6:1', 'test-amExample3.R:11:1', 'test-amExample4.R:10:1',     'test-ggData.R:11:1'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-allelematch_6-amUnique_negative.R:31:5'): Validation of arguments to amUnique() is working ──   Error: allelematch: multilocusMap length mismatch.   Backtrace:       ▆    1. ├─testthat::expect_error(...) at test-allelematch_6-amUnique_negative.R:31:5    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 = NA)   ── Failure ('test-amExample1.R:33:9'): amExample1 from pg 5 in allelematchSuppDoc.pdf is 2.5.3 compatible ──   Expected some element of `output` to match string "missing data load for input dataset is 0.005 ".   Actual text:   x | allelematch: assuming genotype columns are in pairs, representing 10 loci   x | allelematch: running amUnique() at 9 different values of alleleMismatch   x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)   x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)   x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)   x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)   x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)   x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)   x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)   x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)   x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)   x | allelematch: missing data load for input dataset is 0.005   x | allelematch: allelic diversity for input dataset is 6.1   x | allelematch: Best guess for optimal parameter at alleleMismatch=2 OR matchThreshold=0.9 OR cutHeight=0.1   x | allelematch: Best guess for unique profile morphology: ZeroSecondMinimum   x | matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity guessMorphology   x | 1 1.00 0.00 0 20 13 0 0 FALSE 0.005 6.1 ZeroSecondMinimum   x | 2 0.95 0.05 1 20 13 0 2 FALSE 0.005 6.1 ZeroSecondMinimum   x | 3 0.90 0.10 2 20 12 0 0 TRUE 0.005 6.1 ZeroSecondMinimum   x | 4 0.85 0.15 3 20 12 0 0 FALSE 0.005 6.1 ZeroSecondMinimum   ... and 5 more.      ── Failure ('test-amExample1.R:34:9'): amExample1 from pg 5 in allelematchSuppDoc.pdf is 2.5.3 compatible ──   Expected some element of `output` to match string "allelic diversity for input dataset is 6.1 ".   Actual text:   x | allelematch: assuming genotype columns are in pairs, representing 10 loci   x | allelematch: running amUnique() at 9 different values of alleleMismatch   x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)   x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)   x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)   x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)   x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)   x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)   x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)   x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)   x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)   x | allelematch: missing data load for input dataset is 0.005   x | allelematch: allelic diversity for input dataset is 6.1   x | allelematch: Best guess for optimal parameter at alleleMismatch=2 OR matchThreshold=0.9 OR cutHeight=0.1   x | allelematch: Best guess for unique profile morphology: ZeroSecondMinimum   x | matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity guessMorphology   x | 1 1.00 0.00 0 20 13 0 0 FALSE 0.005 6.1 ZeroSecondMinimum   x | 2 0.95 0.05 1 20 13 0 2 FALSE 0.005 6.1 ZeroSecondMinimum   x | 3 0.90 0.10 2 20 12 0 0 TRUE 0.005 6.1 ZeroSecondMinimum   x | 4 0.85 0.15 3 20 12 0 0 FALSE 0.005 6.1 ZeroSecondMinimum   ... and 5 more.      ── Failure ('test-amExample2.R:25:9'): amExample2 results from pg 8 in allelematchSuppDoc.pdf 2.5.3 compatible ──   Expected some element of `output` to match string "missing data load for input dataset is 0.046 ".   Actual text:   x | allelematch: assuming genotype columns are in pairs, representing 10 loci   x | allelematch: running amUnique() at 9 different values of alleleMismatch   x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)   x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)   x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)   x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)   x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)   x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)   x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)   x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)   x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)   x | allelematch: missing data load for input dataset is 0.046   x | allelematch: allelic diversity for input dataset is 7.9   x | allelematch: Best guess for optimal parameter at alleleMismatch=3 OR matchThreshold=0.85 OR cutHeight=0.15   x | allelematch: Best guess for unique profile morphology: ZeroSecondMinimum   x | matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity guessMorphology   x | 1 1.00 0.00 0 148 140 0 0 FALSE 0.046 7.9 ZeroSecondMinimum   x | 2 0.95 0.05 1 148 136 0 25 FALSE 0.046 7.9 ZeroSecondMinimum   x | 3 0.90 0.10 2 148 122 0 33 FALSE 0.046 7.9 ZeroSecondMinimum   x | 4 0.85 0.15 3 148 100 0 0 TRUE 0.046 7.9 ZeroSecondMinimum   ... and 5 more.      ── Failure ('test-amExample2.R:26:9'): amExample2 results from pg 8 in allelematchSuppDoc.pdf 2.5.3 compatible ──   Expected some element of `output` to match string "allelic diversity for input dataset is 7.9 ".   Actual text:   x | allelematch: assuming genotype columns are in pairs, representing 10 loci   x | allelematch: running amUnique() at 9 different values of alleleMismatch   x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)   x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)   x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)   x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)   x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)   x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)   x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)   x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)   x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)   x | allelematch: missing data load for input dataset is 0.046   x | allelematch: allelic diversity for input dataset is 7.9   x | allelematch: Best guess for optimal parameter at alleleMismatch=3 OR matchThreshold=0.85 OR cutHeight=0.15   x | allelematch: Best guess for unique profile morphology: ZeroSecondMinimum   x | matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity guessMorphology   x | 1 1.00 0.00 0 148 140 0 0 FALSE 0.046 7.9 ZeroSecondMinimum   x | 2 0.95 0.05 1 148 136 0 25 FALSE 0.046 7.9 ZeroSecondMinimum   x | 3 0.90 0.10 2 148 122 0 33 FALSE 0.046 7.9 ZeroSecondMinimum   x | 4 0.85 0.15 3 148 100 0 0 TRUE 0.046 7.9 ZeroSecondMinimum   ... and 5 more.      ── Failure ('test-amExample3.R:32:9'): amExample3 results from pg 10 in allelematchSuppDoc.pdf are 2.5.3 compatible ──   Expected some element of `output` to match string "missing data load for input dataset is 0.097 ".   Actual text:   x | allelematch: assuming genotype columns are in pairs, representing 10 loci   x | allelematch: running amUnique() at 9 different values of alleleMismatch   x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)   x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)   x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)   x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)   x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)   x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)   x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)   x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)   x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)   x | allelematch: missing data load for input dataset is 0.097   x | allelematch: allelic diversity for input dataset is 8.2   x | allelematch: Best guess for optimal parameter at alleleMismatch=6 OR matchThreshold=0.7 OR cutHeight=0.3   x | allelematch: Best guess for unique profile morphology: NonZeroSecondMinimum   x | allelematch: Use extra caution. Detection of optimal parameter is more error prone with this morphology.   x | matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity guessMorphology   x | 1 1.00 0.00 0 319 291 0 0 FALSE 0.097 8.2 NonZeroSecondMinimum   x | 2 0.95 0.05 1 319 281 0 97 FALSE 0.097 8.2 NonZeroSecondMinimum   x | 3 0.90 0.10 2 319 212 0 103 FALSE 0.097 8.2 NonZeroSecondMinimum   ... and 6 more.      ── Failure ('test-amExample3.R:33:9'): amExample3 results from pg 10 in allelematchSuppDoc.pdf are 2.5.3 compatible ──   Expected some element of `output` to match string "allelic diversity for input dataset is 8.2 ".   Actual text:   x | allelematch: assuming genotype columns are in pairs, representing 10 loci   x | allelematch: running amUnique() at 9 different values of alleleMismatch   x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)   x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)   x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)   x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)   x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)   x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)   x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)   x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)   x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)   x | allelematch: missing data load for input dataset is 0.097   x | allelematch: allelic diversity for input dataset is 8.2   x | allelematch: Best guess for optimal parameter at alleleMismatch=6 OR matchThreshold=0.7 OR cutHeight=0.3   x | allelematch: Best guess for unique profile morphology: NonZeroSecondMinimum   x | allelematch: Use extra caution. Detection of optimal parameter is more error prone with this morphology.   x | matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity guessMorphology   x | 1 1.00 0.00 0 319 291 0 0 FALSE 0.097 8.2 NonZeroSecondMinimum   x | 2 0.95 0.05 1 319 281 0 97 FALSE 0.097 8.2 NonZeroSecondMinimum   x | 3 0.90 0.10 2 319 212 0 103 FALSE 0.097 8.2 NonZeroSecondMinimum   ... and 6 more.      ── Failure ('test-amExample4.R:31:9'): amExample4 results from pg 14 in allelematchSuppDoc.pdf are 2.5.3 compatible ──   Expected some element of `output` to match string "missing data load for input dataset is 0.199 ".   Actual text:   x | allelematch: assuming genotype columns are in pairs, representing 10 loci   x | allelematch: running amUnique() at 9 different values of alleleMismatch   x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)   x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)   x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)   x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)   x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)   x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)   x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)   x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)   x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)   x | allelematch: missing data load for input dataset is 0.199   x | allelematch: allelic diversity for input dataset is 4.8   x | allelematch: Best guess for optimal parameter at alleleMismatch=1 OR matchThreshold=0.95 OR cutHeight=0.05   x | allelematch: Best guess for unique profile morphology: NoSecondMinimum   x | allelematch: Use extra caution. Detection of optimal parameter is more error prone with this morphology.   x | matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity guessMorphology   x | 1 1.00 0.00 0 307 307 0 0 FALSE 0.199 4.8 NoSecondMinimum   x | 2 0.95 0.05 1 307 307 0 42 TRUE 0.199 4.8 NoSecondMinimum   x | 3 0.90 0.10 2 307 283 0 92 FALSE 0.199 4.8 NoSecondMinimum   ... and 6 more.      ── Failure ('test-amExample4.R:32:9'): amExample4 results from pg 14 in allelematchSuppDoc.pdf are 2.5.3 compatible ──   Expected some element of `output` to match string "allelic diversity for input dataset is 4.8 ".   Actual text:   x | allelematch: assuming genotype columns are in pairs, representing 10 loci   x | allelematch: running amUnique() at 9 different values of alleleMismatch   x | allelematch: 1 of 9 (matchThreshold=1, cutHeight=0, alleleMismatch=0)   x | allelematch: 2 of 9 (matchThreshold=0.95, cutHeight=0.05, alleleMismatch=1)   x | allelematch: 3 of 9 (matchThreshold=0.9, cutHeight=0.1, alleleMismatch=2)   x | allelematch: 4 of 9 (matchThreshold=0.85, cutHeight=0.15, alleleMismatch=3)   x | allelematch: 5 of 9 (matchThreshold=0.8, cutHeight=0.2, alleleMismatch=4)   x | allelematch: 6 of 9 (matchThreshold=0.75, cutHeight=0.25, alleleMismatch=5)   x | allelematch: 7 of 9 (matchThreshold=0.7, cutHeight=0.3, alleleMismatch=6)   x | allelematch: 8 of 9 (matchThreshold=0.65, cutHeight=0.35, alleleMismatch=7)   x | allelematch: 9 of 9 (matchThreshold=0.6, cutHeight=0.4, alleleMismatch=8)   x | allelematch: missing data load for input dataset is 0.199   x | allelematch: allelic diversity for input dataset is 4.8   x | allelematch: Best guess for optimal parameter at alleleMismatch=1 OR matchThreshold=0.95 OR cutHeight=0.05   x | allelematch: Best guess for unique profile morphology: NoSecondMinimum   x | allelematch: Use extra caution. Detection of optimal parameter is more error prone with this morphology.   x | matchThreshold cutHeight alleleMismatch samples unique unclassified multipleMatch guessOptimum missingDataLoad allelicDiversity guessMorphology   x | 1 1.00 0.00 0 307 307 0 0 FALSE 0.199 4.8 NoSecondMinimum   x | 2 0.95 0.05 1 307 307 0 42 TRUE 0.199 4.8 NoSecondMinimum   x | 3 0.90 0.10 2 307 283 0 92 FALSE 0.199 4.8 NoSecondMinimum   ... and 6 more.         [ FAIL 9 | WARN 0 | SKIP 20 | PASS 146 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR