* using log directory ‘/Users/ripley/R/packages/tests-devel/amregtest.Rcheck’ * using R Under development (unstable) (2026-07-03 r90206) * using platform: aarch64-apple-darwin25.5.0 * R was compiled by Apple clang version 21.0.0 (clang-2100.1.1.101) GNU Fortran (GCC) 14.2.0 * running under: macOS Tahoe 26.5.2 * using session charset: UTF-8 * current time: 2026-07-05 11:23:32 UTC * using option ‘--no-stop-on-test-error’ * 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 * 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 examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [127s/129s] [127s/129s] 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/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): /var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//RtmpyAg8x5/working_dir/RtmpOUQU1H/pdfc1d32d5f58da Cleaning up 1 leaked TEMP file(s): /var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//RtmpyAg8x5/working_dir/RtmpOUQU1H/pdfc1d3545d27a4 Cleaning up 1 leaked TEMP file(s): /var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//RtmpyAg8x5/working_dir/RtmpOUQU1H/pdfc1d364c2747f Cleaning up 1 leaked TEMP file(s): /var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//RtmpyAg8x5/working_dir/RtmpOUQU1H/pdfc1d33df9df3f Cleaning up 1 leaked TEMP file(s): /var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//RtmpyAg8x5/working_dir/RtmpOUQU1H/pdfc1d33b5e4047 [ 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 ... OK * checking HTML version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/Users/ripley/R/packages/tests-devel/amregtest.Rcheck/00check.log’ for details. 145.26 real 135.85 user 6.81 sys