Last updated on 2026-07-12 12:51:44 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 4.27 | 468.59 | 472.86 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 3.21 | 290.37 | 293.58 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 750.70 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 7.00 | 854.03 | 861.03 | ERROR | |
| r-devel-windows-x86_64 | 1.1.0 | 8.00 | 512.00 | 520.00 | ERROR | |
| r-patched-linux-x86_64 | 1.1.0 | 4.20 | 459.89 | 464.09 | ERROR | |
| r-release-linux-x86_64 | 1.1.0 | 3.72 | 454.73 | 458.45 | ERROR | |
| r-release-macos-arm64 | 1.1.0 | 1.00 | 128.00 | 129.00 | OK | |
| r-release-macos-x86_64 | 1.1.0 | 3.00 | 554.00 | 557.00 | OK | |
| r-release-windows-x86_64 | 1.1.0 | 6.00 | 484.00 | 490.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.1.0 | 1.00 | 137.00 | 138.00 | OK | |
| r-oldrel-macos-x86_64 | 1.1.0 | 3.00 | 541.00 | 544.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 9.00 | 703.00 | 712.00 | ERROR |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [7m/10m]
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/Rtmp3ad2re/pdf1f0bff1a9d21ad
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/Rtmp3ad2re/pdf1f0bff3c086b10
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/Rtmp3ad2re/pdf1f0bff62751fb7
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/Rtmp3ad2re/pdf1f0bff39b0db2a
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/Rtmp3ad2re/pdf1f0bffc91cb9f
[ 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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [264s/338s]
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/RtmpAhsXYh/pdf2950ba5531ac21
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/RtmpAhsXYh/pdf2950ba1a6c8e58
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/RtmpAhsXYh/pdf2950ba750cf202
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/RtmpAhsXYh/pdf2950ba1078538
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/RtmpAhsXYh/pdf2950ba638d7ab0
[ 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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [12m/16m]
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):
/tmp/Rtmp3jryOt/working_dir/Rtmpay83an/pdf2db09138c1f3fa
Cleaning up 1 leaked TEMP file(s):
/tmp/Rtmp3jryOt/working_dir/Rtmpay83an/pdf2db091d6bd5be
Cleaning up 1 leaked TEMP file(s):
/tmp/Rtmp3jryOt/working_dir/Rtmpay83an/pdf2db091589e4441
Cleaning up 1 leaked TEMP file(s):
/tmp/Rtmp3jryOt/working_dir/Rtmpay83an/pdf2db091303429f
Cleaning up 1 leaked TEMP file(s):
/tmp/Rtmp3jryOt/working_dir/Rtmpay83an/pdf2db0917b5ff888
[ 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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [13m/37m]
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):
/tmp/RtmpSodNnp/working_dir/RtmpAOk2Fy/pdf303f341be00ee5
Cleaning up 1 leaked TEMP file(s):
/tmp/RtmpSodNnp/working_dir/RtmpAOk2Fy/pdf303f346426546e
Cleaning up 1 leaked TEMP file(s):
/tmp/RtmpSodNnp/working_dir/RtmpAOk2Fy/pdf303f3454345b8b
Cleaning up 1 leaked TEMP file(s):
/tmp/RtmpSodNnp/working_dir/RtmpAOk2Fy/pdf303f343dc08f34
Cleaning up 1 leaked TEMP file(s):
/tmp/RtmpSodNnp/working_dir/RtmpAOk2Fy/pdf303f34555f5d8
[ 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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [461s]
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):
D:\temp\2026_07_10_01_50_00_10726\Rtmpmokegr/pdf587865533667
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_10_01_50_00_10726\Rtmpmokegr/pdf58784d2f4114
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_10_01_50_00_10726\Rtmpmokegr/pdf587846487f4b
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_10_01_50_00_10726\Rtmpmokegr/pdf587849fe3293
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_10_01_50_00_10726\Rtmpmokegr/pdf587819145ee1
[ 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
Flavor: r-devel-windows-x86_64
Version: 1.1.0
Check: tests
Result: 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
Flavor: r-patched-linux-x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [428s/571s]
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/RtmpOVebnC/pdf3472e94cfcfc46
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/RtmpOVebnC/pdf3472e95955ea19
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/RtmpOVebnC/pdf3472e95e6b41e
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/RtmpOVebnC/pdf3472e949fb78bc
Cleaning up 1 leaked TEMP file(s):
/home/hornik/tmp/scratch/RtmpOVebnC/pdf3472e947d938e8
[ 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
Flavor: r-release-linux-x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [436s]
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):
D:\temp\2026_07_07_01_50_00_16256\RtmpAxE4qE/pdf48242d4768a3
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_07_01_50_00_16256\RtmpAxE4qE/pdf482462be233f
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_07_01_50_00_16256\RtmpAxE4qE/pdf48243cdd2a30
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_07_01_50_00_16256\RtmpAxE4qE/pdf48241a7c75c1
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_07_01_50_00_16256\RtmpAxE4qE/pdf482470f78c0
[ 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
Flavor: r-release-windows-x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [11m]
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):
D:\temp\2026_07_08_01_50_00_3490\Rtmp6x84E2/pdfa41c1a874fe8
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_08_01_50_00_3490\Rtmp6x84E2/pdfa41c47a9d89
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_08_01_50_00_3490\Rtmp6x84E2/pdfa41c66206309
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_08_01_50_00_3490\Rtmp6x84E2/pdfa41c1fe388e
Cleaning up 1 leaked TEMP file(s):
D:\temp\2026_07_08_01_50_00_3490\Rtmp6x84E2/pdfa41c55197213
[ 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
Flavor: r-oldrel-windows-x86_64