Package: amregtest Check: tests New result: ERROR Running ‘testthat.R’ [152s/153s] 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) > > test_check("amregtest") Saving _problems/test-allelematch_1-amDataset-68.R Saving _problems/test-allelematch_1-amDataset_negative-8.R Saving _problems/test-allelematch_2-amMatrix_negative-6.R Saving _problems/test-allelematch_3-amPairwise_negative-14.R Saving _problems/test-allelematch_3-amPairwise_print-29.R Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=1) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=2) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=4) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=1) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=2) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample1, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=4) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=2) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=1, consensusMethod=2) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample2, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=1, consensusMethod=2) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.7, missingMethod=2, consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=1, consensusMethod=4) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.9, missingMethod=2, consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=1, consensusMethod=4) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.95, missingMethod=2, consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=1, consensusMethod=4) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amCluster(amdataExample4, runUntilSingletons=TRUE, cutHeight=0.99, missingMethod=2, consensusMethod=3) Saving _problems/test-allelematch_4-amCluster_print-29.R Saving _problems/test-allelematch_5-amAlleleFreq-63.R Saving _problems/test-allelematch_6-amUnique-76.R Saving _problems/test-allelematch_6-amUnique_negative-14.R Saving _problems/test-allelematch_6-amUnique_print-38.R Saving _problems/test-amExample1-59.R Saving _problems/test-amExample2-36.R Saving _problems/test-amExample2-42.R Saving _problems/test-amExample3-43.R Saving _problems/test-amExample3-49.R Saving _problems/test-amExample4-42.R Saving _problems/test-amExample4-48.R Saving _problems/test-ggData-42.R [ FAIL 18 | WARN 0 | SKIP 7 | PASS 64 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • On CRAN (7): 'test-allelematch_1-amDataset.R:132:1', 'test-allelematch_2-amMatrix.R:2:1', 'test-allelematch_2-amMatrix.R:90:1', 'test-allelematch_3-amPairwise.R:2:1', 'test-allelematch_3-amPairwise.R:68:1', 'test-allelematch_4-amCluster.R:2:1', 'test-allelematch_7-amUniqueProfile.R:2:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-allelematch_1-amDataset.R:68:3'): See how an object of class amDataset is built: ── Error in `print.amDataset(miniDataset1)`: could not find function "print.amDataset" ── Error ('test-allelematch_1-amDataset_negative.R:8:3'): Validation of arguments to amDataset() is working ── Error: allelematch: multilocusDataset must be a matrix or a data.frame Backtrace: ▆ 1. ├─testthat::expect_error(amDataset(NULL), "allelematch: multilocusDataset must be a matrix or a data.frame") at test-allelematch_1-amDataset_negative.R:8:3 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::amDataset(NULL) ── Error ('test-allelematch_2-amMatrix_negative.R:6:5'): Validation of arguments to amMatrix() is working ── Error: allelematch: amDatasetFocal must be an object of class "amDataset"; use amDataset() first Backtrace: ▆ 1. ├─testthat::expect_error(amMatrix(NULL), "allelematch: amDatasetFocal must be an object of class \"amDataset\"") at test-allelematch_2-amMatrix_negative.R:6:5 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::amMatrix(NULL) ── Error ('test-allelematch_3-amPairwise_negative.R:14:5'): Validation of arguments to amPairwise() is working ── Error in `print.amDataset(amdataMini1)`: could not find function "print.amDataset" ── Error ('test-allelematch_3-amPairwise_print.R:29:5'): Print ───────────────── Error in `summary.amPairwise(get(obj))`: could not find function "summary.amPairwise" ── Error ('test-allelematch_4-amCluster_print.R:29:5'): Print ────────────────── Error in `summary.amCluster(get(obj))`: could not find function "summary.amCluster" ── Error ('test-allelematch_5-amAlleleFreq.R:63:7'): Loop the Loop ───────────── Error in `print.amAlleleFreq(af)`: could not find function "print.amAlleleFreq" Backtrace: ▆ 1. └─amregtest (local) snapshot_amAlleleFreq("amdataMini") at test-allelematch_5-amAlleleFreq.R:76:3 ── Error ('test-allelematch_6-amUnique.R:76:7'): Loop the Loop ───────────────── Error in `amCSV.amUnique(ret, csvFile = stdout(), uniqueOnly = FALSE)`: could not find function "amCSV.amUnique" Backtrace: ▆ 1. └─amregtest (local) snapshot_amUnique(amds, cutHeight = ch, doPsib = psi, consensusMethod = cons) at test-allelematch_6-amUnique.R:100:11 ── Error ('test-allelematch_6-amUnique_negative.R:14:5'): Validation of arguments to amUnique() is working ── Error in `print.amDataset(amdataMini1)`: could not find function "print.amDataset" ── Error ('test-allelematch_6-amUnique_print.R:38:5'): Print ─────────────────── Error in `summary.amUnique(get(obj), csv = tmp)`: could not find function "summary.amUnique" ── Error ('test-amExample1.R:57:5'): amExample1 from pg 5 in allelematchSuppDoc.pdf is 2.5.3 compatible ── Error in `summary.amUnique(uniqueExample1, csv = summaryFile <- tempfile("example1_1.csv"))`: could not find function "summary.amUnique" ── Failure ('test-amExample2.R:36:9'): amExample2 results from pg 8 in allelematchSuppDoc.pdf 2.5.3 compatible ── Expected some element of `output` to match regexp "allelematch: assuming genotype columns are in pairs, representing 10 loci$". Actual text: x | allelematch: assuming genotype columns are in pairs, representing 10 loci x | allelematch: amUnique: Clustering genotypes x | allelematch: amUnique: Comparing unique genotypes identified by clustering to all samples x | allelematch: amUnique: Determining allele frequencies of unique genotypes identified by cluster x | allelematch: amUnique: Finding Psib ── Error ('test-amExample2.R:42:9'): amExample2 results from pg 8 in allelematchSuppDoc.pdf 2.5.3 compatible ── Error in `summary.amUnique(uniqueExample2, csv = summaryFile <- tempfile("example2_1.csv"))`: could not find function "summary.amUnique" ── Failure ('test-amExample3.R:43:9'): amExample3 results from pg 10 in allelematchSuppDoc.pdf are 2.5.3 compatible ── Expected some element of `output` to match regexp "allelematch: assuming genotype columns are in pairs, representing 10 loci$". Actual text: x | allelematch: assuming genotype columns are in pairs, representing 10 loci x | allelematch: amUnique: Clustering genotypes x | allelematch: amUnique: Comparing unique genotypes identified by clustering to all samples x | allelematch: amUnique: Determining allele frequencies of unique genotypes identified by cluster x | allelematch: amUnique: Finding Psib ── Error ('test-amExample3.R:49:9'): amExample3 results from pg 10 in allelematchSuppDoc.pdf are 2.5.3 compatible ── Error in `summary.amUnique(uniqueExample3, csv = summaryFile <- tempfile("example3_1.csv"))`: could not find function "summary.amUnique" ── Failure ('test-amExample4.R:42:9'): amExample4 results from pg 14 in allelematchSuppDoc.pdf are 2.5.3 compatible ── Expected some element of `output` to match regexp "allelematch: assuming genotype columns are in pairs, representing 10 loci$". Actual text: x | allelematch: assuming genotype columns are in pairs, representing 10 loci x | allelematch: amUnique: Clustering genotypes x | allelematch: amUnique: Comparing unique genotypes identified by clustering to all samples x | allelematch: amUnique: Determining allele frequencies of unique genotypes identified by cluster x | allelematch: amUnique: Finding Psib ── Error ('test-amExample4.R:48:9'): amExample4 results from pg 14 in allelematchSuppDoc.pdf are 2.5.3 compatible ── Error in `summary.amUnique(uniqueExample4, csv = summaryFile <- tempfile("example4_1.csv"))`: could not find function "summary.amUnique" ── Error ('test-ggData.R:42:9'): amUnique(matchThreshold=0.9) for dataset ggSample ── Error in `summary.amUnique(obj, csv = tmp)`: could not find function "summary.amUnique" Backtrace: ▆ 1. └─amregtest (local) snapshot_amUnique("ggDataset", matchThreshold = 0.9) at test-ggData.R:66:5 [ FAIL 18 | WARN 0 | SKIP 7 | PASS 64 ] Error: ! Test failures. Execution halted