* using log directory 'd:/RCompile/CRANincoming/R-devel/amregtest.Rcheck' * using R Under development (unstable) (2026-06-23 r90186 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-06-24 09:30:28 UTC * checking for file 'amregtest/DESCRIPTION' ... OK * this is package 'amregtest' version '1.0.6' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [11s] OK * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'amregtest' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [488s] ERROR Running 'testthat.R' [487s] 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. 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) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=1) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=2) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataMini, cutHeight=1, doPsib="missing", consensusMethod=4) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=1) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=2) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataMini, cutHeight=1, doPsib="all", consensusMethod=4) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=1) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=2) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="missing", consensusMethod=4) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=1) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=2) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample1, cutHeight=0.9, doPsib="all", consensusMethod=4) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample4, cutHeight=0.7, doPsib="missing", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample4, cutHeight=0.7, doPsib="all", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample4, cutHeight=0.9, doPsib="missing", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample4, cutHeight=0.9, doPsib="all", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample4, cutHeight=0.95, doPsib="missing", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample4, cutHeight=0.95, doPsib="all", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample4, cutHeight=0.99, doPsib="missing", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample4, cutHeight=0.99, doPsib="all", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample4, cutHeight=1, doPsib="missing", consensusMethod=3) Error : allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Rejected : amUnique(amdataExample4, cutHeight=1, doPsib="all", consensusMethod=3) [ FAIL 1 | WARN 8 | SKIP 20 | PASS 164 ] ══ Skipped tests (20) ══════════════════════════════════════════════════════════ • On CRAN (20): 'test-allelematch_1-amDataset.R:32:1', 'test-allelematch_1-amDataset.R:132:1', '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:47:5'): Validation of arguments to amUnique() is working ── Error: allelematch: amCluster: no clusters formed. Please set cutHeight lower and run again. Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-allelematch_6-amUnique_negative.R:47:5 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, alleleMismatch = 5) 8. └─allelematch::amCluster(...) [ FAIL 1 | WARN 8 | SKIP 20 | PASS 164 ] Error: ! Test failures. Cleaning up 4 leaked TEMP file(s): D:\temp\2026_06_24_11_30_17_999\RtmpKeemFz/amPairwise_Y8LUCKAH.htm D:\temp\2026_06_24_11_30_17_999\RtmpKeemFz/amCluster_7E3B9I4P.htm D:\temp\2026_06_24_11_30_17_999\RtmpKeemFz/amUnique_GVLEWBOF.htm D:\temp\2026_06_24_11_30_17_999\RtmpKeemFz/pdf4ddc5aff2c10 Execution halted Warning message: In file.remove(to_remove) : cannot remove file 'D:\temp\2026_06_24_11_30_17_999\RtmpKeemFz/pdf4ddc5aff2c10', reason 'Permission denied' * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR