* using log directory ‘/Users/ripley/R/packages/tests-devel/mispitools.Rcheck’ * using R Under development (unstable) (2026-08-25 r90447) * using platform: aarch64-apple-darwin25.6.0 * R was compiled by Apple clang version 21.0.0 (clang-2100.1.1.101) GNU Fortran (GCC) 14.2.0 * running under: macOS Tahoe 26.6.2 * using session charset: UTF-8 * current time: 2026-08-26 06:39:03 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘mispitools/DESCRIPTION’ ... OK * this is package ‘mispitools’ version ‘2.0.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘mispitools’ can be installed ... [20s/20s] OK * used C++ compiler: ‘Apple clang version 21.0.0 (clang-2100.1.1.101)’ * used SDK: ‘MacOSX26.5.sdk’ * checking C++ specification ... INFO specified C++17 * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [19s/19s] [19s/19s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(mispitools) > > test_check("mispitools") 3 atoms; E[log10 LR | H1] = 1.1 log10_lr p_h1 p_h2 -1 0.1 0.6 0 0.3 0.3 2 0.6 0.1 Saving _problems/test-lr-distribution-85.R Saving _problems/test-lr-distribution-86.R Saving _problems/test-lr-distribution-87.R Saving _problems/test-lr-distribution-88.R Saving _problems/test-lr-distribution-87.R Saving _problems/test-lr-distribution-88.R Saving _problems/test-lr-distribution-85.R Saving _problems/test-lr-distribution-86.R Saving _problems/test-lr-distribution-87.R Saving _problems/test-lr-distribution-88.R Saving _problems/test-lr-distribution-103.R Saving _problems/test-lr-distribution-104.R Saving _problems/test-lr-distribution-105.R marker_id : M1 alleles : 3 (12, 13, 14) mutation : none linkage : none pedigree : 3 individuals type : sex (categorical) observed : F categories : 2 (F, M) reference : marginal error : eps=0.05 Saving _problems/test-per-marker-lr-dist-cpp-141.R Saving _problems/test-per-marker-lr-dist-cpp-141.R Saving _problems/test-per-marker-lr-dist-cpp-151.R Saving _problems/test-per-marker-lr-dist-cpp-151.R Saving _problems/test-per-marker-lr-dist-cpp-151.R Saving _problems/test-per-marker-lr-dist-cpp-151.R Saving _problems/test-per-marker-lr-dist-cpp-174.R Saving _problems/test-per-marker-lr-dist-cpp-174.R Saving _problems/test-per-marker-lr-dist-cpp-174.R Saving _problems/test-per-marker-lr-dist-cpp-174.R [ FAIL 23 | WARN 0 | SKIP 23 | PASS 2446 ] ══ Skipped tests (23) ══════════════════════════════════════════════════════════ • On CRAN (20): 'test-core-modules.R:50:3', 'test-core-modules.R:68:3', 'test-fragility-tools.R:63:3', 'test-vs-pedprobr-cpp.R:108:11', 'test-vs-pedprobr-cpp.R:108:11', 'test-vs-pedprobr-cpp.R:108:11', 'test-vs-pedprobr-cpp.R:108:11', 'test-vs-pedprobr-cpp.R:108:11', 'test-vs-pedprobr-cpp.R:108:11', 'test-vs-pedprobr-linked-mut.R:176:3', 'test-vs-pedprobr-linked-mut.R:248:3', 'test-vs-pedprobr.R:78:9', 'test-vs-pedprobr.R:78:9', 'test-vs-pedprobr.R:78:9', 'test-vs-pedprobr.R:78:9', 'test-vs-pedprobr.R:78:9', 'test-vs-pedprobr.R:78:9', 'test-vs-pedprobr.R:78:9', 'test-vs-pedprobr.R:78:9', 'test-vs-pedprobr.R:78:9' • package built without OpenMP (SHLIB_OPENMP_CXXFLAGS empty) (1): 'test-openmp.R:32:5' • {forensIT} is not installed (2): 'test-vs-forensit-public.R:335:3', 'test-vs-forensit.R:232:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-lr-distribution.R:85:5'): multi-marker exact composition matches lr_dist_compose_R ── Expected `nrow(d)` to equal `nrow(ref)`. Differences: 1/1 mismatches [1] 7257 - 7138 == 119 ── Failure ('test-lr-distribution.R:86:5'): multi-marker exact composition matches lr_dist_compose_R ── Expected `d$log10_lr` to equal `ref$log10_lr`. Differences: Lengths differ: 7257 is not 7138 ── Failure ('test-lr-distribution.R:87:5'): multi-marker exact composition matches lr_dist_compose_R ── Expected `d$p_h1` to equal `ref$p_h1`. Differences: Lengths differ: 7257 is not 7138 ── Failure ('test-lr-distribution.R:88:5'): multi-marker exact composition matches lr_dist_compose_R ── Expected `d$p_h2` to equal `ref$p_h2`. Differences: Lengths differ: 7257 is not 7138 ── Failure ('test-lr-distribution.R:87:5'): multi-marker exact composition matches lr_dist_compose_R ── Expected `d$p_h1` to equal `ref$p_h1`. Differences: 13427/36300 mismatches (average diff: 5.28e-06) [1484] 3.22e-11 - 3.07e-11 == 1.49e-12 [1485] 4.51e-12 - 5.86e-12 == -1.35e-12 [1498] 2.71e-12 - 6.11e-12 == -3.39e-12 [1500] 2.34e-11 - 1.99e-11 == 3.43e-12 [1508] 2.47e-11 - 2.34e-11 == 1.23e-12 [1510] 1.88e-12 - 3.52e-12 == -1.64e-12 [1525] 1.57e-10 - 1.71e-10 == -1.35e-11 [1526] 2.83e-11 - 2.53e-11 == 2.97e-12 [1527] 5.33e-11 - 4.27e-11 == 1.06e-11 ... ── Failure ('test-lr-distribution.R:88:5'): multi-marker exact composition matches lr_dist_compose_R ── Expected `d$p_h2` to equal `ref$p_h2`. Differences: 15458/36300 mismatches (average diff: 3.81e-06) [20] 1.57e-05 - 1.57e-05 == 3.12e-08 [21] 3.01e-06 - 3.04e-06 == -3.12e-08 [25] 1.04e-05 - 1.04e-05 == 1.86e-10 [26] 2.24e-07 - 2.24e-07 == -1.86e-10 [33] 2.52e-05 - 2.56e-05 == -3.29e-07 [34] 1.77e-06 - 1.44e-06 == 3.29e-07 [39] 4.23e-06 - 4.34e-06 == -1.12e-07 [40] 4.89e-06 - 4.78e-06 == 1.12e-07 [42] 7.01e-07 - 7.25e-07 == -2.44e-08 ... ── Failure ('test-lr-distribution.R:85:5'): multi-marker exact composition matches lr_dist_compose_R ── Expected `nrow(d)` to equal `nrow(ref)`. Differences: 1/1 mismatches [1] 37203 - 37108 == 95 ── Failure ('test-lr-distribution.R:86:5'): multi-marker exact composition matches lr_dist_compose_R ── Expected `d$log10_lr` to equal `ref$log10_lr`. Differences: Lengths differ: 37203 is not 37108 ── Failure ('test-lr-distribution.R:87:5'): multi-marker exact composition matches lr_dist_compose_R ── Expected `d$p_h1` to equal `ref$p_h1`. Differences: Lengths differ: 37203 is not 37108 ── Failure ('test-lr-distribution.R:88:5'): multi-marker exact composition matches lr_dist_compose_R ── Expected `d$p_h2` to equal `ref$p_h2`. Differences: Lengths differ: 37203 is not 37108 ── Failure ('test-lr-distribution.R:103:3'): Argentina markers compose against the reference ── Expected `d$log10_lr` to equal `ref$log10_lr`. Differences: Lengths differ: 10651 is not 10429 ── Failure ('test-lr-distribution.R:104:3'): Argentina markers compose against the reference ── Expected `d$p_h1` to equal `ref$p_h1`. Differences: Lengths differ: 10651 is not 10429 ── Failure ('test-lr-distribution.R:105:3'): Argentina markers compose against the reference ── Expected `d$p_h2` to equal `ref$p_h2`. Differences: Lengths differ: 10651 is not 10429 ── Failure ('test-per-marker-lr-dist-cpp.R:141:3'): cpp_per_marker_lr_dist matches R-ref on halfSibPed K=3 mut=equal ── Expected `cpp$p_h1` to equal `ref$p_h1`. Differences: 18/100 mismatches (average diff: 0.000796) [14] 8.11e-05 - 9.33e-05 == -1.22e-05 [15] 2.78e-04 - 2.65e-04 == 1.22e-05 [18] 2.19e-04 - 2.07e-04 == 1.16e-05 [20] 1.16e-05 - 2.32e-05 == -1.16e-05 [26] 6.07e-04 - 6.22e-04 == -1.45e-05 [27] 1.08e-03 - 1.07e-03 == 1.45e-05 [31] 1.35e-03 - 1.34e-03 == 1.15e-05 [33] 2.00e-04 - 2.11e-04 == -1.15e-05 [41] 7.82e-04 - 7.96e-04 == -1.45e-05 ... halfSibPed K=3 mut=equal Backtrace: ▆ 1. └─mispitools (local) expect_lrdist_equal(cpp, ref, info = "halfSibPed K=3 mut=equal") at test-per-marker-lr-dist-cpp.R:141:3 2. └─testthat::expect_equal(cpp$p_h1, ref$p_h1, tolerance = tol, info = info) at test-per-marker-lr-dist-cpp.R:28:3 ── Failure ('test-per-marker-lr-dist-cpp.R:141:3'): cpp_per_marker_lr_dist matches R-ref on halfSibPed K=3 mut=equal ── Expected `cpp$p_h2` to equal `ref$p_h2`. Differences: 18/100 mismatches (average diff: 0.000875) [14] 0.007749 - 0.00891 == -0.001166 [15] 0.026521 - 0.02535 == 0.001166 [18] 0.015661 - 0.01483 == 0.000829 [20] 0.000829 - 0.00166 == -0.000829 [26] 0.029303 - 0.03000 == -0.000700 [27] 0.052189 - 0.05149 == 0.000700 [31] 0.048956 - 0.04854 == 0.000415 [33] 0.007237 - 0.00765 == -0.000415 [41] 0.025234 - 0.02570 == -0.000467 ... halfSibPed K=3 mut=equal Backtrace: ▆ 1. └─mispitools (local) expect_lrdist_equal(cpp, ref, info = "halfSibPed K=3 mut=equal") at test-per-marker-lr-dist-cpp.R:141:3 2. └─testthat::expect_equal(cpp$p_h2, ref$p_h2, tolerance = tol, info = info) at test-per-marker-lr-dist-cpp.R:29:3 ── Failure ('test-per-marker-lr-dist-cpp.R:151:3'): cpp_per_marker_lr_dist matches R-ref on linearPed(2) mut=stepwise ── Expected `length(cpp$log10_lr)` to equal `nrow(ref)`. Differences: 1/1 mismatches [1] 188 - 186 == 2 linearPed(2) K=3 mut=stepwise Backtrace: ▆ 1. └─mispitools (local) expect_lrdist_equal(cpp, ref, info = "linearPed(2) K=3 mut=stepwise") at test-per-marker-lr-dist-cpp.R:151:3 2. └─testthat::expect_equal(length(cpp$log10_lr), nrow(ref), info = info) at test-per-marker-lr-dist-cpp.R:26:3 ── Failure ('test-per-marker-lr-dist-cpp.R:151:3'): cpp_per_marker_lr_dist matches R-ref on linearPed(2) mut=stepwise ── Expected `cpp$log10_lr` to equal `ref$log10_lr`. Differences: Lengths differ: 188 is not 186 linearPed(2) K=3 mut=stepwise Backtrace: ▆ 1. └─mispitools (local) expect_lrdist_equal(cpp, ref, info = "linearPed(2) K=3 mut=stepwise") at test-per-marker-lr-dist-cpp.R:151:3 2. └─testthat::expect_equal(...) at test-per-marker-lr-dist-cpp.R:27:3 ── Failure ('test-per-marker-lr-dist-cpp.R:151:3'): cpp_per_marker_lr_dist matches R-ref on linearPed(2) mut=stepwise ── Expected `cpp$p_h1` to equal `ref$p_h1`. Differences: Lengths differ: 188 is not 186 linearPed(2) K=3 mut=stepwise Backtrace: ▆ 1. └─mispitools (local) expect_lrdist_equal(cpp, ref, info = "linearPed(2) K=3 mut=stepwise") at test-per-marker-lr-dist-cpp.R:151:3 2. └─testthat::expect_equal(cpp$p_h1, ref$p_h1, tolerance = tol, info = info) at test-per-marker-lr-dist-cpp.R:28:3 ── Failure ('test-per-marker-lr-dist-cpp.R:151:3'): cpp_per_marker_lr_dist matches R-ref on linearPed(2) mut=stepwise ── Expected `cpp$p_h2` to equal `ref$p_h2`. Differences: Lengths differ: 188 is not 186 linearPed(2) K=3 mut=stepwise Backtrace: ▆ 1. └─mispitools (local) expect_lrdist_equal(cpp, ref, info = "linearPed(2) K=3 mut=stepwise") at test-per-marker-lr-dist-cpp.R:151:3 2. └─testthat::expect_equal(cpp$p_h2, ref$p_h2, tolerance = tol, info = info) at test-per-marker-lr-dist-cpp.R:29:3 ── Failure ('test-per-marker-lr-dist-cpp.R:174:3'): cpp_per_marker_lr_dist matches R-ref on trio K=4 mut=stepwise ── Expected `length(cpp$log10_lr)` to equal `nrow(ref)`. Differences: 1/1 mismatches [1] 523 - 519 == 4 trio K=4 mut=stepwise Backtrace: ▆ 1. └─mispitools (local) expect_lrdist_equal(cpp, ref, info = "trio K=4 mut=stepwise") at test-per-marker-lr-dist-cpp.R:174:3 2. └─testthat::expect_equal(length(cpp$log10_lr), nrow(ref), info = info) at test-per-marker-lr-dist-cpp.R:26:3 ── Failure ('test-per-marker-lr-dist-cpp.R:174:3'): cpp_per_marker_lr_dist matches R-ref on trio K=4 mut=stepwise ── Expected `cpp$log10_lr` to equal `ref$log10_lr`. Differences: Lengths differ: 523 is not 519 trio K=4 mut=stepwise Backtrace: ▆ 1. └─mispitools (local) expect_lrdist_equal(cpp, ref, info = "trio K=4 mut=stepwise") at test-per-marker-lr-dist-cpp.R:174:3 2. └─testthat::expect_equal(...) at test-per-marker-lr-dist-cpp.R:27:3 ── Failure ('test-per-marker-lr-dist-cpp.R:174:3'): cpp_per_marker_lr_dist matches R-ref on trio K=4 mut=stepwise ── Expected `cpp$p_h1` to equal `ref$p_h1`. Differences: Lengths differ: 523 is not 519 trio K=4 mut=stepwise Backtrace: ▆ 1. └─mispitools (local) expect_lrdist_equal(cpp, ref, info = "trio K=4 mut=stepwise") at test-per-marker-lr-dist-cpp.R:174:3 2. └─testthat::expect_equal(cpp$p_h1, ref$p_h1, tolerance = tol, info = info) at test-per-marker-lr-dist-cpp.R:28:3 ── Failure ('test-per-marker-lr-dist-cpp.R:174:3'): cpp_per_marker_lr_dist matches R-ref on trio K=4 mut=stepwise ── Expected `cpp$p_h2` to equal `ref$p_h2`. Differences: Lengths differ: 523 is not 519 trio K=4 mut=stepwise Backtrace: ▆ 1. └─mispitools (local) expect_lrdist_equal(cpp, ref, info = "trio K=4 mut=stepwise") at test-per-marker-lr-dist-cpp.R:174:3 2. └─testthat::expect_equal(cpp$p_h2, ref$p_h2, tolerance = tol, info = info) at test-per-marker-lr-dist-cpp.R:29:3 [ FAIL 23 | WARN 0 | SKIP 23 | PASS 2446 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [13s/13s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/Users/ripley/R/packages/tests-devel/mispitools.Rcheck/00check.log’ for details. 109.76 real 88.31 user 16.19 sys