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Type 'q()' to quit R. > library(testthat) > library(mvMAPIT) > > test_check("mvMAPIT") 2026-02-21 00:28:46.068829 DEBUG:mvmapit:Running in normal test mode. 2026-02-21 00:28:46.078845 DEBUG:mvmapit:Genotype matrix: 2 x 10 2026-02-21 00:28:46.086922 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2026-02-21 00:28:46.088292 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-21 00:28:46.089617 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2026-02-21 00:28:46.090818 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-21 00:28:46.092413 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:46.093953 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2026-02-21 00:28:46.215299 DEBUG:mvmapit:Running in normal test mode. 2026-02-21 00:28:46.216894 DEBUG:mvmapit:Genotype matrix: 2 x 10 2026-02-21 00:28:46.218135 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2026-02-21 00:28:46.219421 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-21 00:28:46.220702 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2026-02-21 00:28:46.2219 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-21 00:28:46.223348 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:46.224655 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2026-02-21 00:28:46.276824 DEBUG:mvmapit:Running in normal test mode. 2026-02-21 00:28:46.278363 DEBUG:mvmapit:Genotype matrix: 2 x 10 2026-02-21 00:28:46.279575 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2026-02-21 00:28:46.280837 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-21 00:28:46.282087 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2026-02-21 00:28:46.283247 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-21 00:28:46.284642 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:46.285916 DEBUG:mvmapit:Calculated mean time of execution. Return list. # A tibble: 2 × 3 id trait p 1 1 cauchy 0.719 2 2 cauchy 0.349 # A tibble: 2 × 3 id trait p 1 1 cauchy 0.719 2 2 cauchy 0.349 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:46.598091 DEBUG:mvmapit:Running in normal test mode. 2026-02-21 00:28:46.599909 DEBUG:mvmapit:Genotype matrix: 2 x 10 2026-02-21 00:28:46.601257 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2026-02-21 00:28:46.602661 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-21 00:28:46.604059 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2026-02-21 00:28:46.605344 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-21 00:28:46.606972 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:46.608445 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2026-02-21 00:28:46.660795 INFO:mvmapit:Running davies C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:46.716526 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:46.717739 INFO:mvmapit:0 p-values of variance components are significant with alpha = 0.050000 2026-02-21 00:28:46.718785 INFO:mvmapit:0 positions are significant with alpha = 0.050000 2026-02-21 00:28:46.719734 INFO:mvmapit:Running davies C++ routine on selected SNPs. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ************ warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ************* warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ************ warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric *************| warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ************ warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ************* warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ************ warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric *************| warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ***** warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ***** warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ***** warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ***** warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ***** warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ***** warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ***** warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ***** warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric ***** warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric *****| warning: eig_sym(): given matrix is not symmetric warning: eig_sym(): given matrix is not symmetric 2026-02-21 00:28:46.969971 DEBUG:mvmapit:Running in hybrid test mode. 2026-02-21 00:28:46.971666 DEBUG:mvmapit:Genotype matrix: 2 x 10 2026-02-21 00:28:46.972966 DEBUG:mvmapit:Phenotype matrix: 1 x 10 2026-02-21 00:28:46.974237 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-21 00:28:46.975497 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2026-02-21 00:28:46.976669 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-21 00:28:46.978067 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:46.979217 INFO:mvmapit:0 p-values of variance components are significant with alpha = 0.050000 2026-02-21 00:28:46.980231 INFO:mvmapit:0 positions are significant with alpha = 0.050000 2026-02-21 00:28:46.981202 INFO:mvmapit:Running davies C++ routine on selected SNPs. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:46.984663 DEBUG:mvmapit:Calculated mean time of execution. Return list. # A tibble: 2 × 3 id trait p 1 1 P1 0.499 2 2 P1 0.502 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:47.08634 DEBUG:mvmapit:Running in normal test mode. 2026-02-21 00:28:47.087873 DEBUG:mvmapit:Genotype matrix: 20 x 10 2026-02-21 00:28:47.089095 DEBUG:mvmapit:Phenotype matrix: 2 x 10 2026-02-21 00:28:47.090547 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-21 00:28:47.091959 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 20 x 10 2026-02-21 00:28:47.093138 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-21 00:28:47.094835 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:47.096315 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2026-02-21 00:28:47.905229 DEBUG:mvmapit:Running in normal test mode. 2026-02-21 00:28:47.906866 DEBUG:mvmapit:Genotype matrix: 3 x 10 2026-02-21 00:28:47.908097 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2026-02-21 00:28:47.909387 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-21 00:28:47.910671 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 3 x 10 2026-02-21 00:28:47.911856 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-21 00:28:47.913309 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-21 00:28:47.91461 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2026-02-21 00:28:47.915911 DEBUG:mvmapit:Set pve to NA if not in varianIndex. [ FAIL 0 | WARN 1 | SKIP 1 | PASS 50 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-simulate_data.R:353:1' [ FAIL 0 | WARN 1 | SKIP 1 | PASS 50 ] > > proc.time() user system elapsed 2.57 0.35 2.92