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Type 'q()' to quit R. > library(testthat) > library(mvMAPIT) > > test_check("mvMAPIT") 2026-02-20 23:18:51.946649 DEBUG:mvmapit:Running in normal test mode. 2026-02-20 23:18:51.956419 DEBUG:mvmapit:Genotype matrix: 2 x 10 2026-02-20 23:18:51.964574 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2026-02-20 23:18:51.965992 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-20 23:18:51.967321 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2026-02-20 23:18:51.968496 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-20 23:18:51.9701 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:51.971812 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2026-02-20 23:18:52.093449 DEBUG:mvmapit:Running in normal test mode. 2026-02-20 23:18:52.095029 DEBUG:mvmapit:Genotype matrix: 2 x 10 2026-02-20 23:18:52.096259 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2026-02-20 23:18:52.097544 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-20 23:18:52.098823 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2026-02-20 23:18:52.100009 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-20 23:18:52.101628 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:52.102934 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2026-02-20 23:18:52.15476 DEBUG:mvmapit:Running in normal test mode. 2026-02-20 23:18:52.156251 DEBUG:mvmapit:Genotype matrix: 2 x 10 2026-02-20 23:18:52.157453 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2026-02-20 23:18:52.158692 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-20 23:18:52.159936 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2026-02-20 23:18:52.161088 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-20 23:18:52.16249 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:52.163767 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:52.468595 DEBUG:mvmapit:Running in normal test mode. 2026-02-20 23:18:52.47043 DEBUG:mvmapit:Genotype matrix: 2 x 10 2026-02-20 23:18:52.471808 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2026-02-20 23:18:52.47326 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-20 23:18:52.47467 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2026-02-20 23:18:52.476045 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-20 23:18:52.477717 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:52.479255 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2026-02-20 23:18:52.531097 INFO:mvmapit:Running davies C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:52.586992 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:52.588208 INFO:mvmapit:0 p-values of variance components are significant with alpha = 0.050000 2026-02-20 23:18:52.589252 INFO:mvmapit:0 positions are significant with alpha = 0.050000 2026-02-20 23:18:52.590209 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 2026-02-20 23:18:52.853336 DEBUG:mvmapit:Running in hybrid test mode. 2026-02-20 23:18:52.854966 DEBUG:mvmapit:Genotype matrix: 2 x 10 2026-02-20 23:18:52.856202 DEBUG:mvmapit:Phenotype matrix: 1 x 10 2026-02-20 23:18:52.857459 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-20 23:18:52.858713 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2026-02-20 23:18:52.859899 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-20 23:18:52.861304 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:52.862458 INFO:mvmapit:0 p-values of variance components are significant with alpha = 0.050000 2026-02-20 23:18:52.863475 INFO:mvmapit:0 positions are significant with alpha = 0.050000 2026-02-20 23:18:52.864414 INFO:mvmapit:Running davies C++ routine on selected SNPs. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:52.867884 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:52.969871 DEBUG:mvmapit:Running in normal test mode. 2026-02-20 23:18:52.971403 DEBUG:mvmapit:Genotype matrix: 20 x 10 2026-02-20 23:18:52.972646 DEBUG:mvmapit:Phenotype matrix: 2 x 10 2026-02-20 23:18:52.974059 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-20 23:18:52.975487 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 20 x 10 2026-02-20 23:18:52.976688 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-20 23:18:52.978417 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:52.979899 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2026-02-20 23:18:53.784587 DEBUG:mvmapit:Running in normal test mode. 2026-02-20 23:18:53.786179 DEBUG:mvmapit:Genotype matrix: 3 x 10 2026-02-20 23:18:53.787413 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2026-02-20 23:18:53.788716 DEBUG:mvmapit:Number of zero variance variants: 0 2026-02-20 23:18:53.789986 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 3 x 10 2026-02-20 23:18:53.791162 DEBUG:mvmapit:Scale X matrix appropriately. 2026-02-20 23:18:53.792602 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2026-02-20 23:18:53.793897 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2026-02-20 23:18:53.795194 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 2.62 0.34 2.90