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Type 'q()' to quit R. > library(testthat) > library(mvMAPIT) > > test_check("mvMAPIT") 2023-09-25 19:33:23.419681 DEBUG:mvmapit:Running in normal test mode. 2023-09-25 19:33:23.430105 DEBUG:mvmapit:Genotype matrix: 2 x 10 2023-09-25 19:33:23.438415 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2023-09-25 19:33:23.439803 DEBUG:mvmapit:Number of zero variance variants: 0 2023-09-25 19:33:23.441131 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2023-09-25 19:33:23.442302 DEBUG:mvmapit:Scale X matrix appropriately. 2023-09-25 19:33:23.44394 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.445496 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2023-09-25 19:33:23.501407 DEBUG:mvmapit:Running in normal test mode. 2023-09-25 19:33:23.503024 DEBUG:mvmapit:Genotype matrix: 2 x 10 2023-09-25 19:33:23.509858 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2023-09-25 19:33:23.511112 DEBUG:mvmapit:Number of zero variance variants: 0 2023-09-25 19:33:23.512354 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2023-09-25 19:33:23.513515 DEBUG:mvmapit:Scale X matrix appropriately. 2023-09-25 19:33:23.514898 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.516169 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2023-09-25 19:33:23.550326 DEBUG:mvmapit:Running in normal test mode. 2023-09-25 19:33:23.551816 DEBUG:mvmapit:Genotype matrix: 2 x 10 2023-09-25 19:33:23.553086 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2023-09-25 19:33:23.554329 DEBUG:mvmapit:Number of zero variance variants: 0 2023-09-25 19:33:23.555576 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2023-09-25 19:33:23.556728 DEBUG:mvmapit:Scale X matrix appropriately. 2023-09-25 19:33:23.558108 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.55937 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.701889 DEBUG:mvmapit:Running in normal test mode. 2023-09-25 19:33:23.703414 DEBUG:mvmapit:Genotype matrix: 2 x 10 2023-09-25 19:33:23.704554 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2023-09-25 19:33:23.705715 DEBUG:mvmapit:Number of zero variance variants: 0 2023-09-25 19:33:23.706882 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2023-09-25 19:33:23.707969 DEBUG:mvmapit:Scale X matrix appropriately. 2023-09-25 19:33:23.709281 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.710547 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2023-09-25 19:33:23.732543 INFO:mvmapit:Running davies C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.762092 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.763226 INFO:mvmapit:0 p-values of variance components are significant with alpha = 0.050000 2023-09-25 19:33:23.764184 INFO:mvmapit:0 positions are significant with alpha = 0.050000 2023-09-25 19:33:23.765047 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 2023-09-25 19:33:23.898894 DEBUG:mvmapit:Running in hybrid test mode. 2023-09-25 19:33:23.900445 DEBUG:mvmapit:Genotype matrix: 2 x 10 2023-09-25 19:33:23.901649 DEBUG:mvmapit:Phenotype matrix: 1 x 10 2023-09-25 19:33:23.902883 DEBUG:mvmapit:Number of zero variance variants: 0 2023-09-25 19:33:23.904126 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 2 x 10 2023-09-25 19:33:23.90528 DEBUG:mvmapit:Scale X matrix appropriately. 2023-09-25 19:33:23.906664 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.907818 INFO:mvmapit:0 p-values of variance components are significant with alpha = 0.050000 2023-09-25 19:33:23.908827 INFO:mvmapit:0 positions are significant with alpha = 0.050000 2023-09-25 19:33:23.909748 INFO:mvmapit:Running davies C++ routine on selected SNPs. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.913233 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.969077 DEBUG:mvmapit:Running in normal test mode. 2023-09-25 19:33:23.970617 DEBUG:mvmapit:Genotype matrix: 20 x 10 2023-09-25 19:33:23.971821 DEBUG:mvmapit:Phenotype matrix: 2 x 10 2023-09-25 19:33:23.97322 DEBUG:mvmapit:Number of zero variance variants: 0 2023-09-25 19:33:23.974743 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 20 x 10 2023-09-25 19:33:23.975911 DEBUG:mvmapit:Scale X matrix appropriately. 2023-09-25 19:33:23.977586 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:23.979084 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2023-09-25 19:33:24.881066 DEBUG:mvmapit:Running in normal test mode. 2023-09-25 19:33:24.882587 DEBUG:mvmapit:Genotype matrix: 3 x 10 2023-09-25 19:33:24.883787 DEBUG:mvmapit:Phenotype matrix: 3 x 10 2023-09-25 19:33:24.885041 DEBUG:mvmapit:Number of zero variance variants: 0 2023-09-25 19:33:24.886301 DEBUG:mvmapit:Genotype matrix after removing zero variance variants: 3 x 10 2023-09-25 19:33:24.887462 DEBUG:mvmapit:Scale X matrix appropriately. 2023-09-25 19:33:24.888853 INFO:mvmapit:Running normal C++ routine. 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 2023-09-25 19:33:24.890133 DEBUG:mvmapit:Calculated mean time of execution. Return list. 2023-09-25 19:33:24.89139 DEBUG:mvmapit:Set pve to NA if not in varianIndex. [ FAIL 0 | WARN 0 | SKIP 1 | PASS 46 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-simulate_data.R:353:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 46 ] > > proc.time() user system elapsed 2.29 0.25 2.54