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Type 'q()' to quit R. > # 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(serosv) > > test_check("serosv") Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not SAMPLING FOR MODEL 'prevalence_correction' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.0001 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup) Chain 1: Iteration: 200 / 2000 [ 10%] (Warmup) Chain 1: Iteration: 400 / 2000 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2000 [ 25%] (Sampling) Chain 1: Iteration: 700 / 2000 [ 35%] (Sampling) Chain 1: Iteration: 900 / 2000 [ 45%] (Sampling) Chain 1: Iteration: 1100 / 2000 [ 55%] (Sampling) Chain 1: Iteration: 1300 / 2000 [ 65%] (Sampling) Chain 1: Iteration: 1500 / 2000 [ 75%] (Sampling) Chain 1: Iteration: 1700 / 2000 [ 85%] (Sampling) Chain 1: Iteration: 1900 / 2000 [ 95%] (Sampling) Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 0.598 seconds (Warm-up) Chain 1: 0.838 seconds (Sampling) Chain 1: 1.436 seconds (Total) Chain 1: SAMPLING FOR MODEL 'fra_2' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 5.6e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.56 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup) Chain 1: Iteration: 200 / 2000 [ 10%] (Warmup) Chain 1: Iteration: 400 / 2000 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2000 [ 25%] (Sampling) Chain 1: Iteration: 700 / 2000 [ 35%] (Sampling) Chain 1: Iteration: 900 / 2000 [ 45%] (Sampling) Chain 1: Iteration: 1100 / 2000 [ 55%] (Sampling) Chain 1: Iteration: 1300 / 2000 [ 65%] (Sampling) Chain 1: Iteration: 1500 / 2000 [ 75%] (Sampling) Chain 1: Iteration: 1700 / 2000 [ 85%] (Sampling) Chain 1: Iteration: 1900 / 2000 [ 95%] (Sampling) Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 1.462 seconds (Warm-up) Chain 1: 0.89 seconds (Sampling) Chain 1: 2.352 seconds (Total) Chain 1: SAMPLING FOR MODEL 'fra_3' NOW (CHAIN 1). Chain 1: Rejecting initial value: Chain 1: Log probability evaluates to log(0), i.e. negative infinity. Chain 1: Stan can't start sampling from this initial value. Chain 1: Rejecting initial value: Chain 1: Log probability evaluates to log(0), i.e. negative infinity. Chain 1: Stan can't start sampling from this initial value. Chain 1: Rejecting initial value: Chain 1: Log probability evaluates to log(0), i.e. negative infinity. Chain 1: Stan can't start sampling from this initial value. Chain 1: Chain 1: Gradient evaluation took 7.4e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.74 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup) Chain 1: Iteration: 200 / 2000 [ 10%] (Warmup) Chain 1: Iteration: 400 / 2000 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2000 [ 25%] (Sampling) Chain 1: Iteration: 700 / 2000 [ 35%] (Sampling) Chain 1: Iteration: 900 / 2000 [ 45%] (Sampling) Chain 1: Iteration: 1100 / 2000 [ 55%] (Sampling) Chain 1: Iteration: 1300 / 2000 [ 65%] (Sampling) Chain 1: Iteration: 1500 / 2000 [ 75%] (Sampling) Chain 1: Iteration: 1700 / 2000 [ 85%] (Sampling) Chain 1: Iteration: 1900 / 2000 [ 95%] (Sampling) Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 3.044 seconds (Warm-up) Chain 1: 5.326 seconds (Sampling) Chain 1: 8.37 seconds (Total) Chain 1: SAMPLING FOR MODEL 'log_logistic' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 4.2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup) Chain 1: Iteration: 200 / 2000 [ 10%] (Warmup) Chain 1: Iteration: 400 / 2000 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2000 [ 25%] (Sampling) Chain 1: Iteration: 700 / 2000 [ 35%] (Sampling) Chain 1: Iteration: 900 / 2000 [ 45%] (Sampling) Chain 1: Iteration: 1100 / 2000 [ 55%] (Sampling) Chain 1: Iteration: 1300 / 2000 [ 65%] (Sampling) Chain 1: Iteration: 1500 / 2000 [ 75%] (Sampling) Chain 1: Iteration: 1700 / 2000 [ 85%] (Sampling) Chain 1: Iteration: 1900 / 2000 [ 95%] (Sampling) Chain 1: Iteration: 2000 / 2000 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 0.908 seconds (Warm-up) Chain 1: 0.375 seconds (Sampling) Chain 1: 1.283 seconds (Total) Chain 1: Maximum number of PQL iterations: 20 iteration 1 iteration 2 iteration 3 iteration 4 Maximum number of PQL iterations: 20 iteration 1 iteration 2 iteration 3 iteration 4 [ FAIL 0 | WARN 2 | SKIP 0 | PASS 54 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 54 ] > > proc.time() user system elapsed 70.32 3.76 74.07