Package: Cyclops Check: tests New result: ERROR Running ‘testthat.R’ [14s/17s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > test_check("Cyclops") Loading required package: Cyclops Sorting outcomes by stratumId and rowId Sorting covariates by covariateId, stratumId, and rowId Sparseness = 98.87 % Sorting covariates by covariateId and rowId Using cross-validation selector type byRow Performing 10-fold cross-validation [seed = 1744185802] with data partitions of sizes 100 100 100 100 100 100 100 100 100 100 Using 1 thread(s) Starting var = 0.0113 (default) Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #1 Rep #1 pred log like = -30.7941 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #2 Rep #1 pred log like = -35.7735 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #3 Rep #1 pred log like = -32.4429 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #4 Rep #1 pred log like = -37.4555 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #5 Rep #1 pred log like = -42.5695 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #6 Rep #1 pred log like = -35.7735 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #7 Rep #1 pred log like = -27.5291 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #8 Rep #1 pred log like = -30.7941 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #9 Rep #1 pred log like = -30.7941 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #10 Rep #1 pred log like = -25.9128 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #1 Rep #2 pred log like = -35.7735 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #2 Rep #2 pred log like = -37.4555 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #3 Rep #2 pred log like = -30.7941 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #4 Rep #2 pred log like = -27.5291 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #5 Rep #2 pred log like = -35.7735 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #6 Rep #2 pred log like = -29.1562 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #7 Rep #2 pred log like = -24.3071 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #8 Rep #2 pred log like = -39.1488 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #9 Rep #2 pred log like = -37.4555 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #10 Rep #2 pred log like = -32.4429 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #1 Rep #3 pred log like = -22.7119 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #2 Rep #3 pred log like = -34.1027 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #3 Rep #3 pred log like = -39.1488 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #4 Rep #3 pred log like = -35.7735 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #5 Rep #3 pred log like = -19.553 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #6 Rep #3 pred log like = -39.1488 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #7 Rep #3 pred log like = -39.1488 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #8 Rep #3 pred log like = -35.7735 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #9 Rep #3 pred log like = -34.1027 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #10 Rep #3 pred log like = -30.7941 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #1 Rep #4 pred log like = -29.1562 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #2 Rep #4 pred log like = -30.7941 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #3 Rep #4 pred log like = -35.7735 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #4 Rep #4 pred log like = -37.4555 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #5 Rep #4 pred log like = -40.8534 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #6 Rep #4 pred log like = -27.5291 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #7 Rep #4 pred log like = -35.7735 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #8 Rep #4 pred log like = -32.4429 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #9 Rep #4 pred log like = -34.1027 Running at Laplace(13.3038) None Grid-point #1 at 0.0113 Fold #10 Rep #4 pred log like = -25.9128 AvgPred = -32.9932 with stdev = 5.15082 Completed at 0.0113 Next point at 0.113 with value 0 and continue = 1 search[ 0.0113 ] = -32.9932(5.15082) Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #1 Rep #1 pred log like = -30.7941 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #2 Rep #1 pred log like = -35.7735 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #3 Rep #1 pred log like = -32.4429 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #4 Rep #1 pred log like = -37.4555 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #5 Rep #1 pred log like = -42.5695 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #6 Rep #1 pred log like = -35.7735 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #7 Rep #1 pred log like = -27.5291 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #8 Rep #1 pred log like = -30.7941 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #9 Rep #1 pred log like = -30.7941 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #10 Rep #1 pred log like = -25.9128 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #1 Rep #2 pred log like = -35.7735 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #2 Rep #2 pred log like = -37.4555 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #3 Rep #2 pred log like = -30.7941 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #4 Rep #2 pred log like = -27.5291 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #5 Rep #2 pred log like = -35.7735 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #6 Rep #2 pred log like = -29.1562 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #7 Rep #2 pred log like = -24.3071 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #8 Rep #2 pred log like = -39.1488 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #9 Rep #2 pred log like = -37.4555 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #10 Rep #2 pred log like = -32.4429 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #1 Rep #3 pred log like = -22.7119 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #2 Rep #3 pred log like = -34.1027 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #3 Rep #3 pred log like = -39.1488 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #4 Rep #3 pred log like = -35.7735 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #5 Rep #3 pred log like = -19.553 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #6 Rep #3 pred log like = -39.1488 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #7 Rep #3 pred log like = -39.1488 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #8 Rep #3 pred log like = -35.7735 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #9 Rep #3 pred log like = -34.1027 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #10 Rep #3 pred log like = -30.7941 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #1 Rep #4 pred log like = -29.1562 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #2 Rep #4 pred log like = -30.7941 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #3 Rep #4 pred log like = -35.7735 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #4 Rep #4 pred log like = -37.4555 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #5 Rep #4 pred log like = -40.8534 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #6 Rep #4 pred log like = -27.5291 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #7 Rep #4 pred log like = -35.7735 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #8 Rep #4 pred log like = -32.4429 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #9 Rep #4 pred log like = -34.1027 Running at Laplace(4.20703) None Grid-point #2 at 0.113 Fold #10 Rep #4 pred log like = -25.9128 AvgPred = -32.9932 with stdev = 5.15082 Completed at 0.113 Next point at 1.13 with value 0 and continue = 1 search[ 0.0113 ] = -32.9932(5.15082) search[ 0.113 ] = -32.9932(5.15082) Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #1 Rep #1 pred log like = -30.7513 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #2 Rep #1 pred log like = -35.6937 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #3 Rep #1 pred log like = -32.3382 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #4 Rep #1 pred log like = -37.4235 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #5 Rep #1 pred log like = -42.4299 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #6 Rep #1 pred log like = -35.7538 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #7 Rep #1 pred log like = -27.5073 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #8 Rep #1 pred log like = -30.7648 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #9 Rep #1 pred log like = -31.017 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #10 Rep #1 pred log like = -26.2544 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #1 Rep #2 pred log like = -35.6596 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #2 Rep #2 pred log like = -37.3669 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #3 Rep #2 pred log like = -30.7803 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #4 Rep #2 pred log like = -27.4369 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #5 Rep #2 pred log like = -36.5423 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #6 Rep #2 pred log like = -29.3542 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #7 Rep #2 pred log like = -24.2346 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #8 Rep #2 pred log like = -39.1995 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #9 Rep #2 pred log like = -37.3766 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #10 Rep #2 pred log like = -32.423 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #1 Rep #3 pred log like = -22.7105 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #2 Rep #3 pred log like = -34.055 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #3 Rep #3 pred log like = -39.1727 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #4 Rep #3 pred log like = -35.7816 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #5 Rep #3 pred log like = -19.5227 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #6 Rep #3 pred log like = -39.3361 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #7 Rep #3 pred log like = -39.1805 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #8 Rep #3 pred log like = -36.0765 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #9 Rep #3 pred log like = -33.9509 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #10 Rep #3 pred log like = -30.7023 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #1 Rep #4 pred log like = -29.1286 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #2 Rep #4 pred log like = -30.6331 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #3 Rep #4 pred log like = -35.614 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #4 Rep #4 pred log like = -37.4541 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #5 Rep #4 pred log like = -41.0545 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #6 Rep #4 pred log like = -27.4214 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #7 Rep #4 pred log like = -35.8173 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #8 Rep #4 pred log like = -32.423 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #9 Rep #4 pred log like = -34.2894 Running at Laplace(1.33038) None Grid-point #3 at 1.13 Fold #10 Rep #4 pred log like = -25.9245 AvgPred = -33.0139 with stdev = 5.16658 Completed at 1.13 Next point at 0.00113 with value 0 and continue = 1 search[ 0.0113 ] = -32.9932(5.15082) search[ 0.113 ] = -32.9932(5.15082) search[ 1.13 ] = -33.0139(5.16658) Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #1 Rep #1 pred log like = -30.7941 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #2 Rep #1 pred log like = -35.7735 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #3 Rep #1 pred log like = -32.4429 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #4 Rep #1 pred log like = -37.4555 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #5 Rep #1 pred log like = -42.5695 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #6 Rep #1 pred log like = -35.7735 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #7 Rep #1 pred log like = -27.5291 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #8 Rep #1 pred log like = -30.7941 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #9 Rep #1 pred log like = -30.7941 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #10 Rep #1 pred log like = -25.9128 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #1 Rep #2 pred log like = -35.7735 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #2 Rep #2 pred log like = -37.4555 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #3 Rep #2 pred log like = -30.7941 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #4 Rep #2 pred log like = -27.5291 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #5 Rep #2 pred log like = -35.7735 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #6 Rep #2 pred log like = -29.1562 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #7 Rep #2 pred log like = -24.3071 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #8 Rep #2 pred log like = -39.1488 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #9 Rep #2 pred log like = -37.4555 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #10 Rep #2 pred log like = -32.4429 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #1 Rep #3 pred log like = -22.7119 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #2 Rep #3 pred log like = -34.1027 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #3 Rep #3 pred log like = -39.1488 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #4 Rep #3 pred log like = -35.7735 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #5 Rep #3 pred log like = -19.553 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #6 Rep #3 pred log like = -39.1488 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #7 Rep #3 pred log like = -39.1488 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #8 Rep #3 pred log like = -35.7735 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #9 Rep #3 pred log like = -34.1027 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #10 Rep #3 pred log like = -30.7941 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #1 Rep #4 pred log like = -29.1562 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #2 Rep #4 pred log like = -30.7941 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #3 Rep #4 pred log like = -35.7735 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #4 Rep #4 pred log like = -37.4555 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #5 Rep #4 pred log like = -40.8534 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #6 Rep #4 pred log like = -27.5291 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #7 Rep #4 pred log like = -35.7735 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #8 Rep #4 pred log like = -32.4429 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #9 Rep #4 pred log like = -34.1027 Running at Laplace(42.0703) None Grid-point #4 at 0.00113 Fold #10 Rep #4 pred log like = -25.9128 AvgPred = -32.9932 with stdev = 5.15082 Completed at 0.00113 Next point at 0.000113 with value 0 and continue = 1 search[ 0.00113 ] = -32.9932(5.15082) search[ 0.0113 ] = -32.9932(5.15082) search[ 0.113 ] = -32.9932(5.15082) search[ 1.13 ] = -33.0139(5.16658) Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #1 Rep #1 pred log like = -30.7941 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #2 Rep #1 pred log like = -35.7735 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #3 Rep #1 pred log like = -32.4429 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #4 Rep #1 pred log like = -37.4555 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #5 Rep #1 pred log like = -42.5695 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #6 Rep #1 pred log like = -35.7735 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #7 Rep #1 pred log like = -27.5291 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #8 Rep #1 pred log like = -30.7941 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #9 Rep #1 pred log like = -30.7941 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #10 Rep #1 pred log like = -25.9128 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #1 Rep #2 pred log like = -35.7735 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #2 Rep #2 pred log like = -37.4555 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #3 Rep #2 pred log like = -30.7941 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #4 Rep #2 pred log like = -27.5291 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #5 Rep #2 pred log like = -35.7735 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #6 Rep #2 pred log like = -29.1562 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #7 Rep #2 pred log like = -24.3071 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #8 Rep #2 pred log like = -39.1488 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #9 Rep #2 pred log like = -37.4555 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #10 Rep #2 pred log like = -32.4429 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #1 Rep #3 pred log like = -22.7119 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #2 Rep #3 pred log like = -34.1027 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #3 Rep #3 pred log like = -39.1488 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #4 Rep #3 pred log like = -35.7735 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #5 Rep #3 pred log like = -19.553 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #6 Rep #3 pred log like = -39.1488 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #7 Rep #3 pred log like = -39.1488 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #8 Rep #3 pred log like = -35.7735 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #9 Rep #3 pred log like = -34.1027 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #10 Rep #3 pred log like = -30.7941 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #1 Rep #4 pred log like = -29.1562 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #2 Rep #4 pred log like = -30.7941 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #3 Rep #4 pred log like = -35.7735 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #4 Rep #4 pred log like = -37.4555 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #5 Rep #4 pred log like = -40.8534 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #6 Rep #4 pred log like = -27.5291 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #7 Rep #4 pred log like = -35.7735 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #8 Rep #4 pred log like = -32.4429 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #9 Rep #4 pred log like = -34.1027 Running at Laplace(133.038) None Grid-point #5 at 0.000113 Fold #10 Rep #4 pred log like = -25.9128 AvgPred = -32.9932 with stdev = 5.15082 Completed at 0.000113 Next point at 0.00225465 with value -32.9899 and continue = 0 search[ 0.000113 ] = -32.9932(5.15082) search[ 0.00113 ] = -32.9932(5.15082) search[ 0.0113 ] = -32.9932(5.15082) search[ 0.113 ] = -32.9932(5.15082) search[ 1.13 ] = -33.0139(5.16658) Maximum predicted log likelihood (-32.9899) estimated at: 0.00225465 (variance) 29.7835 (lambda) Fitting model at optimal hyperparameter Using prior: Laplace(29.7835) None Sorting outcomes by stratumId and rowId Sorting covariates by covariateId, stratumId, and rowId Sorting outcomes by stratumId, time (descending), y and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Sorting outcomes by stratumId, time (descending), y and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Sorting outcomes by stratumId, time (descending), y and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Sparseness = 75.595 % Sorting covariates by covariateId and rowId Sparseness = 98.96 % Sorting covariates by covariateId and rowId Sorting covariates by covariateId and rowId Sorting covariates by covariateId and rowId Sparseness = 98.96 % Sorting outcomes by rowId Sorting covariates by covariateId and rowId Sparseness = 75.475 % Sorting covariates by covariateId and rowId Sparseness = 75.805 % Sorting covariates by covariateId and rowId Sparseness = 75.15 % Sorting covariates by covariateId and rowId Sparseness = 76.5 % Sorting covariates by covariateId and rowId Sparseness = 76.4 % Sorting covariates by covariateId and rowId Analysis took 0.00893 secs ( 2.6e-05 ) Fitting model using clogit Analysis took 0.114 secs Sparseness = 76.4 % Sorting outcomes by stratumId, time (descending), y and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Sorting outcomes by stratumId, time (descending), y and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Sorting outcomes by stratumId, time (descending), y and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Analysis took 0.0104 secs ( 0.000124 ) Fitting model using coxpht Analysis took 0.00789 secs Using prior: None log post: -153.591 (-153.591 + 0) (iter:1, conv: 0.987315) log post: -140.356 (-140.356 + 0) (iter:2, conv: 0.418345) log post: -132.023 (-132.023 + 0) (iter:3, conv: 0.261265) log post: -126.384 (-126.384 + 0) (iter:4, conv: 0.18403) log post: -122.381 (-122.381 + 0) (iter:5, conv: 0.13696) log post: -119.443 (-119.443 + 0) (iter:6, conv: 0.106924) log post: -117.232 (-117.232 + 0) (iter:7, conv: 0.086332) log post: -115.533 (-115.533 + 0) (iter:8, conv: 0.0714192) log post: -114.208 (-114.208 + 0) (iter:9, conv: 0.0601726) log post: -113.161 (-113.161 + 0) (iter:10, conv: 0.0514226) log post: -112.324 (-112.324 + 0) (iter:11, conv: 0.0444455) log post: -111.651 (-111.651 + 0) (iter:12, conv: 0.0387701) log post: -111.103 (-111.103 + 0) (iter:13, conv: 0.0340776) log post: -110.656 (-110.656 + 0) (iter:14, conv: 0.0301443) log post: -110.289 (-110.289 + 0) (iter:15, conv: 0.0268092) log post: -109.985 (-109.985 + 0) (iter:16, conv: 0.0239533) log post: -109.734 (-109.734 + 0) (iter:17, conv: 0.0214871) log post: -109.524 (-109.524 + 0) (iter:18, conv: 0.0193415) log post: -109.349 (-109.349 + 0) (iter:19, conv: 0.017463) log post: -109.203 (-109.203 + 0) (iter:20, conv: 0.015809) log post: -109.08 (-109.08 + 0) (iter:21, conv: 0.0143454) log post: -108.976 (-108.976 + 0) (iter:22, conv: 0.0130446) log post: -108.889 (-108.889 + 0) (iter:23, conv: 0.011884) log post: -108.815 (-108.815 + 0) (iter:24, conv: 0.0108446) log post: -108.753 (-108.753 + 0) (iter:25, conv: 0.00991073) log post: -108.7 (-108.7 + 0) (iter:26, conv: 0.00906605) log post: -108.655 (-108.655 + 0) (iter:27, conv: 0.00830381) log post: -108.616 (-108.616 + 0) (iter:28, conv: 0.00761432) log post: -108.584 (-108.584 + 0) (iter:29, conv: 0.0069893) log post: -108.556 (-108.556 + 0) (iter:30, conv: 0.0064216) log post: -108.533 (-108.533 + 0) (iter:31, conv: 0.00590505) log post: -108.512 (-108.512 + 0) (iter:32, conv: 0.00543428) log post: -108.495 (-108.495 + 0) (iter:33, conv: 0.0050046) log post: -108.481 (-108.481 + 0) (iter:34, conv: 0.00461189) log post: -108.468 (-108.468 + 0) (iter:35, conv: 0.00425252) log post: -108.457 (-108.457 + 0) (iter:36, conv: 0.00392329) log post: -108.448 (-108.448 + 0) (iter:37, conv: 0.00362136) log post: -108.44 (-108.44 + 0) (iter:38, conv: 0.0033442) log post: -108.433 (-108.433 + 0) (iter:39, conv: 0.00308955) log post: -108.427 (-108.427 + 0) (iter:40, conv: 0.0028554) log post: -108.422 (-108.422 + 0) (iter:41, conv: 0.00263994) log post: -108.418 (-108.418 + 0) (iter:42, conv: 0.00244154) log post: -108.415 (-108.415 + 0) (iter:43, conv: 0.00225873) log post: -108.411 (-108.411 + 0) (iter:44, conv: 0.0020902) log post: -108.409 (-108.409 + 0) (iter:45, conv: 0.00193474) log post: -108.406 (-108.406 + 0) (iter:46, conv: 0.00179126) log post: -108.404 (-108.404 + 0) (iter:47, conv: 0.00165879) log post: -108.403 (-108.403 + 0) (iter:48, conv: 0.00153643) log post: -108.401 (-108.401 + 0) (iter:49, conv: 0.00142337) log post: -108.4 (-108.4 + 0) (iter:50, conv: 0.00131885) log post: -108.399 (-108.399 + 0) (iter:51, conv: 0.0012222) log post: -108.398 (-108.398 + 0) (iter:52, conv: 0.0011328) log post: -108.397 (-108.397 + 0) (iter:53, conv: 0.00105009) log post: -108.396 (-108.396 + 0) (iter:54, conv: 0.000973536) log post: -108.396 (-108.396 + 0) (iter:55, conv: 0.000902672) log post: -108.395 (-108.395 + 0) (iter:56, conv: 0.000837057) log post: -108.395 (-108.395 + 0) (iter:57, conv: 0.00077629) log post: -108.394 (-108.394 + 0) (iter:58, conv: 0.000720002) log post: -108.394 (-108.394 + 0) (iter:59, conv: 0.000667853) log post: -108.394 (-108.394 + 0) (iter:60, conv: 0.00061953) log post: -108.393 (-108.393 + 0) (iter:61, conv: 0.000574747) log post: -108.393 (-108.393 + 0) (iter:62, conv: 0.000533238) log post: -108.393 (-108.393 + 0) (iter:63, conv: 0.000494758) log post: -108.393 (-108.393 + 0) (iter:64, conv: 0.000459082) log post: -108.393 (-108.393 + 0) (iter:65, conv: 0.000426002) log post: -108.393 (-108.393 + 0) (iter:66, conv: 0.000395326) log post: -108.393 (-108.393 + 0) (iter:67, conv: 0.000366876) log post: -108.393 (-108.393 + 0) (iter:68, conv: 0.000340489) log post: -108.392 (-108.392 + 0) (iter:69, conv: 0.000316012) log post: -108.392 (-108.392 + 0) (iter:70, conv: 0.000293306) log post: -108.392 (-108.392 + 0) (iter:71, conv: 0.000272241) log post: -108.392 (-108.392 + 0) (iter:72, conv: 0.000252697) log post: -108.392 (-108.392 + 0) (iter:73, conv: 0.000234563) log post: -108.392 (-108.392 + 0) (iter:74, conv: 0.000217736) log post: -108.392 (-108.392 + 0) (iter:75, conv: 0.000202122) log post: -108.392 (-108.392 + 0) (iter:76, conv: 0.000187632) log post: -108.392 (-108.392 + 0) (iter:77, conv: 0.000174185) log post: -108.392 (-108.392 + 0) (iter:78, conv: 0.000161705) log post: -108.392 (-108.392 + 0) (iter:79, conv: 0.000150122) log post: -108.392 (-108.392 + 0) (iter:80, conv: 0.000139371) log post: -108.392 (-108.392 + 0) (iter:81, conv: 0.000129392) log post: -108.392 (-108.392 + 0) (iter:82, conv: 0.000120129) log post: -108.392 (-108.392 + 0) (iter:83, conv: 0.000111531) log post: -108.392 (-108.392 + 0) (iter:84, conv: 0.00010355) log post: -108.392 (-108.392 + 0) (iter:85, conv: 9.61414e-05) log post: -108.392 (-108.392 + 0) (iter:86, conv: 8.92637e-05) log post: -108.392 (-108.392 + 0) (iter:87, conv: 8.28789e-05) log post: -108.392 (-108.392 + 0) (iter:88, conv: 7.69515e-05) log post: -108.392 (-108.392 + 0) (iter:89, conv: 7.14487e-05) log post: -108.392 (-108.392 + 0) (iter:90, conv: 6.634e-05) log post: -108.392 (-108.392 + 0) (iter:91, conv: 6.1597e-05) log post: -108.392 (-108.392 + 0) (iter:92, conv: 5.71936e-05) log post: -108.392 (-108.392 + 0) (iter:93, conv: 5.31053e-05) log post: -108.392 (-108.392 + 0) (iter:94, conv: 4.93095e-05) log post: -108.392 (-108.392 + 0) (iter:95, conv: 4.57854e-05) log post: -108.392 (-108.392 + 0) (iter:96, conv: 4.25133e-05) log post: -108.392 (-108.392 + 0) (iter:97, conv: 3.94753e-05) log post: -108.392 (-108.392 + 0) (iter:98, conv: 3.66545e-05) log post: -108.392 (-108.392 + 0) (iter:99, conv: 3.40355e-05) log post: -108.392 (-108.392 + 0) (iter:100, conv: 3.16037e-05) log post: -108.392 (-108.392 + 0) (iter:101, conv: 2.93458e-05) log post: -108.392 (-108.392 + 0) (iter:102, conv: 2.72492e-05) log post: -108.392 (-108.392 + 0) (iter:103, conv: 2.53026e-05) log post: -108.392 (-108.392 + 0) (iter:104, conv: 2.34951e-05) log post: -108.392 (-108.392 + 0) (iter:105, conv: 2.18167e-05) log post: -108.392 (-108.392 + 0) (iter:106, conv: 2.02583e-05) log post: -108.392 (-108.392 + 0) (iter:107, conv: 1.88113e-05) log post: -108.392 (-108.392 + 0) (iter:108, conv: 1.74677e-05) log post: -108.392 (-108.392 + 0) (iter:109, conv: 1.62201e-05) log post: -108.392 (-108.392 + 0) (iter:110, conv: 1.50616e-05) log post: -108.392 (-108.392 + 0) (iter:111, conv: 1.39859e-05) log post: -108.392 (-108.392 + 0) (iter:112, conv: 1.2987e-05) log post: -108.392 (-108.392 + 0) (iter:113, conv: 1.20595e-05) log post: -108.392 (-108.392 + 0) (iter:114, conv: 1.11982e-05) log post: -108.392 (-108.392 + 0) (iter:115, conv: 1.03985e-05) log post: -108.392 (-108.392 + 0) (iter:116, conv: 9.65589e-06) log post: -108.392 (-108.392 + 0) (iter:117, conv: 8.96633e-06) log post: -108.392 (-108.392 + 0) (iter:118, conv: 8.32602e-06) log post: -108.392 (-108.392 + 0) (iter:119, conv: 7.73144e-06) log post: -108.392 (-108.392 + 0) (iter:120, conv: 7.17933e-06) log post: -108.392 (-108.392 + 0) (iter:121, conv: 6.66666e-06) log post: -108.392 (-108.392 + 0) (iter:122, conv: 6.1906e-06) log post: -108.392 (-108.392 + 0) (iter:123, conv: 5.74853e-06) log post: -108.392 (-108.392 + 0) (iter:124, conv: 5.33804e-06) log post: -108.392 (-108.392 + 0) (iter:125, conv: 4.95687e-06) log post: -108.392 (-108.392 + 0) (iter:126, conv: 4.60291e-06) log post: -108.392 (-108.392 + 0) (iter:127, conv: 4.27423e-06) log post: -108.392 (-108.392 + 0) (iter:128, conv: 3.96903e-06) log post: -108.392 (-108.392 + 0) (iter:129, conv: 3.68562e-06) log post: -108.392 (-108.392 + 0) (iter:130, conv: 3.42245e-06) log post: -108.392 (-108.392 + 0) (iter:131, conv: 3.17807e-06) log post: -108.392 (-108.392 + 0) (iter:132, conv: 2.95114e-06) log post: -108.392 (-108.392 + 0) (iter:133, conv: 2.74042e-06) log post: -108.392 (-108.392 + 0) (iter:134, conv: 2.54474e-06) log post: -108.392 (-108.392 + 0) (iter:135, conv: 2.36304e-06) log post: -108.392 (-108.392 + 0) (iter:136, conv: 2.19431e-06) log post: -108.392 (-108.392 + 0) (iter:137, conv: 2.03763e-06) log post: -108.392 (-108.392 + 0) (iter:138, conv: 1.89214e-06) log post: -108.392 (-108.392 + 0) (iter:139, conv: 1.75703e-06) log post: -108.392 (-108.392 + 0) (iter:140, conv: 1.63158e-06) log post: -108.392 (-108.392 + 0) (iter:141, conv: 1.51508e-06) log post: -108.392 (-108.392 + 0) (iter:142, conv: 1.4069e-06) log post: -108.392 (-108.392 + 0) (iter:143, conv: 1.30644e-06) log post: -108.392 (-108.392 + 0) (iter:144, conv: 1.21316e-06) log post: -108.392 (-108.392 + 0) (iter:145, conv: 1.12654e-06) log post: -108.392 (-108.392 + 0) (iter:146, conv: 1.0461e-06) log post: -108.392 (-108.392 + 0) (iter:147, conv: 9.71411e-07) Reached convergence criterion Using prior: Laplace(1.41421) None KKT Swindle count 1, activeSet size = 1 update time: 1.5436e-05 in 3 iterations. Inactive set violations: 1 KKT Swindle count 2, activeSet size = 2 update time: 0.000893163 in 134 iterations. Sparseness = 99.012 % Sorting outcomes by stratumId, time (descending), y and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Generating censoring weights Generating censoring weights Sorting outcomes by stratumId, time (descending), y and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Sorting outcomes by stratumId, time (descending), y and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Using cross-validation selector type byRow Performing 10-fold cross-validation [seed = 1744185811] with data partitions of sizes 1 1 1 1 1 1 1 1 1 0 Using 1 thread(s) Starting var = 0.333333 (default) Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #1 Rep #1 pred log like = 20.3427 Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #2 Rep #1 pred log like = 44.5701 Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #3 Rep #1 pred log like = 24.9454 Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #4 Rep #1 pred log like = 106.597 Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #5 Rep #1 pred log like = 14.674 Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #6 Rep #1 pred log like = 112.869 Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #7 Rep #1 pred log like = 59.4944 Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #8 Rep #1 pred log like = 79.8291 Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #9 Rep #1 pred log like = 33.625 Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #10 Rep #1 pred log like = 0 AvgPred = 49.6947 with stdev = 36.9968 Completed at 0.333333 Next point at 3.33333 with value 0 and continue = 1 search[ 0.333333 ] = 49.6947(36.9968) Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #1 Rep #1 pred log like = 20.3443 Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #2 Rep #1 pred log like = 44.6337 Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #3 Rep #1 pred log like = 24.7929 Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #4 Rep #1 pred log like = 106.149 Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #5 Rep #1 pred log like = 14.5878 Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #6 Rep #1 pred log like = 110.219 Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #7 Rep #1 pred log like = 57.3441 Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #8 Rep #1 pred log like = 79.7694 Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #9 Rep #1 pred log like = 32.8915 Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #10 Rep #1 pred log like = 0 AvgPred = 49.0732 with stdev = 36.4706 Completed at 3.33333 Next point at 0.0333333 with value 0 and continue = 1 search[ 0.333333 ] = 49.6947(36.9968) search[ 3.33333 ] = 49.0732(36.4706) Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #1 Rep #1 pred log like = 20.3273 Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #2 Rep #1 pred log like = 43.169 Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #3 Rep #1 pred log like = 25.0614 Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #4 Rep #1 pred log like = 107.806 Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #5 Rep #1 pred log like = 15.7525 Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #6 Rep #1 pred log like = 118.443 Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #7 Rep #1 pred log like = 60.6085 Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #8 Rep #1 pred log like = 79.6334 Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #9 Rep #1 pred log like = 34.0061 Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #10 Rep #1 pred log like = 0 AvgPred = 50.4807 with stdev = 38.0685 Completed at 0.0333333 Next point at 0.00333333 with value 0 and continue = 1 search[ 0.0333333 ] = 50.4807(38.0685) search[ 0.333333 ] = 49.6947(36.9968) search[ 3.33333 ] = 49.0732(36.4706) Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #1 Rep #1 pred log like = 19.9614 Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #2 Rep #1 pred log like = 42.498 Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #3 Rep #1 pred log like = 25.4635 Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #4 Rep #1 pred log like = 106.001 Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #5 Rep #1 pred log like = 16.8111 Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #6 Rep #1 pred log like = 118.246 Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #7 Rep #1 pred log like = 62.1884 Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #8 Rep #1 pred log like = 79.0526 Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #9 Rep #1 pred log like = 33.9945 Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #10 Rep #1 pred log like = 0 AvgPred = 50.4216 with stdev = 37.6865 Completed at 0.00333333 Next point at 0.00390597 with value 50.4732 and continue = 0 search[ 0.00333333 ] = 50.4216(37.6865) search[ 0.0333333 ] = 50.4807(38.0685) search[ 0.333333 ] = 49.6947(36.9968) search[ 3.33333 ] = 49.0732(36.4706) Maximum predicted log likelihood (50.4732) estimated at: 0.00390597 (variance) 22.6282 (lambda) Fitting model at optimal hyperparameter Using prior: Laplace(22.6282) None Sparseness = 80.112 % Sorting covariates by covariateId, stratumId, and rowId Using cross-validation selector type byPid Performing 10-fold cross-validation [seed = 123] with data partitions of sizes 100 100 100 100 100 100 100 100 100 100 Using 1 thread(s) Starting var = 0.1 Running at Laplace(4.47214) None Grid-point #1 at 0.1 Fold #1 Rep #1 pred log like = -14146.5 Running at Laplace(4.47214) None Grid-point #1 at 0.1 Fold #2 Rep #1 pred log like = -13824.3 Running at Laplace(4.47214) None Grid-point #1 at 0.1 Fold #3 Rep #1 pred log like = -13922.5 Running at Laplace(4.47214) None Grid-point #1 at 0.1 Fold #4 Rep #1 pred log like = -12009.7 Running at Laplace(4.47214) None Grid-point #1 at 0.1 Fold #5 Rep #1 pred log like = -13190.5 Running at Laplace(4.47214) None Grid-point #1 at 0.1 Fold #6 Rep #1 pred log like = -14032 Running at Laplace(4.47214) None Grid-point #1 at 0.1 Fold #7 Rep #1 pred log like = -13053.7 Running at Laplace(4.47214) None Grid-point #1 at 0.1 Fold #8 Rep #1 pred log like = -13911.1 Running at Laplace(4.47214) None Grid-point #1 at 0.1 Fold #9 Rep #1 pred log like = -13560.8 Running at Laplace(4.47214) None Grid-point #1 at 0.1 Fold #10 Rep #1 pred log like = -13052.5 AvgPred = -13470.4 with stdev = 621.67 Completed at 0.1 Next point at 1 with value 0 and continue = 1 search[ 0.1 ] = -13470.4(621.67) Running at Laplace(1.41421) None Grid-point #2 at 1 Fold #1 Rep #1 pred log like = -14146.5 Running at Laplace(1.41421) None Grid-point #2 at 1 Fold #2 Rep #1 pred log like = -13824.3 Running at Laplace(1.41421) None Grid-point #2 at 1 Fold #3 Rep #1 pred log like = -13922.5 Running at Laplace(1.41421) None Grid-point #2 at 1 Fold #4 Rep #1 pred log like = -12009.7 Running at Laplace(1.41421) None Grid-point #2 at 1 Fold #5 Rep #1 pred log like = -13190.5 Running at Laplace(1.41421) None Grid-point #2 at 1 Fold #6 Rep #1 pred log like = -14032 Running at Laplace(1.41421) None Grid-point #2 at 1 Fold #7 Rep #1 pred log like = -13053.7 Running at Laplace(1.41421) None Grid-point #2 at 1 Fold #8 Rep #1 pred log like = -13911.1 Running at Laplace(1.41421) None Grid-point #2 at 1 Fold #9 Rep #1 pred log like = -13560.8 Running at Laplace(1.41421) None Grid-point #2 at 1 Fold #10 Rep #1 pred log like = -13052.4 AvgPred = -13470.4 with stdev = 621.671 Completed at 1 Next point at 0.01 with value 0 and continue = 1 search[ 0.1 ] = -13470.4(621.67) search[ 1 ] = -13470.4(621.671) Running at Laplace(14.1421) None Grid-point #3 at 0.01 Fold #1 Rep #1 pred log like = -14146.5 Running at Laplace(14.1421) None Grid-point #3 at 0.01 Fold #2 Rep #1 pred log like = -13824.3 Running at Laplace(14.1421) None Grid-point #3 at 0.01 Fold #3 Rep #1 pred log like = -13922.5 Running at Laplace(14.1421) None Grid-point #3 at 0.01 Fold #4 Rep #1 pred log like = -12009.7 Running at Laplace(14.1421) None Grid-point #3 at 0.01 Fold #5 Rep #1 pred log like = -13190.3 Running at Laplace(14.1421) None Grid-point #3 at 0.01 Fold #6 Rep #1 pred log like = -14031.9 Running at Laplace(14.1421) None Grid-point #3 at 0.01 Fold #7 Rep #1 pred log like = -13053.7 Running at Laplace(14.1421) None Grid-point #3 at 0.01 Fold #8 Rep #1 pred log like = -13911.1 Running at Laplace(14.1421) None Grid-point #3 at 0.01 Fold #9 Rep #1 pred log like = -13560.8 Running at Laplace(14.1421) None Grid-point #3 at 0.01 Fold #10 Rep #1 pred log like = -13052.6 AvgPred = -13470.3 with stdev = 621.666 Completed at 0.01 Next point at 0.001 with value 0 and continue = 1 search[ 0.01 ] = -13470.3(621.666) search[ 0.1 ] = -13470.4(621.67) search[ 1 ] = -13470.4(621.671) Running at Laplace(44.7214) None Grid-point #4 at 0.001 Fold #1 Rep #1 pred log like = -14146.6 Running at Laplace(44.7214) None Grid-point #4 at 0.001 Fold #2 Rep #1 pred log like = -13824.2 Running at Laplace(44.7214) None Grid-point #4 at 0.001 Fold #3 Rep #1 pred log like = -13922.5 Running at Laplace(44.7214) None Grid-point #4 at 0.001 Fold #4 Rep #1 pred log like = -12009.6 Running at Laplace(44.7214) None Grid-point #4 at 0.001 Fold #5 Rep #1 pred log like = -13189.8 Running at Laplace(44.7214) None Grid-point #4 at 0.001 Fold #6 Rep #1 pred log like = -14031.6 Running at Laplace(44.7214) None Grid-point #4 at 0.001 Fold #7 Rep #1 pred log like = -13053.7 Running at Laplace(44.7214) None Grid-point #4 at 0.001 Fold #8 Rep #1 pred log like = -13911.2 Running at Laplace(44.7214) None Grid-point #4 at 0.001 Fold #9 Rep #1 pred log like = -13561 Running at Laplace(44.7214) None Grid-point #4 at 0.001 Fold #10 Rep #1 pred log like = -13052.9 AvgPred = -13470.3 with stdev = 621.685 Completed at 0.001 Next point at 0.0001 with value 0 and continue = 1 search[ 0.001 ] = -13470.3(621.685) search[ 0.01 ] = -13470.3(621.666) search[ 0.1 ] = -13470.4(621.67) search[ 1 ] = -13470.4(621.671) Running at Laplace(141.421) None Grid-point #5 at 0.0001 Fold #1 Rep #1 pred log like = -14146.6 Running at Laplace(141.421) None Grid-point #5 at 0.0001 Fold #2 Rep #1 pred log like = -13824.4 Running at Laplace(141.421) None Grid-point #5 at 0.0001 Fold #3 Rep #1 pred log like = -13922.3 Running at Laplace(141.421) None Grid-point #5 at 0.0001 Fold #4 Rep #1 pred log like = -12009.6 Running at Laplace(141.421) None Grid-point #5 at 0.0001 Fold #5 Rep #1 pred log like = -13189 Running at Laplace(141.421) None Grid-point #5 at 0.0001 Fold #6 Rep #1 pred log like = -14030.9 Running at Laplace(141.421) None Grid-point #5 at 0.0001 Fold #7 Rep #1 pred log like = -13053.6 Running at Laplace(141.421) None Grid-point #5 at 0.0001 Fold #8 Rep #1 pred log like = -13911.5 Running at Laplace(141.421) None Grid-point #5 at 0.0001 Fold #9 Rep #1 pred log like = -13561 Running at Laplace(141.421) None Grid-point #5 at 0.0001 Fold #10 Rep #1 pred log like = -13053.1 AvgPred = -13470.2 with stdev = 621.656 Completed at 0.0001 Next point at 1e-05 with value 0 and continue = 1 search[ 0.0001 ] = -13470.2(621.656) search[ 0.001 ] = -13470.3(621.685) search[ 0.01 ] = -13470.3(621.666) search[ 0.1 ] = -13470.4(621.67) search[ 1 ] = -13470.4(621.671) Running at Laplace(447.214) None Grid-point #6 at 1e-05 Fold #1 Rep #1 pred log like = -14146.6 Running at Laplace(447.214) None Grid-point #6 at 1e-05 Fold #2 Rep #1 pred log like = -13825.3 Running at Laplace(447.214) None Grid-point #6 at 1e-05 Fold #3 Rep #1 pred log like = -13922.8 Running at Laplace(447.214) None Grid-point #6 at 1e-05 Fold #4 Rep #1 pred log like = -12011.1 Running at Laplace(447.214) None Grid-point #6 at 1e-05 Fold #5 Rep #1 pred log like = -13189.7 Running at Laplace(447.214) None Grid-point #6 at 1e-05 Fold #6 Rep #1 pred log like = -14031.3 Running at Laplace(447.214) None Grid-point #6 at 1e-05 Fold #7 Rep #1 pred log like = -13054.9 Running at Laplace(447.214) None Grid-point #6 at 1e-05 Fold #8 Rep #1 pred log like = -13912.9 Running at Laplace(447.214) None Grid-point #6 at 1e-05 Fold #9 Rep #1 pred log like = -13562 Running at Laplace(447.214) None Grid-point #6 at 1e-05 Fold #10 Rep #1 pred log like = -13054.1 AvgPred = -13471.1 with stdev = 621.373 Completed at 1e-05 Next point at 0.0125877 with value -13470.2 and continue = 0 search[ 1e-05 ] = -13471.1(621.373) search[ 0.0001 ] = -13470.2(621.656) search[ 0.001 ] = -13470.3(621.685) search[ 0.01 ] = -13470.3(621.666) search[ 0.1 ] = -13470.4(621.67) search[ 1 ] = -13470.4(621.671) Maximum predicted log likelihood (-13470.2) estimated at: 0.0125877 (variance) 12.605 (lambda) Fitting model at optimal hyperparameter Using prior: Laplace(12.605) None Sparseness = 80.112 % Sorting outcomes by stratumId, time (descending), y and rowId Sorting covariates by covariateId, stratumId, time (descending), y, and rowId Sparseness = 99.09 % Sorting covariates by covariateId and rowId [ FAIL 2 | WARN 3 | SKIP 28 | PASS 309 ] ══ Skipped tests (28) ══════════════════════════════════════════════════════════ • Current not working (1): 'test-offsetPoisson.R:41:5' • GPU not available (6): 'test-gpucox.R:12:5', 'test-gpucox.R:37:5', 'test-gpucox.R:63:5', 'test-gpucox.R:88:5', 'test-gpucox.R:118:5', 'test-timevaryingCox.R:8:5' • On CRAN (11): 'test-cv.R:37:5', 'test-cv.R:110:5', 'test-cv.R:148:5', 'test-dataConversionStratified.R:113:3', 'test-largeBernoulli.R:26:5', 'test-largeBernoulli.R:73:5', 'test-outOfSample.R:7:5', 'test-parameterizedPriors.R:88:5', 'test-smallExactCLR.R:9:5', 'test-smallExactCLR.R:32:5', 'test-weighted_cv.R:5:5' • Takes much too longer (1): 'test-largeProfileLikelihood.R:7:5' • empty test (8): 'test-believedBroken.R:75:1', 'test-cprViaSql.R:5:1', 'test-multitypePoisson.R:113:1', 'test-multitypePoisson.R:146:1', 'test-recenter.R:6:1', 'test-recenter.R:28:1', 'test-sqlConstructor.R:99:1', 'test-weighting.R:259:1' • for debugging purposes; simulation takes too long (1): 'test-floatingPoint.R:57:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-predict.R:23:5'): Test predict for Poisson regression ──────── `predictOriginal` not equal to `predictNew`. Names: 9996 string mismatches ── Failure ('test-predict.R:43:5'): Test predict for logistic regression ─────── `predictOriginal` not equal to `predictNew`. Names: 9993 string mismatches [ FAIL 2 | WARN 3 | SKIP 28 | PASS 309 ] Error: Test failures Execution halted Package: FeatureExtraction Check: tests New result: ERROR Running ‘testBigQuery.R’ [0s/0s] Running ‘testOracle.R’ [0s/0s] Running ‘testPostgres.R’ [0s/0s] Running ‘testRedshift.R’ [0s/0s] Running ‘testSnowflake.R’ [0s/0s] Running ‘testSpark.R’ [0s/0s] Running ‘testSqlServer.R’ [0s/0s] Running ‘testSqlite.R’ [221s/221s] Running the tests in ‘tests/testSqlite.R’ failed. Complete output: > library(testthat) > options(dbms = "sqlite") > runTestsOnEunomia <- TRUE > if (runTestsOnEunomia) { + test_check("FeatureExtraction") + } Loading required package: FeatureExtraction Loading required package: DatabaseConnector Loading required package: Andromeda Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union ************* Testing on sqlite ************* attempting to download GiBleed trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Content type 'application/zip' length 6861852 bytes (6.5 MB) ================================================== downloaded 6.5 MB attempting to extract and load: /home/hornik/tmp/scratch/RtmpblU2Ci/GiBleed_5.3.zip to: /home/hornik/tmp/scratch/RtmpblU2Ci/GiBleed_5.3.sqlite Connecting using SQLite driver Executing SQL took 0.0326 secs Cohorts created in table main.cohort Sending temp tables to server Constructing features on server Fetching data from server Fetching data took 0.716 secs Constructing features on server Fetching data from server Fetching data took 0.461 secs # CovariateData object Cohorts of interest IDs: 1, 2 Inherits from Andromeda: # Andromeda object # Physical location: /home/hornik/tmp/scratch/RtmpblU2Ci/file35623d41d1c67c.duckdb Tables: $analysisRef (analysisId, analysisName, domainId, startDay, endDay, isBinary, missingMeansZero) $covariateRef (covariateId, covariateName, analysisId, conceptId) $covariates (cohortDefinitionId, covariateId, covariateValue, rowId) Constructing features on server Fetching data from server Fetching data took 0.432 secs Sending temp tables to server Constructing features on server Fetching data from server Fetching data took 0.407 secs Sending temp tables to server Constructing features on server Fetching data from server Fetching data took 0.419 secs Constructing features on server Fetching data from server Fetching data took 0.37 secs Constructing features on server Fetching data from server Fetching data took 0.832 secs Constructing features on server Fetching data from server Fetching data took 0.407 secs Sending temp tables to server Constructing features on server Fetching data from server Fetching data took 0.5 secs Constructing features on server Fetching data from server Fetching data took 0.771 secs Constructing features on server Fetching data from server Fetching data took 0.386 secs Constructing features on server Fetching data from server Fetching data took 0.37 secs Constructing features on server Fetching data from server Fetching data took 1.49 secs Constructing features on server Fetching data from server Fetching data took 0.799 secs Constructing features on server Fetching data from server Fetching data took 0.402 secs Constructing features on server Fetching data from server Fetching data took 0.444 secs Constructing features on server Fetching data from server Fetching data took 0.508 secs Sending temp tables to server Constructing features on server Fetching data from server Fetching data took 0.529 secs Sending temp tables to server Constructing features on server Fetching data from server Fetching data took 0.599 secs Sending temp tables to server Constructing features on server Fetching data from server Fetching data took 0.344 secs Sending temp tables to server Constructing features on server Fetching data from server Fetching data took 0.423 secs Tidying covariates took 0.559 secs Removing 1 redundant covariates Removing 1 infrequent covariates Normalizing covariates Tidying covariates took 1.45 secs Sending temp tables to server Constructing features on server Fetching data from server Fetching data took 0.759 secs Removing 0 redundant covariate ID - time ID combinations Removing 0 infrequent covariates Normalizing covariates Tidying covariates took 2 secs [ FAIL 2 | WARN 5 | SKIP 82 | PASS 124 ] ══ Skipped tests (82) ══════════════════════════════════════════════════════════ • On CRAN (26): 'test-Aggregation.R:6:3', 'test-CompareCohorts.R:42:3', 'test-CovariateData.R:55:3', 'test-CovariateData.R:99:3', 'test-CovariateData.R:160:3', 'test-CovariateData.R:174:3', 'test-GetCohortBasedCovariates.R:489:3', 'test-GetCohortBasedCovariates.R:500:3', 'test-GetCohortBasedCovariates.R:511:3', 'test-GetCohortBasedCovariates.R:522:3', 'test-GetCohortBasedCovariates.R:533:3', 'test-GetCohortBasedCovariates.R:544:3', 'test-GetCohortBasedCovariates.R:555:3', 'test-GetCohortBasedCovariates.R:566:3', 'test-GetCovariates.R:63:3', 'test-GetCovariates.R:87:3', 'test-GetCovariates.R:100:3', 'test-GetCovariates.R:113:3', 'test-GetCovariatesFromCohortAttributes.R:30:3', 'test-GetCovariatesFromCohortAttributes.R:51:3', 'test-GetCovariatesFromCohortAttributes.R:79:3', 'test-GetCovariatesTemporalSequence.R:83:3', 'test-GetDefaultCovariates.R:6:3', 'test-HelperFunctions.R:31:3', 'test-Table1.R:85:3', 'test-Table1.R:146:3' • dbms == "oracle" is not TRUE (14): 'test-GetCohortBasedCovariates.R:796:3', 'test-GetCohortBasedCovariates.R:808:3', 'test-GetCohortBasedCovariates.R:820:3', 'test-GetCohortBasedCovariates.R:832:3', 'test-GetCohortBasedCovariates.R:844:3', 'test-GetCohortBasedCovariates.R:856:3', 'test-GetCohortBasedCovariates.R:868:3', 'test-GetCohortBasedCovariates.R:880:3', 'test-GetCohortBasedCovariates.R:892:3', 'test-query-no-fail.R:162:3', 'test-query-no-fail.R:344:3', 'test-query-no-fail.R:450:3', 'test-query-no-fail.R:558:3', 'test-spot-checks.R:204:3' • dbms == "postgresql" is not TRUE (14): 'test-GetCohortBasedCovariates.R:578:3', 'test-GetCohortBasedCovariates.R:590:3', 'test-GetCohortBasedCovariates.R:602:3', 'test-GetCohortBasedCovariates.R:614:3', 'test-GetCohortBasedCovariates.R:626:3', 'test-GetCohortBasedCovariates.R:638:3', 'test-GetCohortBasedCovariates.R:650:3', 'test-GetCohortBasedCovariates.R:662:3', 'test-GetCohortBasedCovariates.R:674:3', 'test-query-no-fail.R:146:3', 'test-query-no-fail.R:328:3', 'test-query-no-fail.R:434:3', 'test-query-no-fail.R:542:3', 'test-spot-checks.R:190:3' • dbms == "redshift" is not TRUE (14): 'test-GetCohortBasedCovariates.R:905:3', 'test-GetCohortBasedCovariates.R:917:3', 'test-GetCohortBasedCovariates.R:929:3', 'test-GetCohortBasedCovariates.R:941:3', 'test-GetCohortBasedCovariates.R:953:3', 'test-GetCohortBasedCovariates.R:965:3', 'test-GetCohortBasedCovariates.R:977:3', 'test-GetCohortBasedCovariates.R:989:3', 'test-GetCohortBasedCovariates.R:1001:3', 'test-query-no-fail.R:170:3', 'test-query-no-fail.R:352:3', 'test-query-no-fail.R:458:3', 'test-query-no-fail.R:566:3', 'test-spot-checks.R:211:3' • dbms == "sql server" is not TRUE (14): 'test-GetCohortBasedCovariates.R:687:3', 'test-GetCohortBasedCovariates.R:699:3', 'test-GetCohortBasedCovariates.R:711:3', 'test-GetCohortBasedCovariates.R:723:3', 'test-GetCohortBasedCovariates.R:735:3', 'test-GetCohortBasedCovariates.R:747:3', 'test-GetCohortBasedCovariates.R:759:3', 'test-GetCohortBasedCovariates.R:771:3', 'test-GetCohortBasedCovariates.R:783:3', 'test-query-no-fail.R:154:3', 'test-query-no-fail.R:336:3', 'test-query-no-fail.R:442:3', 'test-query-no-fail.R:550:3', 'test-spot-checks.R:197:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-CompareCohorts.R:19:3'): Test stdDiff continuous variable computation ── Error in `file.rename(file.path(tempDir, duckdbFilenameInZip), newFileName)`: 'from' and 'to' are of different lengths Backtrace: ▆ 1. └─FeatureExtraction::loadCovariateData(getTestResourceFilePath("continuousCovariateData.zip")) at test-CompareCohorts.R:19:3 2. └─Andromeda::loadAndromeda(file) 3. └─base::file.rename(file.path(tempDir, duckdbFilenameInZip), newFileName) ── Error ('test-HelperFunctions.R:21:3'): Test helper functions for non-aggregated covariate data ── Error in `DBI::dbSendQuery(connection, sql)`: rapi_prepare: Failed to prepare query SELECT covariateId, SUM(covariateValue) AS sumValue, SUM(covariateValue / 890.0) AS averageValue FROM ( SELECT "...1".*, covariateRef.covariateId AS covariateId, covariateName, conceptId, valueAsConceptId, collisions, rowId, covariateValue FROM ( SELECT analysisRef.* FROM analysisRef WHERE (isBinary = 'Y') ) "...1" INNER JOIN covariateRef ON ("...1".analysisId = covariateRef.analysisId) INNER JOIN covariates ON (covariateRef.covariateId = covariates.covariateId) ) q01 GROUP BY covariateId Error: Binder Error: Ambiguous reference to column name "rowId" (use: "covariateRef.rowId" or "covariates.rowId") Backtrace: ▆ 1. ├─FeatureExtraction::aggregateCovariates(covariateData) at test-HelperFunctions.R:21:3 2. │ ├─methods (local) `$<-`(`*tmp*`, "covariates", value = ``) 3. │ └─Andromeda (local) `$<-`(`*tmp*`, "covariates", value = ``) 4. │ ├─methods (local) `[[<-`(`*tmp*`, name, value = ``) 5. │ └─Andromeda (local) `[[<-`(`*tmp*`, name, value = ``) 6. │ └─Andromeda (local) .local(x, i, ..., value) 7. │ └─Andromeda::batchApply(value, doBatchedAppend) 8. │ ├─DBI::dbSendQuery(connection, sql) 9. │ └─DBI::dbSendQuery(connection, sql) 10. │ └─duckdb (local) .local(conn, statement, ...) 11. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env) 12. │ ├─rlang::try_fetch(...) 13. │ │ ├─base::tryCatch(...) 14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ │ └─base::withCallingHandlers(...) 18. │ └─duckdb:::rapi_prepare(conn, query, env) 19. └─base::.handleSimpleError(...) 20. └─rlang (local) h(simpleError(msg, call)) 21. └─handlers[[1L]](cnd) 22. └─duckdb:::rethrow_error_from_rapi(e, call) 23. └─rlang::abort(msg, call = call) [ FAIL 2 | WARN 5 | SKIP 82 | PASS 124 ] Error: Test failures Executing SQL took 0.00457 secs Execution halted Package: TreatmentPatterns Check: tests New result: ERROR Running ‘testthat.R’ [234s/129s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # 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(TreatmentPatterns) > > test_check("TreatmentPatterns") Starting 2 test processes [ FAIL 16 | WARN 0 | SKIP 60 | PASS 108 ] ══ Skipped tests (60) ══════════════════════════════════════════════════════════ • Eunomia [2.0.0] bug (8): 'test-CDMInterfaceDBC.R:6:3', 'test-CDMInterfaceDBC.R:24:3', 'test-CDMInterfaceDBC.R:53:3', 'test-CDMInterfaceDBC.R:80:3', 'test-CDMInterfaceDBC.R:117:3', 'test-multipleCohortTables.R:68:3', 'test-computePathways.R:8:3', 'test-computePathways.R:53:3' • On CRAN (45): 'test-CDMInterface.R:7:3', 'test-export.R:314:3', 'test-export.R:381:3', 'test-export.R:428:3', 'test-export.R:470:3', 'test-export.R:514:3', 'test-export.R:589:3', 'test-export.R:657:3', 'test-export.R:685:3', 'test-pathwaysLogical.R:8:3', 'test-pathwaysLogical.R:50:3', 'test-pathwaysLogical.R:94:3', 'test-pathwaysLogical.R:138:3', 'test-pathwaysLogical.R:182:3', 'test-pathwaysLogical.R:225:3', 'test-pathwaysLogical.R:270:3', 'test-pathwaysLogical.R:315:3', 'test-pathwaysLogical.R:359:3', 'test-pathwaysLogical.R:403:3', 'test-pathwaysLogical.R:447:3', 'test-pathwaysLogical.R:491:3', 'test-pathwaysLogical.R:535:3', 'test-pathwaysLogical.R:579:3', 'test-pathwaysLogical.R:624:3', 'test-pathwaysLogical.R:669:3', 'test-pathwaysLogical.R:712:3', 'test-pathwaysLogical.R:756:3', 'test-pathwaysLogical.R:800:3', 'test-pathwaysLogical.R:845:3', 'test-pathwaysLogical.R:887:3', 'test-pathwaysLogical.R:929:3', 'test-pathwaysLogical.R:971:3', 'test-pathwaysLogical.R:1013:3', 'test-pathwaysLogical.R:1055:3', 'test-pathwaysLogical.R:1098:3', 'test-pathwaysLogical.R:1144:3', 'test-pathwaysLogical.R:1188:3', 'test-pathwaysLogical.R:1232:3', 'test-pathwaysLogical.R:1276:3', 'test-pathwaysLogical.R:1322:3', 'test-pathwaysLogical.R:1369:3', 'test-pathwaysLogical.R:1416:3', 'test-pathwaysLogical.R:1462:3', 'test-pathwaysMultipleTargetsLogical.R:19:3', 'test-pathwaysMultipleTargetsLogical.R:225:3' • On Linux (7): 'test-executeTreatmentPatterns.R:10:3', 'test-export.R:30:3', 'test-export.R:99:3', 'test-export.R:149:3', 'test-export.R:193:3', 'test-export.R:237:3', 'test-computePathways.R:720:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-CDMInterfaceCDMC.R:78:3'): Method: fetchCohortTable ──────────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─cdmInterface$fetchCohortTable(...) at test-CDMInterfaceCDMC.R:78:3 2. │ └─private$cdmconFetchCohortTable(...) 3. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 4. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 5. │ └─Andromeda (local) .local(x, i, ..., value) 6. │ ├─DBI::dbExecute(x, sql) 7. │ └─DBI::dbExecute(x, sql) 8. │ ├─DBI::dbSendStatement(conn, statement, ...) 9. │ └─DBI::dbSendStatement(conn, statement, ...) 10. │ ├─DBI::dbSendQuery(conn, statement, ...) 11. │ └─duckdb::dbSendQuery(conn, statement, ...) 12. │ └─duckdb (local) .local(conn, statement, ...) 13. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 14. │ └─duckdb:::duckdb_execute(res) 15. │ └─duckdb:::rethrow_rapi_execute(...) 16. │ ├─rlang::try_fetch(...) 17. │ │ ├─base::tryCatch(...) 18. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 19. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 20. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 21. │ │ └─base::withCallingHandlers(...) 22. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 23. └─base::.handleSimpleError(...) 24. └─rlang (local) h(simpleError(msg, call)) 25. └─handlers[[1L]](cnd) 26. └─duckdb:::rethrow_error_from_rapi(e, call) 27. └─rlang::abort(msg, call = call) ── Error ('test-TreatmentPatternsResults.R:5:3'): Method: new(data.frame) ────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::executeTreatmentPatterns(...) at test-TreatmentPatternsResults.R:5:3 2. │ └─TreatmentPatterns::computePathways(...) 3. │ └─cdmInterface$fetchCohortTable(...) 4. │ └─private$cdmconFetchCohortTable(...) 5. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 7. │ └─Andromeda (local) .local(x, i, ..., value) 8. │ ├─DBI::dbExecute(x, sql) 9. │ └─DBI::dbExecute(x, sql) 10. │ ├─DBI::dbSendStatement(conn, statement, ...) 11. │ └─DBI::dbSendStatement(conn, statement, ...) 12. │ ├─DBI::dbSendQuery(conn, statement, ...) 13. │ └─duckdb::dbSendQuery(conn, statement, ...) 14. │ └─duckdb (local) .local(conn, statement, ...) 15. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 16. │ └─duckdb:::duckdb_execute(res) 17. │ └─duckdb:::rethrow_rapi_execute(...) 18. │ ├─rlang::try_fetch(...) 19. │ │ ├─base::tryCatch(...) 20. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 21. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 22. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 23. │ │ └─base::withCallingHandlers(...) 24. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 25. └─base::.handleSimpleError(...) 26. └─rlang (local) h(simpleError(msg, call)) 27. └─handlers[[1L]](cnd) 28. └─duckdb:::rethrow_error_from_rapi(e, call) 29. └─rlang::abort(msg, call = call) ── Error ('test-executeTreatmentPatterns.R:30:3'): CDMConnector ──────────────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::executeTreatmentPatterns(...) at test-executeTreatmentPatterns.R:30:3 2. │ └─TreatmentPatterns::computePathways(...) 3. │ └─cdmInterface$fetchCohortTable(...) 4. │ └─private$cdmconFetchCohortTable(...) 5. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 7. │ └─Andromeda (local) .local(x, i, ..., value) 8. │ ├─DBI::dbExecute(x, sql) 9. │ └─DBI::dbExecute(x, sql) 10. │ ├─DBI::dbSendStatement(conn, statement, ...) 11. │ └─DBI::dbSendStatement(conn, statement, ...) 12. │ ├─DBI::dbSendQuery(conn, statement, ...) 13. │ └─duckdb::dbSendQuery(conn, statement, ...) 14. │ └─duckdb (local) .local(conn, statement, ...) 15. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 16. │ └─duckdb:::duckdb_execute(res) 17. │ └─duckdb:::rethrow_rapi_execute(...) 18. │ ├─rlang::try_fetch(...) 19. │ │ ├─base::tryCatch(...) 20. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 21. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 22. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 23. │ │ └─base::withCallingHandlers(...) 24. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 25. └─base::.handleSimpleError(...) 26. └─rlang (local) h(simpleError(msg, call)) 27. └─handlers[[1L]](cnd) 28. └─duckdb:::rethrow_error_from_rapi(e, call) 29. └─rlang::abort(msg, call = call) ── Error ('test-multipleCohortTables.R:45:3'): multiple cohort_tables ────────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::computePathways(...) at test-multipleCohortTables.R:45:3 2. │ └─cdmInterface$fetchCohortTable(...) 3. │ └─private$cdmconFetchCohortTable(...) 4. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 5. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) .local(x, i, ..., value) 7. │ ├─DBI::dbExecute(x, sql) 8. │ └─DBI::dbExecute(x, sql) 9. │ ├─DBI::dbSendStatement(conn, statement, ...) 10. │ └─DBI::dbSendStatement(conn, statement, ...) 11. │ ├─DBI::dbSendQuery(conn, statement, ...) 12. │ └─duckdb::dbSendQuery(conn, statement, ...) 13. │ └─duckdb (local) .local(conn, statement, ...) 14. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 15. │ └─duckdb:::duckdb_execute(res) 16. │ └─duckdb:::rethrow_rapi_execute(...) 17. │ ├─rlang::try_fetch(...) 18. │ │ ├─base::tryCatch(...) 19. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 20. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 22. │ │ └─base::withCallingHandlers(...) 23. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 24. └─base::.handleSimpleError(...) 25. └─rlang (local) h(simpleError(msg, call)) 26. └─handlers[[1L]](cnd) 27. └─duckdb:::rethrow_error_from_rapi(e, call) 28. └─rlang::abort(msg, call = call) ── Error ('test-pathwaysMultipleTargetsLogical.R:341:3'): Events outside target ── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::computePathways(...) at test-pathwaysMultipleTargetsLogical.R:341:3 2. │ └─cdmInterface$fetchCohortTable(...) 3. │ └─private$cdmconFetchCohortTable(...) 4. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 5. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) .local(x, i, ..., value) 7. │ ├─DBI::dbExecute(x, sql) 8. │ └─DBI::dbExecute(x, sql) 9. │ ├─DBI::dbSendStatement(conn, statement, ...) 10. │ └─DBI::dbSendStatement(conn, statement, ...) 11. │ ├─DBI::dbSendQuery(conn, statement, ...) 12. │ └─duckdb::dbSendQuery(conn, statement, ...) 13. │ └─duckdb (local) .local(conn, statement, ...) 14. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 15. │ └─duckdb:::duckdb_execute(res) 16. │ └─duckdb:::rethrow_rapi_execute(...) 17. │ ├─rlang::try_fetch(...) 18. │ │ ├─base::tryCatch(...) 19. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 20. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 22. │ │ └─base::withCallingHandlers(...) 23. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 24. └─base::.handleSimpleError(...) 25. └─rlang (local) h(simpleError(msg, call)) 26. └─handlers[[1L]](cnd) 27. └─duckdb:::rethrow_error_from_rapi(e, call) 28. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:34:3'): computePathways CDMConnector ───────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─testthat::expect_message(...) at test-computePathways.R:34:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─testthat::expect_message(...) 8. │ └─testthat:::expect_condition_matching(...) 9. │ └─testthat:::quasi_capture(...) 10. │ ├─testthat (local) .capture(...) 11. │ │ └─base::withCallingHandlers(...) 12. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 13. ├─testthat::expect_message(...) 14. │ └─testthat:::expect_condition_matching(...) 15. │ └─testthat:::quasi_capture(...) 16. │ ├─testthat (local) .capture(...) 17. │ │ └─base::withCallingHandlers(...) 18. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 19. ├─TreatmentPatterns::computePathways(...) 20. │ └─cdmInterface$fetchCohortTable(...) 21. │ └─private$cdmconFetchCohortTable(...) 22. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 23. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 24. │ └─Andromeda (local) .local(x, i, ..., value) 25. │ ├─DBI::dbExecute(x, sql) 26. │ └─DBI::dbExecute(x, sql) 27. │ ├─DBI::dbSendStatement(conn, statement, ...) 28. │ └─DBI::dbSendStatement(conn, statement, ...) 29. │ ├─DBI::dbSendQuery(conn, statement, ...) 30. │ └─duckdb::dbSendQuery(conn, statement, ...) 31. │ └─duckdb (local) .local(conn, statement, ...) 32. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 33. │ └─duckdb:::duckdb_execute(res) 34. │ └─duckdb:::rethrow_rapi_execute(...) 35. │ ├─rlang::try_fetch(...) 36. │ │ ├─base::tryCatch(...) 37. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 38. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 39. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 40. │ │ └─base::withCallingHandlers(...) 41. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 42. └─base::.handleSimpleError(...) 43. └─rlang (local) h(simpleError(msg, call)) 44. └─handlers[[1L]](cnd) 45. └─duckdb:::rethrow_error_from_rapi(e, call) 46. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:80:3'): includeTreatments ──────────────────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::computePathways(...) at test-computePathways.R:80:3 2. │ └─cdmInterface$fetchCohortTable(...) 3. │ └─private$cdmconFetchCohortTable(...) 4. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 5. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) .local(x, i, ..., value) 7. │ ├─DBI::dbExecute(x, sql) 8. │ └─DBI::dbExecute(x, sql) 9. │ ├─DBI::dbSendStatement(conn, statement, ...) 10. │ └─DBI::dbSendStatement(conn, statement, ...) 11. │ ├─DBI::dbSendQuery(conn, statement, ...) 12. │ └─duckdb::dbSendQuery(conn, statement, ...) 13. │ └─duckdb (local) .local(conn, statement, ...) 14. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 15. │ └─duckdb:::duckdb_execute(res) 16. │ └─duckdb:::rethrow_rapi_execute(...) 17. │ ├─rlang::try_fetch(...) 18. │ │ ├─base::tryCatch(...) 19. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 20. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 22. │ │ └─base::withCallingHandlers(...) 23. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 24. └─base::.handleSimpleError(...) 25. └─rlang (local) h(simpleError(msg, call)) 26. └─handlers[[1L]](cnd) 27. └─duckdb:::rethrow_error_from_rapi(e, call) 28. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:144:3'): indexDateOffset ───────────────────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─testthat::expect_message(...) at test-computePathways.R:144:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─TreatmentPatterns::computePathways(...) 8. │ └─cdmInterface$fetchCohortTable(...) 9. │ └─private$cdmconFetchCohortTable(...) 10. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 11. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 12. │ └─Andromeda (local) .local(x, i, ..., value) 13. │ ├─DBI::dbExecute(x, sql) 14. │ └─DBI::dbExecute(x, sql) 15. │ ├─DBI::dbSendStatement(conn, statement, ...) 16. │ └─DBI::dbSendStatement(conn, statement, ...) 17. │ ├─DBI::dbSendQuery(conn, statement, ...) 18. │ └─duckdb::dbSendQuery(conn, statement, ...) 19. │ └─duckdb (local) .local(conn, statement, ...) 20. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 21. │ └─duckdb:::duckdb_execute(res) 22. │ └─duckdb:::rethrow_rapi_execute(...) 23. │ ├─rlang::try_fetch(...) 24. │ │ ├─base::tryCatch(...) 25. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 26. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 27. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 28. │ │ └─base::withCallingHandlers(...) 29. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 30. └─base::.handleSimpleError(...) 31. └─rlang (local) h(simpleError(msg, call)) 32. └─handlers[[1L]](cnd) 33. └─duckdb:::rethrow_error_from_rapi(e, call) 34. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:194:3'): splitEventCohorts ─────────────────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::computePathways(...) at test-computePathways.R:194:3 2. │ └─cdmInterface$fetchCohortTable(...) 3. │ └─private$cdmconFetchCohortTable(...) 4. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 5. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) .local(x, i, ..., value) 7. │ ├─DBI::dbExecute(x, sql) 8. │ └─DBI::dbExecute(x, sql) 9. │ ├─DBI::dbSendStatement(conn, statement, ...) 10. │ └─DBI::dbSendStatement(conn, statement, ...) 11. │ ├─DBI::dbSendQuery(conn, statement, ...) 12. │ └─duckdb::dbSendQuery(conn, statement, ...) 13. │ └─duckdb (local) .local(conn, statement, ...) 14. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 15. │ └─duckdb:::duckdb_execute(res) 16. │ └─duckdb:::rethrow_rapi_execute(...) 17. │ ├─rlang::try_fetch(...) 18. │ │ ├─base::tryCatch(...) 19. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 20. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 22. │ │ └─base::withCallingHandlers(...) 23. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 24. └─base::.handleSimpleError(...) 25. └─rlang (local) h(simpleError(msg, call)) 26. └─handlers[[1L]](cnd) 27. └─duckdb:::rethrow_error_from_rapi(e, call) 28. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:247:3'): eraCollapseSize ───────────────────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::computePathways(...) at test-computePathways.R:247:3 2. │ └─cdmInterface$fetchCohortTable(...) 3. │ └─private$cdmconFetchCohortTable(...) 4. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 5. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) .local(x, i, ..., value) 7. │ ├─DBI::dbExecute(x, sql) 8. │ └─DBI::dbExecute(x, sql) 9. │ ├─DBI::dbSendStatement(conn, statement, ...) 10. │ └─DBI::dbSendStatement(conn, statement, ...) 11. │ ├─DBI::dbSendQuery(conn, statement, ...) 12. │ └─duckdb::dbSendQuery(conn, statement, ...) 13. │ └─duckdb (local) .local(conn, statement, ...) 14. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 15. │ └─duckdb:::duckdb_execute(res) 16. │ └─duckdb:::rethrow_rapi_execute(...) 17. │ ├─rlang::try_fetch(...) 18. │ │ ├─base::tryCatch(...) 19. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 20. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 22. │ │ └─base::withCallingHandlers(...) 23. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 24. └─base::.handleSimpleError(...) 25. └─rlang (local) h(simpleError(msg, call)) 26. └─handlers[[1L]](cnd) 27. └─duckdb:::rethrow_error_from_rapi(e, call) 28. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:314:3'): minPostCombinationDuration: 30 ────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::computePathways(...) at test-computePathways.R:314:3 2. │ └─cdmInterface$fetchCohortTable(...) 3. │ └─private$cdmconFetchCohortTable(...) 4. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 5. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) .local(x, i, ..., value) 7. │ ├─DBI::dbExecute(x, sql) 8. │ └─DBI::dbExecute(x, sql) 9. │ ├─DBI::dbSendStatement(conn, statement, ...) 10. │ └─DBI::dbSendStatement(conn, statement, ...) 11. │ ├─DBI::dbSendQuery(conn, statement, ...) 12. │ └─duckdb::dbSendQuery(conn, statement, ...) 13. │ └─duckdb (local) .local(conn, statement, ...) 14. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 15. │ └─duckdb:::duckdb_execute(res) 16. │ └─duckdb:::rethrow_rapi_execute(...) 17. │ ├─rlang::try_fetch(...) 18. │ │ ├─base::tryCatch(...) 19. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 20. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 22. │ │ └─base::withCallingHandlers(...) 23. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 24. └─base::.handleSimpleError(...) 25. └─rlang (local) h(simpleError(msg, call)) 26. └─handlers[[1L]](cnd) 27. └─duckdb:::rethrow_error_from_rapi(e, call) 28. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:415:3'): filterTreatments ──────────────────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::computePathways(...) at test-computePathways.R:415:3 2. │ └─cdmInterface$fetchCohortTable(...) 3. │ └─private$cdmconFetchCohortTable(...) 4. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 5. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) .local(x, i, ..., value) 7. │ ├─DBI::dbExecute(x, sql) 8. │ └─DBI::dbExecute(x, sql) 9. │ ├─DBI::dbSendStatement(conn, statement, ...) 10. │ └─DBI::dbSendStatement(conn, statement, ...) 11. │ ├─DBI::dbSendQuery(conn, statement, ...) 12. │ └─duckdb::dbSendQuery(conn, statement, ...) 13. │ └─duckdb (local) .local(conn, statement, ...) 14. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 15. │ └─duckdb:::duckdb_execute(res) 16. │ └─duckdb:::rethrow_rapi_execute(...) 17. │ ├─rlang::try_fetch(...) 18. │ │ ├─base::tryCatch(...) 19. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 20. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 22. │ │ └─base::withCallingHandlers(...) 23. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 24. └─base::.handleSimpleError(...) 25. └─rlang (local) h(simpleError(msg, call)) 26. └─handlers[[1L]](cnd) 27. └─duckdb:::rethrow_error_from_rapi(e, call) 28. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:578:3'): FRFS combination ──────────────────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::computePathways(...) at test-computePathways.R:578:3 2. │ └─cdmInterface$fetchCohortTable(...) 3. │ └─private$cdmconFetchCohortTable(...) 4. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 5. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) .local(x, i, ..., value) 7. │ ├─DBI::dbExecute(x, sql) 8. │ └─DBI::dbExecute(x, sql) 9. │ ├─DBI::dbSendStatement(conn, statement, ...) 10. │ └─DBI::dbSendStatement(conn, statement, ...) 11. │ ├─DBI::dbSendQuery(conn, statement, ...) 12. │ └─duckdb::dbSendQuery(conn, statement, ...) 13. │ └─duckdb (local) .local(conn, statement, ...) 14. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 15. │ └─duckdb:::duckdb_execute(res) 16. │ └─duckdb:::rethrow_rapi_execute(...) 17. │ ├─rlang::try_fetch(...) 18. │ │ ├─base::tryCatch(...) 19. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 20. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 22. │ │ └─base::withCallingHandlers(...) 23. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 24. └─base::.handleSimpleError(...) 25. └─rlang (local) h(simpleError(msg, call)) 26. └─handlers[[1L]](cnd) 27. └─duckdb:::rethrow_error_from_rapi(e, call) 28. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:631:3'): LRFS combination ──────────────────── Error in `duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)`: rapi_execute: Failed to run query Error: Conversion Error: Unimplemented type for cast (DATE -> INTEGER) LINE 5: CAST(cohort_start_date AS INTEGER) AS cohort_start_date, ^ Backtrace: ▆ 1. ├─TreatmentPatterns::computePathways(...) at test-computePathways.R:631:3 2. │ └─cdmInterface$fetchCohortTable(...) 3. │ └─private$cdmconFetchCohortTable(...) 4. │ ├─methods (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 5. │ └─Andromeda (local) `[[<-`(`*tmp*`, andromedaTableName, value = ``) 6. │ └─Andromeda (local) .local(x, i, ..., value) 7. │ ├─DBI::dbExecute(x, sql) 8. │ └─DBI::dbExecute(x, sql) 9. │ ├─DBI::dbSendStatement(conn, statement, ...) 10. │ └─DBI::dbSendStatement(conn, statement, ...) 11. │ ├─DBI::dbSendQuery(conn, statement, ...) 12. │ └─duckdb::dbSendQuery(conn, statement, ...) 13. │ └─duckdb (local) .local(conn, statement, ...) 14. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 15. │ └─duckdb:::duckdb_execute(res) 16. │ └─duckdb:::rethrow_rapi_execute(...) 17. │ ├─rlang::try_fetch(...) 18. │ │ ├─base::tryCatch(...) 19. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 20. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 22. │ │ └─base::withCallingHandlers(...) 23. │ └─duckdb:::rapi_execute(stmt, arrow, integer64) 24. └─base::.handleSimpleError(...) 25. └─rlang (local) h(simpleError(msg, call)) 26. └─handlers[[1L]](cnd) 27. └─duckdb:::rethrow_error_from_rapi(e, call) 28. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:667:5'): No target records ─────────────────── Error in `dbSendQuery(conn, statement, ...)`: rapi_prepare: Failed to prepare query CREATE TABLE targetCohorts AS SELECT q01.*, startDate + 0.0 AS indexDate FROM ( SELECT q01.*, CAST(format(startDate, '%Y') AS NUMERIC) AS indexYear FROM ( SELECT cohortTable.*, 'target' AS "type" FROM cohortTable WHERE (cohortId IN (9.0)) ) q01 ) q01 Error: Binder Error: No function matches the given name and argument types 'format(INTEGER, STRING_LITERAL)'. You might need to add explicit type casts. Candidate functions: format(VARCHAR, [ANY...]) -> VARCHAR LINE 3: SELECT q01.*, CAST(format(startDate, '%Y') AS NUMERIC) AS indexYear ^ Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-computePathways.R:666:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─TreatmentPatterns::computePathways(...) at test-computePathways.R:667:5 8. │ └─TreatmentPatterns:::constructPathways(settings = args, andromeda = andromeda) 9. │ └─TreatmentPatterns:::createTreatmentHistory(...) 10. │ ├─methods (local) `$<-`(`*tmp*`, "targetCohorts", value = ``) 11. │ └─Andromeda (local) `$<-`(`*tmp*`, "targetCohorts", value = ``) 12. │ ├─methods (local) `[[<-`(`*tmp*`, name, value = ``) 13. │ └─Andromeda (local) `[[<-`(`*tmp*`, name, value = ``) 14. │ └─Andromeda (local) .local(x, i, ..., value) 15. │ ├─DBI::dbExecute(x, sql) 16. │ └─DBI::dbExecute(x, sql) 17. │ ├─DBI::dbSendStatement(conn, statement, ...) 18. │ └─DBI::dbSendStatement(conn, statement, ...) 19. │ ├─DBI::dbSendQuery(conn, statement, ...) 20. │ └─duckdb::dbSendQuery(conn, statement, ...) 21. │ └─duckdb (local) .local(conn, statement, ...) 22. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env) 23. │ ├─rlang::try_fetch(...) 24. │ │ ├─base::tryCatch(...) 25. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 26. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 27. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 28. │ │ └─base::withCallingHandlers(...) 29. │ └─duckdb:::rapi_prepare(conn, query, env) 30. └─base::.handleSimpleError(...) 31. └─rlang (local) h(simpleError(msg, call)) 32. └─handlers[[1L]](cnd) 33. └─duckdb:::rethrow_error_from_rapi(e, call) 34. └─rlang::abort(msg, call = call) ── Error ('test-computePathways.R:689:5'): Empty cohort table ────────────────── Error in `dbSendQuery(conn, statement, ...)`: rapi_prepare: Failed to prepare query CREATE TABLE targetCohorts AS SELECT q01.*, startDate + 0.0 AS indexDate FROM ( SELECT q01.*, CAST(format(startDate, '%Y') AS NUMERIC) AS indexYear FROM ( SELECT cohortTable.*, 'target' AS "type" FROM cohortTable WHERE (cohortId IN (8)) ) q01 ) q01 Error: Binder Error: No function matches the given name and argument types 'format(INTEGER, STRING_LITERAL)'. You might need to add explicit type casts. Candidate functions: format(VARCHAR, [ANY...]) -> VARCHAR LINE 3: SELECT q01.*, CAST(format(startDate, '%Y') AS NUMERIC) AS indexYear ^ Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-computePathways.R:688:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─TreatmentPatterns::computePathways(...) at test-computePathways.R:689:5 8. │ └─TreatmentPatterns:::constructPathways(settings = args, andromeda = andromeda) 9. │ └─TreatmentPatterns:::createTreatmentHistory(...) 10. │ ├─methods (local) `$<-`(`*tmp*`, "targetCohorts", value = ``) 11. │ └─Andromeda (local) `$<-`(`*tmp*`, "targetCohorts", value = ``) 12. │ ├─methods (local) `[[<-`(`*tmp*`, name, value = ``) 13. │ └─Andromeda (local) `[[<-`(`*tmp*`, name, value = ``) 14. │ └─Andromeda (local) .local(x, i, ..., value) 15. │ ├─DBI::dbExecute(x, sql) 16. │ └─DBI::dbExecute(x, sql) 17. │ ├─DBI::dbSendStatement(conn, statement, ...) 18. │ └─DBI::dbSendStatement(conn, statement, ...) 19. │ ├─DBI::dbSendQuery(conn, statement, ...) 20. │ └─duckdb::dbSendQuery(conn, statement, ...) 21. │ └─duckdb (local) .local(conn, statement, ...) 22. │ └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env) 23. │ ├─rlang::try_fetch(...) 24. │ │ ├─base::tryCatch(...) 25. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 26. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 27. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 28. │ │ └─base::withCallingHandlers(...) 29. │ └─duckdb:::rapi_prepare(conn, query, env) 30. └─base::.handleSimpleError(...) 31. └─rlang (local) h(simpleError(msg, call)) 32. └─handlers[[1L]](cnd) 33. └─duckdb:::rethrow_error_from_rapi(e, call) 34. └─rlang::abort(msg, call = call) [ FAIL 16 | WARN 0 | SKIP 60 | PASS 108 ] Error: Test failures Execution halted