Last updated on 2026-10-24 14:49:38 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.7.1 | 210.19 | 333.72 | 543.91 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.7.1 | 184.38 | 244.26 | 428.64 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.7.1 | 168.00 | 248.01 | 416.01 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 3.7.1 | 240.00 | 240.89 | 480.89 | OK | |
| r-devel-windows-x86_64 | 3.7.1 | 283.00 | 465.00 | 748.00 | OK | |
| r-patched-linux-x86_64 | 3.7.1 | 257.49 | 322.07 | 579.56 | OK | |
| r-release-linux-x86_64 | 3.7.1 | 250.91 | 321.57 | 572.48 | OK | |
| r-release-macos-arm64 | 3.7.1 | 51.00 | 53.00 | 104.00 | OK | |
| r-release-macos-x86_64 | 3.7.1 | 147.00 | 340.00 | 487.00 | OK | |
| r-release-windows-x86_64 | 3.7.1 | 294.00 | 396.00 | 690.00 | OK | |
| r-oldrel-macos-arm64 | 3.7.1 | 43.00 | 64.00 | 107.00 | OK | |
| r-oldrel-macos-x86_64 | 3.7.1 | 143.00 | 323.00 | 466.00 | OK | |
| r-oldrel-windows-x86_64 | 3.7.1 | 351.00 | 532.00 | 883.00 | OK |
Version: 3.7.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [168s/237s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("Cyclops")
Loading required package: Cyclops
Sparseness = 52.175 %
Sorting outcomes by rowId
Sorting covariates by covariateId and rowId
Sorting outcomes by rowId
Sorting covariates by covariateId and rowId
Sparseness = 52.175 %
Sorting outcomes by rowId
Sorting covariates by covariateId and rowId
Sorting outcomes by rowId
Sorting covariates by covariateId and rowId
Sparseness = 52.175 %
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 and rowId
Sorting covariates by covariateId, stratumId, and rowId
Sparseness = 98.99 %
Sorting covariates by covariateId and rowId
Using cross-validation selector type byRow
Performing 10-fold cross-validation [seed = 1792756063] with data partitions of sizes 100 100 100 100 100 100 100 100 100 100
Using 1 thread(s)
Starting var = 0.0101 (default)
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #1 Rep #1 pred log like = -44.0616
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #2 Rep #1 pred log like = -31.8582
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #3 Rep #1 pred log like = -26.803
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #4 Rep #1 pred log like = -37.0171
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #5 Rep #1 pred log like = -30.1617
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #6 Rep #1 pred log like = -31.8582
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #7 Rep #1 pred log like = -35.2858
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #8 Rep #1 pred log like = -25.1406
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #9 Rep #1 pred log like = -31.8582
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #10 Rep #1 pred log like = -30.1617
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #1 Rep #2 pred log like = -26.803
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #2 Rep #2 pred log like = -33.5661
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #3 Rep #2 pred log like = -21.8491
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #4 Rep #2 pred log like = -25.1406
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #5 Rep #2 pred log like = -42.2824
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #6 Rep #2 pred log like = -25.1406
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #7 Rep #2 pred log like = -51.3019
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #8 Rep #2 pred log like = -38.7602
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #9 Rep #2 pred log like = -37.0171
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #10 Rep #2 pred log like = -23.4893
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #1 Rep #3 pred log like = -47.6568
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #2 Rep #3 pred log like = -38.7602
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #3 Rep #3 pred log like = -35.2858
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #4 Rep #3 pred log like = -31.8582
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #5 Rep #3 pred log like = -28.4767
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #6 Rep #3 pred log like = -38.7602
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #7 Rep #3 pred log like = -31.8582
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #8 Rep #3 pred log like = -15.397
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #9 Rep #3 pred log like = -31.8582
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #10 Rep #3 pred log like = -25.1406
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #1 Rep #4 pred log like = -21.8491
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #2 Rep #4 pred log like = -26.803
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #3 Rep #4 pred log like = -45.853
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #4 Rep #4 pred log like = -44.0616
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #5 Rep #4 pred log like = -38.7602
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #6 Rep #4 pred log like = -18.6015
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #7 Rep #4 pred log like = -28.4767
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #8 Rep #4 pred log like = -42.2824
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #9 Rep #4 pred log like = -26.803
Running at Laplace(14.072) None Grid-point #1 at 0.0101 Fold #10 Rep #4 pred log like = -31.8582
AvgPred = -32.4989 with stdev = 8.09463
Completed at 0.0101
Next point at 0.101 with value 0 and continue = 1
search[ 0.0101 ] = -32.4989(8.09463)
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #1 Rep #1 pred log like = -44.0616
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #2 Rep #1 pred log like = -31.8582
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #3 Rep #1 pred log like = -26.803
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #4 Rep #1 pred log like = -37.0171
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #5 Rep #1 pred log like = -30.1617
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #6 Rep #1 pred log like = -31.8582
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #7 Rep #1 pred log like = -35.2858
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #8 Rep #1 pred log like = -25.1406
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #9 Rep #1 pred log like = -31.8721
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #10 Rep #1 pred log like = -30.1617
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #1 Rep #2 pred log like = -26.803
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #2 Rep #2 pred log like = -33.5661
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #3 Rep #2 pred log like = -21.855
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #4 Rep #2 pred log like = -25.1406
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #5 Rep #2 pred log like = -42.2824
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #6 Rep #2 pred log like = -25.1406
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #7 Rep #2 pred log like = -51.3019
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #8 Rep #2 pred log like = -38.7602
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #9 Rep #2 pred log like = -37.0171
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #10 Rep #2 pred log like = -23.4893
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #1 Rep #3 pred log like = -47.6568
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #2 Rep #3 pred log like = -38.7602
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #3 Rep #3 pred log like = -35.2858
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #4 Rep #3 pred log like = -31.8582
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #5 Rep #3 pred log like = -28.4767
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #6 Rep #3 pred log like = -38.7602
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #7 Rep #3 pred log like = -31.8582
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #8 Rep #3 pred log like = -15.397
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #9 Rep #3 pred log like = -31.8582
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #10 Rep #3 pred log like = -25.1406
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #1 Rep #4 pred log like = -21.8491
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #2 Rep #4 pred log like = -26.803
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #3 Rep #4 pred log like = -45.853
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #4 Rep #4 pred log like = -44.0616
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #5 Rep #4 pred log like = -38.7602
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #6 Rep #4 pred log like = -18.6015
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #7 Rep #4 pred log like = -28.4767
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #8 Rep #4 pred log like = -42.2824
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #9 Rep #4 pred log like = -26.803
Running at Laplace(4.44994) None Grid-point #2 at 0.101 Fold #10 Rep #4 pred log like = -31.8582
AvgPred = -32.4994 with stdev = 8.0944
Completed at 0.101
Next point at 0.00101 with value 0 and continue = 1
search[ 0.0101 ] = -32.4989(8.09463)
search[ 0.101 ] = -32.4994(8.0944)
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #1 Rep #1 pred log like = -44.0616
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #2 Rep #1 pred log like = -31.8582
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #3 Rep #1 pred log like = -26.803
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #4 Rep #1 pred log like = -37.0171
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #5 Rep #1 pred log like = -30.1617
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #6 Rep #1 pred log like = -31.8582
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #7 Rep #1 pred log like = -35.2858
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #8 Rep #1 pred log like = -25.1406
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #9 Rep #1 pred log like = -31.8582
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #10 Rep #1 pred log like = -30.1617
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #1 Rep #2 pred log like = -26.803
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #2 Rep #2 pred log like = -33.5661
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #3 Rep #2 pred log like = -21.8491
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #4 Rep #2 pred log like = -25.1406
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #5 Rep #2 pred log like = -42.2824
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #6 Rep #2 pred log like = -25.1406
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #7 Rep #2 pred log like = -51.3019
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #8 Rep #2 pred log like = -38.7602
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #9 Rep #2 pred log like = -37.0171
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #10 Rep #2 pred log like = -23.4893
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #1 Rep #3 pred log like = -47.6568
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #2 Rep #3 pred log like = -38.7602
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #3 Rep #3 pred log like = -35.2858
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #4 Rep #3 pred log like = -31.8582
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #5 Rep #3 pred log like = -28.4767
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #6 Rep #3 pred log like = -38.7602
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #7 Rep #3 pred log like = -31.8582
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #8 Rep #3 pred log like = -15.397
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #9 Rep #3 pred log like = -31.8582
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #10 Rep #3 pred log like = -25.1406
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #1 Rep #4 pred log like = -21.8491
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #2 Rep #4 pred log like = -26.803
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #3 Rep #4 pred log like = -45.853
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #4 Rep #4 pred log like = -44.0616
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #5 Rep #4 pred log like = -38.7602
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #6 Rep #4 pred log like = -18.6015
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #7 Rep #4 pred log like = -28.4767
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #8 Rep #4 pred log like = -42.2824
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #9 Rep #4 pred log like = -26.803
Running at Laplace(44.4994) None Grid-point #3 at 0.00101 Fold #10 Rep #4 pred log like = -31.8582
AvgPred = -32.4989 with stdev = 8.09463
Completed at 0.00101
Next point at 0.000101 with value 0 and continue = 1
search[ 0.00101 ] = -32.4989(8.09463)
search[ 0.0101 ] = -32.4989(8.09463)
search[ 0.101 ] = -32.4994(8.0944)
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #1 Rep #1 pred log like = -44.0616
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #2 Rep #1 pred log like = -31.8582
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #3 Rep #1 pred log like = -26.803
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #4 Rep #1 pred log like = -37.0171
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #5 Rep #1 pred log like = -30.1617
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #6 Rep #1 pred log like = -31.8582
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #7 Rep #1 pred log like = -35.2858
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #8 Rep #1 pred log like = -25.1406
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #9 Rep #1 pred log like = -31.8582
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #10 Rep #1 pred log like = -30.1617
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #1 Rep #2 pred log like = -26.803
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #2 Rep #2 pred log like = -33.5661
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #3 Rep #2 pred log like = -21.8491
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #4 Rep #2 pred log like = -25.1406
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #5 Rep #2 pred log like = -42.2824
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #6 Rep #2 pred log like = -25.1406
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #7 Rep #2 pred log like = -51.3019
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #8 Rep #2 pred log like = -38.7602
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #9 Rep #2 pred log like = -37.0171
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #10 Rep #2 pred log like = -23.4893
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #1 Rep #3 pred log like = -47.6568
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #2 Rep #3 pred log like = -38.7602
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #3 Rep #3 pred log like = -35.2858
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #4 Rep #3 pred log like = -31.8582
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #5 Rep #3 pred log like = -28.4767
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #6 Rep #3 pred log like = -38.7602
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #7 Rep #3 pred log like = -31.8582
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #8 Rep #3 pred log like = -15.397
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #9 Rep #3 pred log like = -31.8582
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #10 Rep #3 pred log like = -25.1406
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #1 Rep #4 pred log like = -21.8491
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #2 Rep #4 pred log like = -26.803
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #3 Rep #4 pred log like = -45.853
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #4 Rep #4 pred log like = -44.0616
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #5 Rep #4 pred log like = -38.7602
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #6 Rep #4 pred log like = -18.6015
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #7 Rep #4 pred log like = -28.4767
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #8 Rep #4 pred log like = -42.2824
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #9 Rep #4 pred log like = -26.803
Running at Laplace(140.72) None Grid-point #4 at 0.000101 Fold #10 Rep #4 pred log like = -31.8582
AvgPred = -32.4989 with stdev = 8.09463
Completed at 0.000101
Next point at 0.000802272 with value -32.4988 and continue = 0
search[ 0.000101 ] = -32.4989(8.09463)
search[ 0.00101 ] = -32.4989(8.09463)
search[ 0.0101 ] = -32.4989(8.09463)
search[ 0.101 ] = -32.4994(8.0944)
Maximum predicted log likelihood (-32.4988) estimated at:
0.000802272 (variance)
49.9292 (lambda)
Fitting model at optimal hyperparameter
Using prior: Laplace(49.9292) 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 = 75.605 %
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 = 76.15 %
Sorting covariates by covariateId and rowId
Sparseness = 75.695 %
Sorting covariates by covariateId and rowId
Sparseness = 75.9 %
Sorting covariates by covariateId and rowId
Sparseness = 75.3 %
Sorting covariates by covariateId and rowId
Saving _problems/test-residuals-9.R
Saving _problems/test-residuals-29.R
Saving _problems/test-residuals-58.R
Sparseness = 13.23 %
Sorting outcomes by stratumId, time (descending), y and rowId
Sorting covariates by covariateId, stratumId, time (descending), y, and rowId
Saving _problems/test-residuals-134.R
Saving _problems/test-residuals-161.R
Sparseness = 76.4 %
Sorting covariates by covariateId and rowId
Analysis took 0.0117 secs ( 0.00025 )
Fitting model using clogit
Analysis took 0.14 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 0.0149 secs ( 0.000191 )
Fitting model using coxpht
Analysis took 0.0103 secs
Using prior: None
log post: -153.562 (-153.562 + 0) (iter:1, conv: 1.49516)
log post: -140.336 (-140.336 + 0) (iter:2, conv: 0.417984)
log post: -132.01 (-132.01 + 0) (iter:3, conv: 0.261069)
log post: -126.375 (-126.375 + 0) (iter:4, conv: 0.183922)
log post: -122.375 (-122.375 + 0) (iter:5, conv: 0.136891)
log post: -119.439 (-119.439 + 0) (iter:6, conv: 0.106878)
log post: -117.228 (-117.228 + 0) (iter:7, conv: 0.0862994)
log post: -115.53 (-115.53 + 0) (iter:8, conv: 0.071395)
log post: -114.206 (-114.206 + 0) (iter:9, conv: 0.060154)
log post: -113.159 (-113.159 + 0) (iter:10, conv: 0.051408)
log post: -112.323 (-112.323 + 0) (iter:11, conv: 0.0444337)
log post: -111.649 (-111.649 + 0) (iter:12, conv: 0.0387604)
log post: -111.102 (-111.102 + 0) (iter:13, conv: 0.0340695)
log post: -110.655 (-110.655 + 0) (iter:14, conv: 0.0301375)
log post: -110.288 (-110.288 + 0) (iter:15, conv: 0.0268034)
log post: -109.985 (-109.985 + 0) (iter:16, conv: 0.0239483)
log post: -109.733 (-109.733 + 0) (iter:17, conv: 0.0214827)
log post: -109.524 (-109.524 + 0) (iter:18, conv: 0.0193378)
log post: -109.349 (-109.349 + 0) (iter:19, conv: 0.0174597)
log post: -109.202 (-109.202 + 0) (iter:20, conv: 0.0158061)
log post: -109.079 (-109.079 + 0) (iter:21, conv: 0.0143429)
log post: -108.976 (-108.976 + 0) (iter:22, conv: 0.0130423)
log post: -108.889 (-108.889 + 0) (iter:23, conv: 0.0118819)
log post: -108.815 (-108.815 + 0) (iter:24, conv: 0.0108428)
log post: -108.752 (-108.752 + 0) (iter:25, conv: 0.00990905)
log post: -108.7 (-108.7 + 0) (iter:26, conv: 0.00906454)
log post: -108.655 (-108.655 + 0) (iter:27, conv: 0.00830244)
log post: -108.616 (-108.616 + 0) (iter:28, conv: 0.00761308)
log post: -108.584 (-108.584 + 0) (iter:29, conv: 0.00698817)
log post: -108.556 (-108.556 + 0) (iter:30, conv: 0.00642058)
log post: -108.533 (-108.533 + 0) (iter:31, conv: 0.00590412)
log post: -108.512 (-108.512 + 0) (iter:32, conv: 0.00543344)
log post: -108.495 (-108.495 + 0) (iter:33, conv: 0.00500383)
log post: -108.48 (-108.48 + 0) (iter:34, conv: 0.00461118)
log post: -108.468 (-108.468 + 0) (iter:35, conv: 0.00425187)
log post: -108.457 (-108.457 + 0) (iter:36, conv: 0.00392269)
log post: -108.448 (-108.448 + 0) (iter:37, conv: 0.00362081)
log post: -108.44 (-108.44 + 0) (iter:38, conv: 0.00334369)
log post: -108.433 (-108.433 + 0) (iter:39, conv: 0.00308909)
log post: -108.427 (-108.427 + 0) (iter:40, conv: 0.00285498)
log post: -108.422 (-108.422 + 0) (iter:41, conv: 0.00263955)
log post: -108.418 (-108.418 + 0) (iter:42, conv: 0.00244118)
log post: -108.415 (-108.415 + 0) (iter:43, conv: 0.0022584)
log post: -108.411 (-108.411 + 0) (iter:44, conv: 0.00208989)
log post: -108.409 (-108.409 + 0) (iter:45, conv: 0.00193445)
log post: -108.406 (-108.406 + 0) (iter:46, conv: 0.001791)
log post: -108.404 (-108.404 + 0) (iter:47, conv: 0.00165855)
log post: -108.403 (-108.403 + 0) (iter:48, conv: 0.00153621)
log post: -108.401 (-108.401 + 0) (iter:49, conv: 0.00142316)
log post: -108.4 (-108.4 + 0) (iter:50, conv: 0.00131866)
log post: -108.399 (-108.399 + 0) (iter:51, conv: 0.00122202)
log post: -108.398 (-108.398 + 0) (iter:52, conv: 0.00113264)
log post: -108.397 (-108.397 + 0) (iter:53, conv: 0.00104994)
log post: -108.396 (-108.396 + 0) (iter:54, conv: 0.000973398)
log post: -108.396 (-108.396 + 0) (iter:55, conv: 0.000902544)
log post: -108.395 (-108.395 + 0) (iter:56, conv: 0.000836938)
log post: -108.395 (-108.395 + 0) (iter:57, conv: 0.00077618)
log post: -108.394 (-108.394 + 0) (iter:58, conv: 0.0007199)
log post: -108.394 (-108.394 + 0) (iter:59, conv: 0.000667758)
log post: -108.394 (-108.394 + 0) (iter:60, conv: 0.000619443)
log post: -108.393 (-108.393 + 0) (iter:61, conv: 0.000574666)
log post: -108.393 (-108.393 + 0) (iter:62, conv: 0.000533163)
log post: -108.393 (-108.393 + 0) (iter:63, conv: 0.000494688)
log post: -108.393 (-108.393 + 0) (iter:64, conv: 0.000459018)
log post: -108.393 (-108.393 + 0) (iter:65, conv: 0.000425942)
log post: -108.393 (-108.393 + 0) (iter:66, conv: 0.000395271)
log post: -108.393 (-108.393 + 0) (iter:67, conv: 0.000366825)
log post: -108.393 (-108.393 + 0) (iter:68, conv: 0.000340441)
log post: -108.392 (-108.392 + 0) (iter:69, conv: 0.000315968)
log post: -108.392 (-108.392 + 0) (iter:70, conv: 0.000293265)
log post: -108.392 (-108.392 + 0) (iter:71, conv: 0.000272203)
log post: -108.392 (-108.392 + 0) (iter:72, conv: 0.000252661)
log post: -108.392 (-108.392 + 0) (iter:73, conv: 0.00023453)
log post: -108.392 (-108.392 + 0) (iter:74, conv: 0.000217706)
log post: -108.392 (-108.392 + 0) (iter:75, conv: 0.000202094)
log post: -108.392 (-108.392 + 0) (iter:76, conv: 0.000187606)
log post: -108.392 (-108.392 + 0) (iter:77, conv: 0.00017416)
log post: -108.392 (-108.392 + 0) (iter:78, conv: 0.000161682)
log post: -108.392 (-108.392 + 0) (iter:79, conv: 0.000150101)
log post: -108.392 (-108.392 + 0) (iter:80, conv: 0.000139351)
log post: -108.392 (-108.392 + 0) (iter:81, conv: 0.000129374)
log post: -108.392 (-108.392 + 0) (iter:82, conv: 0.000120112)
log post: -108.392 (-108.392 + 0) (iter:83, conv: 0.000111516)
log post: -108.392 (-108.392 + 0) (iter:84, conv: 0.000103536)
log post: -108.392 (-108.392 + 0) (iter:85, conv: 9.6128e-05)
log post: -108.392 (-108.392 + 0) (iter:86, conv: 8.92512e-05)
log post: -108.392 (-108.392 + 0) (iter:87, conv: 8.28673e-05)
log post: -108.392 (-108.392 + 0) (iter:88, conv: 7.69408e-05)
log post: -108.392 (-108.392 + 0) (iter:89, conv: 7.14387e-05)
log post: -108.392 (-108.392 + 0) (iter:90, conv: 6.63307e-05)
log post: -108.392 (-108.392 + 0) (iter:91, conv: 6.15884e-05)
log post: -108.392 (-108.392 + 0) (iter:92, conv: 5.71856e-05)
log post: -108.392 (-108.392 + 0) (iter:93, conv: 5.30979e-05)
log post: -108.392 (-108.392 + 0) (iter:94, conv: 4.93026e-05)
log post: -108.392 (-108.392 + 0) (iter:95, conv: 4.5779e-05)
log post: -108.392 (-108.392 + 0) (iter:96, conv: 4.25074e-05)
log post: -108.392 (-108.392 + 0) (iter:97, conv: 3.94698e-05)
log post: -108.392 (-108.392 + 0) (iter:98, conv: 3.66494e-05)
log post: -108.392 (-108.392 + 0) (iter:99, conv: 3.40307e-05)
log post: -108.392 (-108.392 + 0) (iter:100, conv: 3.15993e-05)
log post: -108.392 (-108.392 + 0) (iter:101, conv: 2.93417e-05)
log post: -108.392 (-108.392 + 0) (iter:102, conv: 2.72454e-05)
log post: -108.392 (-108.392 + 0) (iter:103, conv: 2.5299e-05)
log post: -108.392 (-108.392 + 0) (iter:104, conv: 2.34918e-05)
log post: -108.392 (-108.392 + 0) (iter:105, conv: 2.18137e-05)
log post: -108.392 (-108.392 + 0) (iter:106, conv: 2.02555e-05)
log post: -108.392 (-108.392 + 0) (iter:107, conv: 1.88087e-05)
log post: -108.392 (-108.392 + 0) (iter:108, conv: 1.74652e-05)
log post: -108.392 (-108.392 + 0) (iter:109, conv: 1.62178e-05)
log post: -108.392 (-108.392 + 0) (iter:110, conv: 1.50595e-05)
log post: -108.392 (-108.392 + 0) (iter:111, conv: 1.39839e-05)
log post: -108.392 (-108.392 + 0) (iter:112, conv: 1.29852e-05)
log post: -108.392 (-108.392 + 0) (iter:113, conv: 1.20578e-05)
log post: -108.392 (-108.392 + 0) (iter:114, conv: 1.11967e-05)
log post: -108.392 (-108.392 + 0) (iter:115, conv: 1.0397e-05)
log post: -108.392 (-108.392 + 0) (iter:116, conv: 9.65454e-06)
log post: -108.392 (-108.392 + 0) (iter:117, conv: 8.96507e-06)
log post: -108.392 (-108.392 + 0) (iter:118, conv: 8.32486e-06)
log post: -108.392 (-108.392 + 0) (iter:119, conv: 7.73036e-06)
log post: -108.392 (-108.392 + 0) (iter:120, conv: 7.17833e-06)
log post: -108.392 (-108.392 + 0) (iter:121, conv: 6.66573e-06)
log post: -108.392 (-108.392 + 0) (iter:122, conv: 6.18973e-06)
log post: -108.392 (-108.392 + 0) (iter:123, conv: 5.74773e-06)
log post: -108.392 (-108.392 + 0) (iter:124, conv: 5.3373e-06)
log post: -108.392 (-108.392 + 0) (iter:125, conv: 4.95617e-06)
log post: -108.392 (-108.392 + 0) (iter:126, conv: 4.60227e-06)
log post: -108.392 (-108.392 + 0) (iter:127, conv: 4.27364e-06)
log post: -108.392 (-108.392 + 0) (iter:128, conv: 3.96847e-06)
log post: -108.392 (-108.392 + 0) (iter:129, conv: 3.6851e-06)
log post: -108.392 (-108.392 + 0) (iter:130, conv: 3.42197e-06)
log post: -108.392 (-108.392 + 0) (iter:131, conv: 3.17762e-06)
log post: -108.392 (-108.392 + 0) (iter:132, conv: 2.95073e-06)
log post: -108.392 (-108.392 + 0) (iter:133, conv: 2.74003e-06)
log post: -108.392 (-108.392 + 0) (iter:134, conv: 2.54439e-06)
log post: -108.392 (-108.392 + 0) (iter:135, conv: 2.36271e-06)
log post: -108.392 (-108.392 + 0) (iter:136, conv: 2.194e-06)
log post: -108.392 (-108.392 + 0) (iter:137, conv: 2.03734e-06)
log post: -108.392 (-108.392 + 0) (iter:138, conv: 1.89187e-06)
log post: -108.392 (-108.392 + 0) (iter:139, conv: 1.75679e-06)
log post: -108.392 (-108.392 + 0) (iter:140, conv: 1.63135e-06)
log post: -108.392 (-108.392 + 0) (iter:141, conv: 1.51487e-06)
log post: -108.392 (-108.392 + 0) (iter:142, conv: 1.4067e-06)
log post: -108.392 (-108.392 + 0) (iter:143, conv: 1.30626e-06)
log post: -108.392 (-108.392 + 0) (iter:144, conv: 1.21299e-06)
log post: -108.392 (-108.392 + 0) (iter:145, conv: 1.12638e-06)
log post: -108.392 (-108.392 + 0) (iter:146, conv: 1.04596e-06)
log post: -108.392 (-108.392 + 0) (iter:147, conv: 9.71275e-07) Reached convergence criterion
Using prior: Laplace(1.41421) None
KKT Swindle count 1, activeSet size = 1
update time: 1.3109e-05 in 1 iterations.
Inactive set violations: 1
KKT Swindle count 2, activeSet size = 2
update time: 0.00090787 in 134 iterations.
Saving _problems/test-smallCox-61.R
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
Saving _problems/test-survfit-23.R
Saving _problems/test-survfit-51.R
Saving _problems/test-survfit-77.R
Saving _problems/test-survfit-104.R
Using cross-validation selector type byRow
Performing 10-fold cross-validation [seed = 1792756082] 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 = 33.625
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #2 Rep #1 pred log like = 24.9457
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #3 Rep #1 pred log like = 106.597
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #4 Rep #1 pred log like = 44.5696
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #5 Rep #1 pred log like = 59.491
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #6 Rep #1 pred log like = 20.3427
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #7 Rep #1 pred log like = 14.674
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 = 112.869
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #10 Rep #1 pred log like = 0
AvgPred = 49.6943 with stdev = 36.9967
Completed at 0.333333
Next point at 3.33333 with value 0 and continue = 1
search[ 0.333333 ] = 49.6943(36.9967)
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #1 Rep #1 pred log like = 32.8915
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #2 Rep #1 pred log like = 24.792
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #3 Rep #1 pred log like = 106.149
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #4 Rep #1 pred log like = 44.6337
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #5 Rep #1 pred log like = 57.3394
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #6 Rep #1 pred log like = 20.3443
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #7 Rep #1 pred log like = 14.5878
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #8 Rep #1 pred log like = 79.7695
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #9 Rep #1 pred log like = 110.219
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #10 Rep #1 pred log like = 0
AvgPred = 49.0726 with stdev = 36.4705
Completed at 3.33333
Next point at 0.0333333 with value 0 and continue = 1
search[ 0.333333 ] = 49.6943(36.9967)
search[ 3.33333 ] = 49.0726(36.4705)
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #1 Rep #1 pred log like = 34.0061
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #2 Rep #1 pred log like = 25.0614
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #3 Rep #1 pred log like = 107.806
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #4 Rep #1 pred log like = 43.169
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #5 Rep #1 pred log like = 60.6085
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #6 Rep #1 pred log like = 20.3273
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #7 Rep #1 pred log like = 15.7525
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 = 118.443
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 ] = 49.6943(36.9967)
search[ 3.33333 ] = 49.0726(36.4705)
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #1 Rep #1 pred log like = 33.9945
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #2 Rep #1 pred log like = 25.4635
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #3 Rep #1 pred log like = 106.001
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #4 Rep #1 pred log like = 42.498
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #5 Rep #1 pred log like = 62.1884
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #6 Rep #1 pred log like = 19.9614
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #7 Rep #1 pred log like = 16.8111
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 = 118.246
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 0.00390425 with value 50.4732 and continue = 0
search[ 0.00333333 ] = 50.4216(37.6865)
search[ 0.0333333 ] = 50.4807(38.0685)
search[ 0.333333 ] = 49.6943(36.9967)
search[ 3.33333 ] = 49.0726(36.4705)
Maximum predicted log likelihood (50.4732) estimated at:
0.00390425 (variance)
22.6332 (lambda)
Fitting model at optimal hyperparameter
Using prior: Laplace(22.6332) None
Warning: BLR gradient is ill-conditioned
Enforcing convergence!
Performing 10-fold cross-validation [seed = 1792756082] 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 = 33.6279
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #2 Rep #1 pred log like = 24.9429
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #3 Rep #1 pred log like = 106.597
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #4 Rep #1 pred log like = 44.5491
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #5 Rep #1 pred log like = 59.4612
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #6 Rep #1 pred log like = 20.3426
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #7 Rep #1 pred log like = 14.6737
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #8 Rep #1 pred log like = 79.8289
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #9 Rep #1 pred log like = 112.876
Running at Laplace(2.44949) None Grid-point #1 at 0.333333 Fold #10 Rep #1 pred log like = 0
AvgPred = 49.69 with stdev = 36.9974
Completed at 0.333333
Next point at 3.33333 with value 0 and continue = 1
search[ 0.333333 ] = 49.69(36.9974)
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #1 Rep #1 pred log like = 32.9161
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #2 Rep #1 pred log like = 24.7804
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #3 Rep #1 pred log like = 106.151
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #4 Rep #1 pred log like = 44.6612
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #5 Rep #1 pred log like = 57.2991
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #6 Rep #1 pred log like = 20.3443
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #7 Rep #1 pred log like = 14.5906
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #8 Rep #1 pred log like = 79.7712
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #9 Rep #1 pred log like = 110.229
Running at Laplace(0.774597) None Grid-point #2 at 3.33333 Fold #10 Rep #1 pred log like = 0
AvgPred = 49.0743 with stdev = 36.4707
Completed at 3.33333
Next point at 0.0333333 with value 0 and continue = 1
search[ 0.333333 ] = 49.69(36.9974)
search[ 3.33333 ] = 49.0743(36.4707)
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #1 Rep #1 pred log like = 34.0058
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #2 Rep #1 pred log like = 25.063
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #3 Rep #1 pred log like = 107.809
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #4 Rep #1 pred log like = 43.169
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #5 Rep #1 pred log like = 60.6085
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #6 Rep #1 pred log like = 20.3269
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #7 Rep #1 pred log like = 15.7527
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #8 Rep #1 pred log like = 79.6331
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #9 Rep #1 pred log like = 118.447
Running at Laplace(7.74597) None Grid-point #3 at 0.0333333 Fold #10 Rep #1 pred log like = 0
AvgPred = 50.4816 with stdev = 38.0697
Completed at 0.0333333
Next point at 0.00333333 with value 0 and continue = 1
search[ 0.0333333 ] = 50.4816(38.0697)
search[ 0.333333 ] = 49.69(36.9974)
search[ 3.33333 ] = 49.0743(36.4707)
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #1 Rep #1 pred log like = 33.9947
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #2 Rep #1 pred log like = 25.464
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #3 Rep #1 pred log like = 106.001
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #4 Rep #1 pred log like = 42.498
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #5 Rep #1 pred log like = 62.1884
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #6 Rep #1 pred log like = 19.9614
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #7 Rep #1 pred log like = 16.8118
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #8 Rep #1 pred log like = 79.055
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #9 Rep #1 pred log like = 118.246
Running at Laplace(24.4949) None Grid-point #4 at 0.00333333 Fold #10 Rep #1 pred log like = 0
AvgPred = 50.422 with stdev = 37.6866
Completed at 0.00333333
Next point at 0.00379385 with value 50.4742 and continue = 0
search[ 0.00333333 ] = 50.422(37.6866)
search[ 0.0333333 ] = 50.4816(38.0697)
search[ 0.333333 ] = 49.69(36.9974)
search[ 3.33333 ] = 49.0743(36.4707)
Maximum predicted log likelihood (50.4742) estimated at:
0.00379385 (variance)
22.9601 (lambda)
Fitting model at optimal hyperparameter
Using prior: Laplace(22.9601) None
Warning: BLR gradient is ill-conditioned
Enforcing convergence!
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 10 | WARN 0 | SKIP 26 | PASS 328 ]
══ Skipped tests (26) ══════════════════════════════════════════════════════════
• 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'
• Needs debugging (1): 'test-profileLikelihood.R:126:2'
• 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'
• empty test (6): 'test-believedBroken.R:75:1', 'test-cprViaSql.R:5:1',
'test-multitypePoisson.R:113:1', 'test-multitypePoisson.R:146:1',
'test-sqlConstructor.R:101:1', 'test-weighting.R:259:1'
• for debugging purposes; simulation takes too long (1):
'test-floatingPoint.R:57:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-residuals.R:9:5'): Check Schoenfeld residuals and PH test, no strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::residuals(gfit, "schoenfeld") at test-residuals.R:9:5
2. └─survival:::residuals.coxph(gfit, "schoenfeld")
3. └─survival:::coxph.getdata(object, y = TRUE, x = TRUE, stratax = TRUE)
4. ├─stats::model.matrix(fit, data = mf)
5. └─survival:::model.matrix.coxph(fit, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-residuals.R:29:5'): Check Schoenfeld residuals and PH test, with strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::residuals(gfit, "schoenfeld") at test-residuals.R:29:5
2. └─survival:::residuals.coxph(gfit, "schoenfeld")
3. └─survival:::coxph.getdata(object, y = TRUE, x = TRUE, stratax = TRUE)
4. ├─stats::model.matrix(fit, data = mf)
5. └─survival:::model.matrix.coxph(fit, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-residuals.R:58:5'): Check Schoenfeld residuals and PH test, with sparse covariates ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::residuals(gfit, "schoenfeld") at test-residuals.R:58:5
2. └─survival:::residuals.coxph(gfit, "schoenfeld")
3. └─survival:::coxph.getdata(object, y = TRUE, x = TRUE, stratax = TRUE)
4. ├─stats::model.matrix(fit, data = mf)
5. └─survival:::model.matrix.coxph(fit, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-residuals.R:134:5'): Check residuals on large Cox regression with weighting ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::residuals(fitCoxph, type = "schoenfeld") at test-residuals.R:134:5
2. └─survival:::residuals.coxph(fitCoxph, type = "schoenfeld")
3. └─survival:::coxph.getdata(object, y = TRUE, x = TRUE, stratax = TRUE)
4. ├─stats::model.matrix(fit, data = mf)
5. └─survival:::model.matrix.coxph(fit, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-residuals.R:161:5'): Check Schoenfeld residuals and PH test, with sparse covariates ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::residuals(gfit, "schoenfeld") at test-residuals.R:161:5
2. └─survival:::residuals.coxph(gfit, "schoenfeld")
3. └─survival:::coxph.getdata(object, y = TRUE, x = TRUE, stratax = TRUE)
4. ├─stats::model.matrix(fit, data = mf)
5. └─survival:::model.matrix.coxph(fit, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-smallCox.R:61:5'): Check very small Cox example with no ties, but with/without strata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─stats::residuals(goldStrat, "schoenfeld") at test-smallCox.R:61:5
2. └─survival:::residuals.coxph(goldStrat, "schoenfeld")
3. └─survival:::coxph.getdata(object, y = TRUE, x = TRUE, stratax = TRUE)
4. ├─stats::model.matrix(fit, data = mf)
5. └─survival:::model.matrix.coxph(fit, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-survfit.R:23:5'): Check very small Cox example with no ties, breslow baseline ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(goldFit) at test-survfit.R:23:5
2. └─survival:::survfit.coxph(goldFit)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-survfit.R:51:5'): Check very small Cox example with time-ties, but no failure ties, breslow baseline ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(goldFit) at test-survfit.R:51:5
2. └─survival:::survfit.coxph(goldFit)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-survfit.R:77:5'): Check very small Cox example with failure ties, no risk-set contribution after tie, breslow baseline ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(goldFit) at test-survfit.R:77:5
2. └─survival:::survfit.coxph(goldFit)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-survfit.R:104:5'): Check very small Cox example with failure ties, with risk-set contribution after tie, breslow baseline ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─survival::survfit(goldFit) at test-survfit.R:104:5
2. └─survival:::survfit.coxph(goldFit)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
[ FAIL 10 | WARN 0 | SKIP 26 | PASS 328 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc