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surv.blackboost breaks when predicting on one data point #309

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hbaniecki opened this issue Jan 13, 2023 · 2 comments
Closed

surv.blackboost breaks when predicting on one data point #309

hbaniecki opened this issue Jan 13, 2023 · 2 comments

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@hbaniecki
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Description

I tried to debug it, and the actual error occurred in this line
https://github.com/mlr-org/mlr3/blob/435c9d13fae39ef3f3f6cf40cbfae6fc9d19a039/R/worker.R#L175-L182

Possibly connected with mlr3extralearners, mboost.

Reproducible example

library(mlr3proba)
#> Loading required package: mlr3
#> Warning: package 'mlr3' was built under R version 4.2.2
library(mlr3extralearners)
library(survival)
task_veteran <- as_task_surv(veteran, time = "time", event = "status", type = "right")
learner_ranger <- lrn("surv.blackboost")
learner_ranger$train(task_veteran)
learner_ranger$predict_newdata(veteran[1, -c(3, 4)])
#> Error in `colnames<-`(`*tmp*`, value = rownames(newdata)): attempt to set 'colnames' on an object with less than two dimensions

Created on 2023-01-13 with reprex v2.0.2

Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.1 (2022-06-23 ucrt)
#>  os       Windows 10 x64 (build 19044)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  English_United Kingdom.utf8
#>  ctype    English_United Kingdom.utf8
#>  tz       Europe/Warsaw
#>  date     2023-01-13
#>  pandoc   2.19.2 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package           * version     date (UTC) lib source
#>  backports           1.4.1       2021-12-13 [1] CRAN (R 4.2.0)
#>  checkmate           2.1.0       2022-04-21 [1] CRAN (R 4.2.2)
#>  cli                 3.4.1       2022-09-23 [1] CRAN (R 4.2.2)
#>  codetools           0.2-18      2020-11-04 [2] CRAN (R 4.2.1)
#>  colorspace          2.0-3       2022-02-21 [1] CRAN (R 4.2.0)
#>  crayon              1.5.0       2022-02-14 [1] CRAN (R 4.2.0)
#>  data.table          1.14.6      2022-11-16 [1] CRAN (R 4.2.2)
#>  dictionar6          0.1.3       2021-09-13 [1] CRAN (R 4.2.2)
#>  digest              0.6.31      2022-12-11 [1] CRAN (R 4.2.2)
#>  distr6              1.6.12      2023-01-13 [1] Github (alan-turing-institute/distr6@6459958)
#>  dplyr               1.0.10      2022-09-01 [1] CRAN (R 4.2.2)
#>  evaluate            0.19        2022-12-13 [1] CRAN (R 4.2.2)
#>  fansi               1.0.3       2022-03-24 [1] CRAN (R 4.2.2)
#>  fastmap             1.1.0       2021-01-25 [1] CRAN (R 4.2.0)
#>  Formula             1.2-4       2020-10-16 [1] CRAN (R 4.2.0)
#>  fs                  1.5.2       2021-12-08 [1] CRAN (R 4.2.0)
#>  future              1.30.0      2022-12-16 [1] CRAN (R 4.2.2)
#>  generics            0.1.2       2022-01-31 [1] CRAN (R 4.2.0)
#>  ggplot2             3.4.0       2022-11-04 [1] CRAN (R 4.2.2)
#>  globals             0.16.2      2022-11-21 [1] CRAN (R 4.2.2)
#>  glue                1.6.2       2022-02-24 [1] CRAN (R 4.2.0)
#>  gtable              0.3.1       2022-09-01 [1] CRAN (R 4.2.1)
#>  highr               0.9         2021-04-16 [1] CRAN (R 4.2.0)
#>  htmltools           0.5.2       2021-08-25 [1] CRAN (R 4.2.0)
#>  inum                1.0-4       2021-04-12 [1] CRAN (R 4.2.1)
#>  knitr               1.40        2022-08-24 [1] CRAN (R 4.2.1)
#>  lattice             0.20-45     2021-09-22 [2] CRAN (R 4.2.1)
#>  lgr                 0.4.4       2022-09-05 [1] CRAN (R 4.2.2)
#>  libcoin             1.0-9       2021-09-27 [1] CRAN (R 4.2.1)
#>  lifecycle           1.0.3       2022-10-07 [1] CRAN (R 4.2.1)
#>  listenv             0.9.0       2022-12-16 [1] CRAN (R 4.2.2)
#>  magrittr            2.0.2       2022-01-26 [1] CRAN (R 4.2.0)
#>  Matrix              1.5-1       2022-09-13 [1] CRAN (R 4.2.1)
#>  mboost              2.9-7       2022-04-26 [1] CRAN (R 4.2.2)
#>  mlr3              * 0.14.1      2022-11-02 [1] CRAN (R 4.2.2)
#>  mlr3extralearners * 0.6.0-9000  2023-01-13 [1] Github (mlr-org/mlr3extralearners@9a343ab)
#>  mlr3misc            0.11.0-9000 2022-11-07 [1] https://mlr-org.r-universe.dev (R 4.2.2)
#>  mlr3pipelines       0.4.2       2022-09-20 [1] CRAN (R 4.2.2)
#>  mlr3proba         * 0.4.16      2023-01-13 [1] Github (mlr-org/mlr3proba@f568abe)
#>  mlr3viz             0.6.0       2023-01-12 [1] CRAN (R 4.2.1)
#>  munsell             0.5.0       2018-06-12 [1] CRAN (R 4.2.0)
#>  mvtnorm             1.1-3       2021-10-08 [1] CRAN (R 4.2.0)
#>  nnls                1.4         2012-03-19 [1] CRAN (R 4.2.0)
#>  ooplah              0.2.0       2022-01-21 [1] CRAN (R 4.2.2)
#>  palmerpenguins      0.1.1       2022-08-15 [1] CRAN (R 4.2.2)
#>  paradox             0.11.0      2022-11-21 [1] CRAN (R 4.2.2)
#>  parallelly          1.33.0      2022-12-14 [1] CRAN (R 4.2.2)
#>  param6              0.2.4       2022-11-09 [1] Github (xoopR/param6@0fa3577)
#>  partykit            1.2-16      2022-06-20 [1] CRAN (R 4.2.1)
#>  pillar              1.8.1       2022-08-19 [1] CRAN (R 4.2.1)
#>  pkgconfig           2.0.3       2019-09-22 [1] CRAN (R 4.2.0)
#>  pracma              2.4.2       2022-09-22 [1] CRAN (R 4.2.2)
#>  purrr               0.3.4       2020-04-17 [1] CRAN (R 4.2.0)
#>  quadprog            1.5-8       2019-11-20 [1] CRAN (R 4.2.0)
#>  R.cache             0.15.0      2021-04-30 [1] CRAN (R 4.2.0)
#>  R.methodsS3         1.8.1       2020-08-26 [1] CRAN (R 4.2.0)
#>  R.oo                1.24.0      2020-08-26 [1] CRAN (R 4.2.0)
#>  R.utils             2.11.0      2021-09-26 [1] CRAN (R 4.2.0)
#>  R6                  2.5.1       2021-08-19 [1] CRAN (R 4.2.0)
#>  Rcpp                1.0.9       2022-07-08 [1] CRAN (R 4.2.2)
#>  reprex              2.0.2       2022-08-17 [1] CRAN (R 4.2.2)
#>  rlang               1.0.6       2022-09-24 [1] CRAN (R 4.2.1)
#>  rmarkdown           2.18        2022-11-09 [1] CRAN (R 4.2.2)
#>  rpart               4.1.16      2022-01-24 [2] CRAN (R 4.2.1)
#>  rstudioapi          0.14        2022-08-22 [1] CRAN (R 4.2.1)
#>  scales              1.2.1       2022-08-20 [1] CRAN (R 4.2.1)
#>  sessioninfo         1.2.2       2021-12-06 [1] CRAN (R 4.2.0)
#>  set6                0.2.5       2022-11-09 [1] Github (xoopR/set6@e65ffee)
#>  stabs               0.6-4       2021-01-29 [1] CRAN (R 4.2.1)
#>  stringi             1.7.6       2021-11-29 [1] CRAN (R 4.2.0)
#>  stringr             1.4.1       2022-08-20 [1] CRAN (R 4.2.1)
#>  styler              1.6.2       2021-09-23 [1] CRAN (R 4.2.0)
#>  survival          * 3.3-1       2022-03-03 [2] CRAN (R 4.2.1)
#>  tibble              3.1.8       2022-07-22 [1] CRAN (R 4.2.1)
#>  tidyselect          1.2.0       2022-10-10 [1] CRAN (R 4.2.2)
#>  utf8                1.2.2       2021-07-24 [1] CRAN (R 4.2.0)
#>  uuid                1.1-0       2022-04-19 [1] CRAN (R 4.2.0)
#>  vctrs               0.5.1       2022-11-16 [1] CRAN (R 4.2.2)
#>  withr               2.5.0       2022-03-03 [1] CRAN (R 4.2.1)
#>  xfun                0.29        2021-12-14 [1] CRAN (R 4.2.0)
#>  yaml                2.3.6       2022-10-18 [1] CRAN (R 4.2.1)
#> 
#>  [1] C:/Users/hbani/AppData/Local/R/win-library/4.2
#>  [2] C:/Program Files/R/R-4.2.1/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────
@hbaniecki
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Author

Found the origin of the problem, and it's solved via boost-R/mboost#118

@RaphaelS1
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Collaborator

Thanks I'm closing then

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