Dear all, I am using caret package to analyze a microarray dataset with feature selection using sbf(). My dataset is 3500 samples with 2200 genes, the outcome Y variable is a factor of 12 levels. I used the following script to run the feature selection:
library(caret) ctrl <- sbfControl(functions=rfSBF, method='repeatedcv', repeats=5) ### x is a matrix of 3500x2200, y is a factor of 12 levels obj <- sbf(x, y, sbfControl=ctrl) But it has been more than 15 hours, the code is still running! My computer has the following specifications: Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz 2.00 GHz, 8 cores 16.0 GB Does anyone know if my script has any issues, or it is normal for sbf() to run this long? Thank you! Andrew > sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 [2] LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.utf8 time zone: America/Los_Angeles tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] caret_6.0-94 lattice_0.21-8 ggplot2_3.4.2 loaded via a namespace (and not attached): [1] utf8_1.2.3 future_1.33.0 generics_0.1.3 [4] class_7.3-22 stringi_1.7.12 pROC_1.18.2 [7] listenv_0.9.0 digest_0.6.32 magrittr_2.0.3 [10] grid_4.3.1 timechange_0.2.0 iterators_1.0.14 [13] foreach_1.5.2 plyr_1.8.8 Matrix_1.5-4.1 [16] ModelMetrics_1.2.2.2 nnet_7.3-19 survival_3.5-5 [19] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 [22] codetools_0.2-19 lava_1.7.2.1 cli_3.6.1 [25] rlang_1.1.1 hardhat_1.3.0 parallelly_1.36.0 [28] future.apply_1.11.0 munsell_0.5.0 splines_4.3.1 [31] withr_2.5.0 prodlim_2023.03.31 tools_4.3.1 [34] parallel_4.3.1 reshape2_1.4.4 dplyr_1.1.2 [37] colorspace_2.1-0 recipes_1.0.6 globals_0.16.2 [40] vctrs_0.6.3 R6_2.5.1 rpart_4.1.19 [43] stats4_4.3.1 lifecycle_1.0.3 lubridate_1.9.2 [46] stringr_1.5.0 MASS_7.3-60 pkgconfig_2.0.3 [49] pillar_1.9.0 gtable_0.3.3 glue_1.6.2 [52] data.table_1.14.8 Rcpp_1.0.10 tibble_3.2.1 [55] tidyselect_1.2.0 nlme_3.1-162 ipred_0.9-14 [58] timeDate_4022.108 gower_1.0.1 compiler_4.3.1 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.