Error with train function in carriage when using glmnet and 2 classes

Question

The following code crashes, for no reason I can distinguish.

library(caret) data(iris) TrainData <- iris[,1:4] TrainClasses <- factor(ifelse(iris[,5]=='versicolor','versicolor','other')) model1 <- train(TrainData,TrainClasses,method='glmnet') 

With the following error:

 Error in { : task 1 failed - "'n' must be a positive integer >= 'x'" 

If sub in another model, for example glm , it works fine. If I use 3 classes, TrainClasses <- iris[,5] , it also works fine.

What about the two classes uniquely causes the glmnet method to fail?

This is version R of version 2.14.0, version 5.09-006 with a carriage, on the windows. The same error occurs on both my mac and linux.

Answer 1

I can’t give you an answer about why you get an error message (since the code works fine on my machine), but I suggest you follow the recommendations in the R-hel Wiring Guide and include more detailed information about your versions and settings .:

 > model1 150 samples 4 predictors 2 classes: 'other', 'versicolor' No pre-processing Resampling: Bootstrap (25 reps) Summary of sample sizes: 150, 150, 150, 150, 150, 150, ... Resampling results across tuning parameters: alpha lambda Accuracy Kappa Accuracy SD Kappa SD 0.1 0.1 0.698 0.19 0.0419 0.0891 0.1 0.462 0.675 0.0311 0.0399 0.0719 # >>> snipped the rest of a page of code 

I have a fairly complete session, and you, of course, would have been different. Conflicts may arise due to functions being masked by other packages that were downloaded later in the session. There were a few warnings when I loaded the carriage just now.

 > sessionInfo() R version 2.14.0 Patched (2011-11-13 r57650) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools stats4 grid splines stats graphics grDevices utils [9] datasets methods base other attached packages: [1] glmnet_1.7.1 Matrix_1.0-1 e1071_1.6 class_7.3-3 [5] caret_5.09-012 foreach_1.3.2 codetools_0.2-8 iterators_1.0.5 [9] cluster_1.14.1 mlogit_0.2-1 maxLik_1.0-2 miscTools_0.6-10 [13] lmtest_0.9-29 statmod_1.4.13 Formula_1.0-1 mvbutils_2.5.101 [17] data.table_1.7.1 party_0.9-99995 vcd_1.2-12 colorspace_1.1-0 [21] strucchange_1.4-6 sandwich_2.2-8 coin_1.0-20 modeltools_0.2-18 [25] lubridate_0.2.5 quantreg_4.71 SparseM_0.89 raster_1.9-41 [29] MASS_7.3-16 ks_1.8.4 misc3d_0.8-1 rgl_0.92.798 [33] mvtnorm_0.9-9991 KernSmooth_2.23-7 sp_0.9-91 latticeExtra_0.6-19 [37] RColorBrewer_1.0-5 zoo_1.7-6 ggplot2_0.8.9 proto_0.3-9.2 [41] reshape_0.8.4 plyr_1.6 rms_3.3-2 Hmisc_3.9-0 [45] survival_2.36-10 sos_1.3-1 brew_1.0-6 lattice_0.20-0 loaded via a namespace (and not attached): [1] compiler_2.14.0 digest_0.5.1 stringr_0.5