R help - Nov 2010 - Sporadic errors when training models using CARET

Hi. I am trying to construct a svmLinear model using the "caret"
package
(see code below). Using the same data, without changing any setting,
sometimes it constructs the model successfully, and sometimes I get an index
out of bounds error. Is this unexpected behaviour? I would appreciate any
insights this issue.


Thanks.
~Kendric

> train.y
 [1] S S S S R R R R R R R R R R R R R R R R R R R R
Levels: R S
> train.x
        m1      m2
1   0.1756  0.6502
2   0.1110 -0.2217
3   0.0837 -0.1809
4  -0.3703 -0.2476
5   8.3825  2.8814
6   5.6400 12.9922
7   7.5537  7.4809
8   3.5005  5.7844
9  16.8541 16.6326
10  9.1851  8.7814
11  1.4405 11.0132
12  9.8795  2.6182
13  8.7151  4.5476
14 -0.2092 -0.7601
15  3.6876  2.5772
16  8.3776  5.0882
17  8.6567  7.2640
18 20.9386 20.1107
19 12.2903  4.7864
20 10.5920  7.5204
21 10.2679  9.5493
22  6.2023 11.2333
23 -5.0720 -4.8701
24  6.6417 11.5139
> svmLinearGrid <- expand.grid(.C=0.1)
> svmLinearFit <- train(train.x, train.y, method="svmLinear",
tuneGrid=svmLinearGrid)
Fitting: C=0.1
Error in indexes[[j]] : subscript out of bounds
> svmLinearFit <- train(train.x, train.y, method="svmLinear",
tuneGrid=svmLinearGrid)
Fitting: C=0.1
maximum number of iterations reached 0.0005031579 0.0005026807maximum number
of iterations reached 0.0002505857 0.0002506714Error in indexes[[j]] :
subscript out of bounds
> svmLinearFit <- train(train.x, train.y, method="svmLinear",
tuneGrid=svmLinearGrid)
Fitting: C=0.1
maximum number of iterations reached 0.0003270061 0.0003269764maximum number
of iterations reached 7.887867e-05 7.866367e-05maximum number of iterations
reached 0.0004087571 0.0004087466Aggregating results
Selecting tuning parameters
Fitting model on full training set


R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] kernlab_0.9-12  pamr_1.47       survival_2.35-8 cluster_1.12.3
 [5] e1071_1.5-24    class_7.3-2     caret_4.70      reshape_0.8.3
 [9] plyr_1.2.1      lattice_0.18-8

loaded via a namespace (and not attached):
[1] grid_2.11.1


-- 
MSc. Candidate
CIHR/MSFHR Training Program in Bioinformatics
University of British Columbia

	[[alternative HTML version deleted]]

Kendric,

I've seen these too and traceback() usually goes back to ksvm(). This
doesn't mean that the error is there, but the results fo traceback()
from you would be helpful.

thanks,

Max

On Mon, Nov 22, 2010 at 6:18 PM, Kendric Wang
<kendricw at interchange.ubc.ca> wrote:
> Hi. I am trying to construct a svmLinear model using the "caret"
package
> (see code below). Using the same data, without changing any setting,
> sometimes it constructs the model successfully, and sometimes I get an
index
> out of bounds error. Is this unexpected behaviour? I would appreciate any
> insights this issue.
>
>
> Thanks.
> ~Kendric
>
>
>> train.y
> ?[1] S S S S R R R R R R R R R R R R R R R R R R R R
> Levels: R S
>
>> train.x
> ? ? ? ?m1 ? ? ?m2
> 1 ? 0.1756 ?0.6502
> 2 ? 0.1110 -0.2217
> 3 ? 0.0837 -0.1809
> 4 ?-0.3703 -0.2476
> 5 ? 8.3825 ?2.8814
> 6 ? 5.6400 12.9922
> 7 ? 7.5537 ?7.4809
> 8 ? 3.5005 ?5.7844
> 9 ?16.8541 16.6326
> 10 ?9.1851 ?8.7814
> 11 ?1.4405 11.0132
> 12 ?9.8795 ?2.6182
> 13 ?8.7151 ?4.5476
> 14 -0.2092 -0.7601
> 15 ?3.6876 ?2.5772
> 16 ?8.3776 ?5.0882
> 17 ?8.6567 ?7.2640
> 18 20.9386 20.1107
> 19 12.2903 ?4.7864
> 20 10.5920 ?7.5204
> 21 10.2679 ?9.5493
> 22 ?6.2023 11.2333
> 23 -5.0720 -4.8701
> 24 ?6.6417 11.5139
>
>> svmLinearGrid <- expand.grid(.C=0.1)
>> svmLinearFit <- train(train.x, train.y,
method="svmLinear",
> tuneGrid=svmLinearGrid)
> Fitting: C=0.1
> Error in indexes[[j]] : subscript out of bounds
>
>> svmLinearFit <- train(train.x, train.y,
method="svmLinear",
> tuneGrid=svmLinearGrid)
> Fitting: C=0.1
> maximum number of iterations reached 0.0005031579 0.0005026807maximum
number
> of iterations reached 0.0002505857 0.0002506714Error in indexes[[j]] :
> subscript out of bounds
>
>> svmLinearFit <- train(train.x, train.y,
method="svmLinear",
> tuneGrid=svmLinearGrid)
> Fitting: C=0.1
> maximum number of iterations reached 0.0003270061 0.0003269764maximum
number
> of iterations reached 7.887867e-05 7.866367e-05maximum number of iterations
> reached 0.0004087571 0.0004087466Aggregating results
> Selecting tuning parameters
> Fitting model on full training set
>
>
> R version 2.11.1 (2010-05-31)
> x86_64-redhat-linux-gnu
>
> locale:
> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C
> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8
> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8
> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C
> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods
> [8] base
>
> other attached packages:
> ?[1] kernlab_0.9-12 ?pamr_1.47 ? ? ? survival_2.35-8 cluster_1.12.3
> ?[5] e1071_1.5-24 ? ?class_7.3-2 ? ? caret_4.70 ? ? ?reshape_0.8.3
> ?[9] plyr_1.2.1 ? ? ?lattice_0.18-8
>
> loaded via a namespace (and not attached):
> [1] grid_2.11.1
>
>
> --
> MSc. Candidate
> CIHR/MSFHR Training Program in Bioinformatics
> University of British Columbia
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
>


-- 

Max