I was walking through the examples of the very nice book "Applied Predictive Modeling" by Max Kuhn and Kjell Johnson, unfortunately I got stuck in one of the examples using the train()
function and one of the GermanCredit
dataset provided by the caret
package for cross-validation of Support Vector Machines:
library(AppliedPredictiveModeling)
library(caret)
# preparing the data
data(GermanCredit)
GermanCredit <- GermanCredit[, -nearZeroVar(GermanCredit)]
GermanCredit$CheckingAccountStatus.lt.0 <- NULL
GermanCredit$SavingsAccountBonds.lt.100 <- NULL
GermanCredit$EmploymentDuration.lt.1 <- NULL
GermanCredit$EmploymentDuration.Unemployed <- NULL
GermanCredit$Personal.Male.Married.Widowed <- NULL
GermanCredit$Property.Unknown <- NULL
GermanCredit$Housing.ForFree <- NULL
set.seed(100)
inTrain <- createDataPartition(GermanCredit$Class, p = .8)[[1]]
GermanCreditTrain <- GermanCredit[ inTrain, ]
GermanCreditTest <- GermanCredit[-inTrain, ]
# Grid selection for `sigma` and `cost` tuning parameters:
library(kernlab)
set.seed(231)
sigDist <- sigest(Class ~ ., data = GermanCreditTrain, frac = 1)
svmTuneGrid <- data.frame(.sigma = sigDist[1], .C = 2^(-2:7))
# SVM classification and cross-validation
svmFit <- train(Class ~ .,
data = GermanCreditTrain,
method = "svmRadial",
preProc = c("center", "scale"),
tuneGrid = svmTuneGrid,
trControl = trainControl(method = "repeatedcv", repeats = 5,
classProbs = TRUE))
and it has thrown this error:
Error in comp(expr, env = envir, options = list(suppressUndefined = TRUE)) :
could not find function "makeCenv"
sometimes this error message:
Loading required package: class
Warning: namespace ‘compiler’ is not available and has been replaced
by .GlobalEnv when processing object ‘GermanCredit’
Error in comp(expr, env = envir, options = list(suppressUndefined = TRUE)) :
could not find function "makeCenv"
In addition: Warning message:
executing %dopar% sequentially: no parallel backend registered
Then I learned that makeCenv()
is in the doMC
package that was suggested as alternative for parallel computation or parallel processing, but I wouldn't go for this package since it is not available in Windows platform, I guess. Any alternative?
Update:
These errors appeared only when the code was run under Rstudio IDE
, things were fine from the default R console, so the problem is local to Rstudio, I guess. The time was a little bit long in R console (about 8min), though, I wonder how to speed up things given the hardware specs mentioned below.
My sessioninfo() output is here (Rstudio):
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] datasets grid splines utils stats graphics grDevices methods
[9] base
other attached packages:
[1] proxy_0.4-10 e1071_1.6-1
[3] class_7.3-9 kernlab_0.9-19
[5] caret_5.17-7 foreach_1.4.1
[7] AppliedPredictiveModeling_1.1-4 CORElearn_0.9.42
[9] rpart_4.1-3 xtable_1.7-1
[11] knitr_1.5 texreg_1.30
[13] pastecs_1.3-15 boot_1.3-9
[15] gridExtra_0.9.1 reshape2_1.2.2
[17] plyr_1.8 scales_0.2.3
[19] ggplot2_0.9.3.1 vcdExtra_0.5-11
[21] gnm_1.0-6 vcd_1.3-1
[23] corrplot_0.73 RColorBrewer_1.0-5
[25] car_2.0-19 Hmisc_3.13-0
[27] Formula_1.1-1 cluster_1.14.4
[29] xlsx_0.5.5 xlsxjars_0.5.0
[31] rJava_0.9-5 lmPerm_1.1-2
[33] coin_1.0-23 survival_2.37-4
[35] GPArotation_2012.3-1 psych_1.3.12
[37] sos_1.3-8 brew_1.0-6
[39] data.table_1.8.10 mice_2.18
[41] nnet_7.3-7 MASS_7.3-29
[43] lattice_0.20-23
loaded via a namespace (and not attached):
[1] codetools_0.2-8 colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4
[5] evaluate_0.5.1 formatR_0.10 gtable_0.1.2 iterators_1.0.6
[9] labeling_0.2 Matrix_1.1-0 modeltools_0.2-21 munsell_0.4.2
[13] mvtnorm_0.9-9996 proto_0.3-10 qvcalc_0.8-8 relimp_1.0-3
[17] stats4_3.0.2 stringr_0.6.2 tcltk_3.0.2 tools_3.0.2
sessionInfo() output from default R console:
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] datasets grDevices grid splines graphics utils stats
[8] methods base
other attached packages:
[1] e1071_1.6-1 class_7.3-9 kernlab_0.9-19 caret_5.17-7
[5] foreach_1.4.1 cluster_1.14.4 lattice_0.20-23 reshape2_1.2.2
[9] plyr_1.8 scales_0.2.3 ggplot2_0.9.3.1 lmPerm_1.1-2
[13] coin_1.0-23 survival_2.37-4 sos_1.3-8 brew_1.0-6
loaded via a namespace (and not attached):
[1] codetools_0.2-8 colorspace_1.2-4 compiler_3.0.2 dichromat_2.0-0
[5] digest_0.6.3 gtable_0.1.2 iterators_1.0.6 labeling_0.2
[9] MASS_7.3-29 modeltools_0.2-21 munsell_0.4.2 mvtnorm_0.9-9996
[13] proto_0.3-10 RColorBrewer_1.0-5 stats4_3.0.2 stringr_0.6.2
[17] tools_3.0.2
Questions:
There must be an interaction with Rstudio
since it worked well in the default R console, based on the two sessionInfo() outputs of default R console and Rstudio, the difference was compiler
package. Strange, this pkg cannot be found in CRAN, I found a note here:
http://www.inside-r.org/r-doc/compiler/compile
saying that load(compiler) would be enough, when I did this in Rstudio: it was not possible with this error message:
Error: package ‘compiler’ was built before R 3.0.0: please re-install it
Update
It worked finally from withing Rstudio after copy & paste the compiler package library from that of default R lib path to that of Rstudio lib path, but still the time is too long (about 8min), I would post a separate question of parallel processing given the hardware below and windows if that would help to find an answer sooner.
train()
function? can you pls issue the R code for this, I would be very grateful indeed.The caret code base is completely independent of doMC or any of the other "do" packages. I don't have a windows system to test with here, but I am 99% sure that this is not a reproducible problem. The package is tested nightly in several places (e.g. R-Forge) and across 3-4 different OS's, including Windows. I have never seen this issue come up, even when I've taught classes on the package to large audiences exclusively using Windows.
My guess is that you accidentally called a doMC function somewhere (even though it was not listed in your sessionInfo out).
It would be helpful if someone else can try to reproduce this error.
Thanks,
Max