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我正在浏览 Max Kuhn 和 Kjell Johnson 的非常好的书“应用预测建模”中的示例,不幸的是,我陷入了使用该train()函数的示例之一和支持交叉验证包GermanCredit提供的数据集之一caret向量机:

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))  

它抛出了这个错误:

Error in comp(expr, env = envir, options = list(suppressUndefined = TRUE)) : 
  could not find function "makeCenv"

有时这个错误信息:

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Warning: namespace ‘compiler’ is not available and has been replaced
by .GlobalEnv when processing object ‘GermanCredit’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

然后我了解到这makeCenv()是在doMC建议作为并行计算或并行处理的替代方案的包中,但我不会选择这个包,因为它在 Windows 平台上不可用,我猜。有什么选择吗?

更新: 这些错误仅在代码运行时出现Rstudio IDE,默认的 R 控制台一切正常,所以问题出在 Rstudio 本地,我猜。R 控制台的时间有点长(大约 8 分钟),不过,鉴于下面提到的硬件规格,我想知道如何加快速度。

我的 sessioninfo() 输出在这里(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      

默认 R 控制台的 sessionInfo() 输出:

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       

问题:

  1. 必须有一个交互,Rstudio因为它在默认 R 控制台中运行良好,基于默认 R 控制台和 Rstudio 的两个 sessionInfo() 输出,区别在于compiler包。奇怪,在 CRAN 中找不到这个 pkg,我在这里找到了一个注释: http://www.inside-r.org/r-doc/compiler/compile 说 load(compiler) 就足够了,当我这样做时Rstudio:无法使用此错误消息:

    错误:包“编译器”是在 R 3.0.0 之前构建的:请重新安装它

更新
在将编译器包库从默认R lib路径复制并粘贴到Rstudio lib路径之后,它终于从withing Rstudio工作了,但是时间仍然太长(大约8分钟),我会发布一个单独的并行处理问题鉴于下面的硬件和 Windows,如果这有助于更快地找到答案。

  1. 我的笔记本电脑是 2.1GHz 双核处理器,3GB,windows 32bit,知道如何用train()函数进行并行处理吗?您能否为此发出 R 代码,我将非常感激。
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2 回答 2

1

插入符号代码库完全独立于 doMC 或任何其他“do”包。我在这里没有要测试的 Windows 系统,但我 99% 确信这不是可重现的问题。该软件包每晚在几个地方(例如 R-Forge)和跨 3-4 个不同的操作系统(包括 Windows)进行测试。我从未见过这个问题出现过,即使我已经专门使用 Windows 向大量受众讲授了有关软件包的课程。

我的猜测是你不小心在某个地方调用了一个 doMC 函数(即使它没有在你的 sessionInfo 中列出)。

如果其他人可以尝试重现此错误,那将很有帮助。

谢谢,

最大限度

于 2014-01-01T21:48:04.210 回答
1

升级 R

    sudo su
    echo "deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/" >> /etc/apt/sources.list
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
    apt-get update
    apt-get upgrade
于 2016-02-17T13:16:49.793 回答