8

昨天我更新了我的 R 包，从那时起并行执行 train 函数失败了。

似乎从工作人员内部调用的某些功能不可用。这些函数至少是 flatTable 和 probFunction。

我在生产机器上遇到了这个问题，并且能够在干净的 Windows 7 x64 VM 上重现它。

我在下面添加了一个最小的工作示例。尊敬的 stackoverflow 用户：感谢您的帮助！

# R 3.0.2 x64, RStudio Version 0.98.490, Windows 7 x64

data(iris)
library(caret) # 6.0-21
library(doParallel) # 1.0.6

model <- "rf"

# Fail
?probFunction
?flatTable

fitControl <- trainControl(
  method = "repeatedcv"
  , number = 5  ## 5-fold CV
  , repeats = 1   ## repeated one times
  , verboseIter =TRUE
)

#### Sequential Version ####

# Runs
train(Species ~ ., data = iris, method = model, trControl = fitControl)

#### Parallelized version ####

# Fails with 
# Error in e$fun(obj, substitute(ex), parent.frame(), e$data) : 
#  worker initialization failed: Error in eval(expr, envir, enclos): could not find function "flatTable"
cl <- makeCluster(3)
registerDoParallel(cl)

train(Species ~ ., data = iris, method = model, trControl = fitControl)

stopCluster(cl)

# Fails with 
# Error in { : task 1 failed - "could not find function "probFunction""
fitControl <- trainControl(
  method = "repeatedcv"
  , number = 5  ## 5-fold CV
  , repeats = 1   ## repeated one times
  , verboseIter =TRUE
  , classProbs = TRUE
)

cl <- makeCluster(3)
registerDoParallel(cl)

train(Species ~ ., data = iris, method = model, trControl = fitControl)

stopCluster(cl)

#### Again sequential version ####

# Fails with
# Error in summary.connection(connection) : invalid connection
train(Species ~ ., data = iris, method = model, trControl = fitControl)

R 会话信息

R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252   

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

other attached packages:
[1] e1071_1.6-1        class_7.3-9        randomForest_4.6-7 doParallel_1.0.6   iterators_1.0.6  
[6] foreach_1.4.1      caret_6.0-21       ggplot2_0.9.3.1    lattice_0.20-23  

loaded via a namespace (and not attached):
[1] car_2.0-19         codetools_0.2-8    colorspace_1.2-4   compiler_3.0.2     dichromat_2.0-0  
 [6] digest_0.6.4       grid_3.0.2         gtable_0.1.2       labeling_0.2       MASS_7.3-29      
[11] munsell_0.4.2      nnet_7.3-7         plyr_1.8           proto_0.3-10       RColorBrewer_1.0-5
[16] reshape2_1.2.2     scales_0.2.3       stringr_0.6.2      tools_3.0.2
4

2 回答 2

7

The error that you're getting is caused by a bug in caret 6.0-21 when using doParallel, doSNOW, and doMPI. It's been fixed in version 6.0-22 in R-forge, but hasn't been released to CRAN yet. If you don't want to wait for the new version to be released, you can:

  1. Downgrade to caret 5.x
  2. Install caret 6.0-22 from R-forge
  3. Install and use doSNOW 1.0.10 from R-forge rather than doParallel

The problem was caused by a change in CRAN policy that forbids the use of the ::: operator, even when referencing non-exported functions from within the same package.

Update

Caret 6.0-22 was released to CRAN on 2014-01-18. This should resolve the reported problem using caret with doSNOW and similar parallel backends.

于 2014-01-09T20:17:05.590 回答
1

could not find function正如@Steve Weston 所建议的那样，第一个错误（ ...）随着新版本的消失而消失，但第二个错误（ Error in summary.connection(connection) : invalid connection）仍然存在。

使用插入符号版本 6.0.84，我可以通过添加allowParallel = F到最后一次连续运行的 trainControl 参数来修复它。

问题中代码的最后一部分更改为：

#### Again sequential version (new) ####

fitControl_new <- trainControl(
  method = "repeatedcv"
  , number = 5  
  , repeats = 1   
  , verboseIter =TRUE
  , classProbs = TRUE
  , allowParallel = F     ## add this argument to overwrite the default TRUE
)

train(Species ~ ., data = iris, method = model, trControl = fitControl_new)
于 2021-01-26T14:01:52.733 回答