readRDS()加载额外的程序包

Question

在什么情况下R中的readRDS()函数会尝试加载包/命名空间？我很惊讶在新的R session 中看到以下内容:

> loadedNamespaces()
[1] "base"      "datasets"  "graphics"  "grDevices" "methods"   "stats"    
[7] "tools"     "utils"    
> x <- readRDS('../../../../data/models/my_model.rds')
There were 19 warnings (use warnings() to see them)
> loadedNamespaces()
 [1] "base"         "class"        "colorspace"   "data.table"  
 [5] "datasets"     "dichromat"    "e1071"        "earth"       
 [9] "evaluate"     "fields"       "formatR"      "gbm"         
[13] "ggthemes"     "graphics"     "grDevices"    "grid"        
[17] "Iso"          "knitr"        "labeling"     "lattice"     
[21] "lubridate"    "MASS"         "methods"      "munsell"     
[25] "plotmo"       "plyr"         "proto"        "quantreg"    
[29] "randomForest" "RColorBrewer" "reshape2"     "rJava"       
[33] "scales"       "spam"         "SparseM"      "splines"     
[37] "stats"        "stringr"      "survival"     "tools"       
[41] "utils"        "wra"          "wra.ops"      "xlsx"        
[45] "xlsxjars"     "xts"          "zoo"     

如果这些新软件包中的任何一个都不可用，则 readRDS()失败。

提到的19条警告是:

> warnings()
Warning messages:
1: replacing previous import ‘hour’ when loading ‘data.table’
2: replacing previous import ‘last’ when loading ‘data.table’
3: replacing previous import ‘mday’ when loading ‘data.table’
4: replacing previous import ‘month’ when loading ‘data.table’
5: replacing previous import ‘quarter’ when loading ‘data.table’
6: replacing previous import ‘wday’ when loading ‘data.table’
7: replacing previous import ‘week’ when loading ‘data.table’
8: replacing previous import ‘yday’ when loading ‘data.table’
9: replacing previous import ‘year’ when loading ‘data.table’
10: replacing previous import ‘here’ when loading ‘plyr’
11: replacing previous import ‘hour’ when loading ‘data.table’
12: replacing previous import ‘last’ when loading ‘data.table’
13: replacing previous import ‘mday’ when loading ‘data.table’
14: replacing previous import ‘month’ when loading ‘data.table’
15: replacing previous import ‘quarter’ when loading ‘data.table’
16: replacing previous import ‘wday’ when loading ‘data.table’
17: replacing previous import ‘week’ when loading ‘data.table’
18: replacing previous import ‘yday’ when loading ‘data.table’
19: replacing previous import ‘year’ when loading ‘data.table’

因此，显然，它先加载了诸如 lubridate然后是 data.table之类的东西，从而随即生成了 namespace 冲突。

FWIW， unserialize()给出相同的结果。

我真正想要的是加载这些对象，而不同时加载保存它们的人当时似乎已经加载的所有东西，这就是它的工作方式。

更新:这是对象 x中的类:

> classes <- function(x) {
    cl <- c()
    for(i in x) {
      cl <- c(cl, if(is.list(i)) c(class(i), classes(i)) else class(i))
    }
    cl
  }
> unique(classes(x))
 [1] "list"              "numeric"           "rq"               
 [4] "terms"             "formula"           "call"             
 [7] "character"         "smooth.spline"     "integer"          
[10] "smooth.spline.fit"

qr来自 quantreg包，其余所有来自 base或 stats。

Answer 1

好的。这可能不是一个有用的答案(需要更多详细信息)，但我认为这至少是“在什么情况下..”这一部分的要求。

首先，我认为它不是特定于readRDS的，但对于可以被save编码的任何load'd对象，其工作方式相同。

“在什么情况下”部分:当保存的对象包含以包/命名空间环境为父环境的环境时。或者当它包含一个环境是包/命名空间环境的函数时。

require(Matrix)
foo <- list(
   a = 1,
   b = new.env(parent=environment(Matrix)),
   c = "c")
save(foo, file="foo.rda")
loadedNamespaces()   # Matrix is there!
detach("package:Matrix")
unloadNamespace("Matrix")
loadedNamespaces()   # no Matrix there!
load("foo.rda")
loadedNamespaces()   # Matrix is back again

并且以下工作也可以:

require(Matrix)
bar <- list(
   a = 1,
   b = force,
   c = "c")
environment(bar$b) <- environment(Matrix)
save(bar, file="bar.rda")
loadedNamespaces()      # Matrix is there!
detach("package:Matrix")
unloadNamespace("Matrix")
loadedNamespaces()      # no Matrix there!
load("bar.rda")
loadedNamespaces()      # Matrix is back!

我没有尝试过，但是没有理由为什么它不应该与 saveRDS/ readRDS一起工作。解决方案:如果这对保存的对象没有害处(即，如果您确定实际上不需要环境)，则可以通过替换父环境来删除它们，例如通过将 parent.env设置为有意义的内容。因此，使用上面的 foo，

parent.env(foo$b) <- baseenv()
save(foo, file="foo.rda")
loadedNamespaces()        # Matrix is there ....
unloadNamespace("Matrix")
loadedNamespaces()        # no Matrix there ...
load("foo.rda")
loadedNamespaces()        # still no Matrix ...