考虑在 R 会话中定义的以下简单函数：
nathanvan@nathanvan-N61Jq:~$ R
R version 3.0.1 (2013-05-16) -- "Good Sport"
... snip ...
> make.a.Matrix <- function(data, nrow, ncol) {
+ require(Matrix)
+ return( Matrix(data, nrow=nrow, ncol=ncol))
+ }
>
> transpose.a.Matrix <- function(data, nrow, ncol ) {
+ return(t( make.a.Matrix(data, nrow=nrow, ncol=ncol) ))
+ }
>
> make.a.Matrix(1:12, 3, 4)
Loading required package: Matrix
Loading required package: lattice
3 x 4 Matrix of class "dgeMatrix"
[,1] [,2] [,3] [,4]
[1,] 1 4 7 10
[2,] 2 5 8 11
[3,] 3 6 9 12
> transpose.a.Matrix(1:12, 3, 4)
4 x 3 Matrix of class "dgeMatrix"
[,1] [,2] [,3]
[1,] 1 2 3
[2,] 4 5 6
[3,] 7 8 9
[4,] 10 11 12
如果我们将这些相同的功能放入一个包中，则该transpose.a.Matrix功能将不再起作用。由于描述包创建过程过于冗长，我只是在此处发布了包的副本。我已经在问题的末尾发布了DESCRIPTION和文件。NAMESPACE如果其他文章是相关的，我也很乐意发布它们。让我知道！
nathanvan@nathanvan-N61Jq:~$ R
R version 3.0.1 (2013-05-16) -- "Good Sport"
... snip ...
> require(minimalbugexample)
Loading required package: minimalbugexample
Loading required package: Matrix
Loading required package: lattice
Loading required package: testthat
> make.a.Matrix(1:12, 3, 4)
3 x 4 Matrix of class "dgeMatrix"
[,1] [,2] [,3] [,4]
[1,] 1 4 7 10
[2,] 2 5 8 11
[3,] 3 6 9 12
> transpose.a.Matrix(1:12, 3, 4)
Error in t.default(make.a.Matrix(data, nrow = nrow, ncol = ncol)) :
argument is not a matrix
> transpose.a.Matrix
function(data, nrow, ncol ) {
return(t( make.a.Matrix(data, nrow=nrow, ncol=ncol) ))
}
<environment: namespace:minimalbugexample>
我认为这里的关键是关于命名空间的一些奇怪的东西。请注意，如果我调试该函数，我可以手动调用Matrix::t它，它会在base::t失败并出现相同错误时工作。
> debug(transpose.a.Matrix)
> transpose.a.Matrix(1:12, 3, 4)
debugging in: transpose.a.Matrix(1:12, 3, 4)
debug at /home/nathanvan/Ubuntu One/workspace/experimental-design/software/minimalbugexample/R/use-Matrix-package.R#31: {
return(t(make.a.Matrix(data, nrow = nrow, ncol = ncol)))
}
Browse[2]> t(Matrix(1:12, 3, 4))
Error in t.default(Matrix(1:12, 3, 4)) : argument is not a matrix
Browse[2]> t
function (x)
UseMethod("t")
<bytecode: 0x46b0a88>
<environment: namespace:base>
Browse[2]> Matrix::t(Matrix(1:12, 3, 4))
4 x 3 Matrix of class "dgeMatrix"
[,1] [,2] [,3]
[1,] 1 2 3
[2,] 4 5 6
[3,] 7 8 9
[4,] 10 11 12
Browse[2]> base::t(Matrix(1:12, 3, 4))
Error in t.default(Matrix(1:12, 3, 4)) : argument is not a matrix
然而 using showMethods，它表明只要 usingt应该找到正确的，即使它没有。
Browse[2]> showMethods('t')
Function: t (package base)
x="ANY"
x="CsparseMatrix"
x="dgeMatrix"
x="diagonalMatrix"
x="dppMatrix"
x="dsCMatrix"
x="dspMatrix"
x="dsTMatrix"
x="dsyMatrix"
x="dtpMatrix"
x="dtrMatrix"
x="dtTMatrix"
x="lgeMatrix"
x="lspMatrix"
x="lsTMatrix"
x="lsyMatrix"
x="ltpMatrix"
x="ltrMatrix"
x="ltTMatrix"
x="matrix"
(inherited from: x="ANY")
x="Matrix"
x="ngeMatrix"
x="nspMatrix"
x="nsTMatrix"
x="nsyMatrix"
x="ntpMatrix"
x="ntrMatrix"
x="ntTMatrix"
x="pMatrix"
x="RsparseMatrix"
x="TsparseMatrix"
现在，我可以通过编辑包的源来“修复”它，以便transpose.a.Matrix函数指定它需要该Matrix::t方法：
transpose.a.Matrix <- function(data, nrow, ncol ) {
require(Matrix)
return(Matrix::t( make.a.Matrix(data, nrow=nrow, ncol=ncol) ))
}
但这似乎不需要它。我错过了什么？
我的说明文件是
Package: minimalbugexample
Title:
Description:
Version: 0.1
Author: Nathan VanHoudnos <nathanvan@letterafterFmail.com>
Maintainer: Nathan VanHoudnos <nathanvan@letterafterFmail.com>
Depends:
R (>= 3.0.1),
Matrix (>= 1.0),
testthat
License: GPL
LazyData: true
Collate:
'minimalbugexample-package.r'
'use-Matrix-package.R'
我的命名空间文件是
export(make.a.Matrix)
export(transpose.a.Matrix)
我可以根据要求发布其他作品。