R Under development (unstable) (2024-10-16 r87241 ucrt) -- "Unsuffered Consequences"
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> #### Thanks to the manipulation in base namespace, see  ../R/zzz.R ,
> #### all the functions (in 'base' or namespaces that import it)
> #### starting with something like
> ####	" x <- as.matrix(x) "  or   " X <- as.array(X) "
> #### will work for 'Matrix'-matrices
> 
> ## for R_DEFAULT_PACKAGES=NULL :
> library(stats)
> library(utils)
> 
> library(Matrix)
> 
> data(KNex, package = "Matrix")
> mm <- KNex$mm
> str(m1 <- mm[1:500, 1:200])
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  ..@ i       : int [1:500] 0 2 25 27 163 165 1 3 4 6 ...
  ..@ p       : int [1:201] 0 6 10 14 18 22 27 31 35 39 ...
  ..@ Dim     : int [1:2] 500 200
  ..@ Dimnames:List of 2
  .. ..$ : NULL
  .. ..$ : NULL
  ..@ x       : num [1:500] 0.277 0.277 0.277 0.277 0.277 ...
  ..@ factors : list()
> m11 <- m1[1:100, 1:20]
> ## These now work thanks to using our as.matrix():
> str(D1 <- dist(m11))
 'dist' num [1:4950] 0.572 0 0.572 0.572 0.434 ...
 - attr(*, "Size")= int 100
 - attr(*, "Diag")= logi FALSE
 - attr(*, "Upper")= logi FALSE
 - attr(*, "method")= chr "euclidean"
 - attr(*, "call")= language dist(x = m11)
> str(rs <- apply(m1, 1, sum))
 num [1:500] 0.277 0.5 0.277 0.5 0.5 ...
> 
> stopifnot(identical(kappa(Matrix(2:5, 2)),
+                     kappa(matrix(2:5, 2))))
> ## used to seg.fault, PR#7984,
> ## because qr() was calling the wrong as.matrix()
> 
> ## also matplot() or pairs().
> 
> ## a regression test for  as.matrix.dist(.) still working
> data(USJudgeRatings, package = "datasets")
> stopifnot(c(43, 43) == dim(as.matrix(d <- dist(USJudgeRatings))))
> 
> m <- Matrix(0:5, 3, 2)
> (m2 <- Matrix(diag(c(3,1))))
2 x 2 diagonal matrix of class "ddiMatrix"
     [,1] [,2]
[1,]    3    .
[2,]    .    1
> (m3 <- crossprod(t(m))) # <- that's an S4 method; nothing "base"
3 x 3 Matrix of class "dpoMatrix"
     [,1] [,2] [,3]
[1,]    9   12   15
[2,]   12   17   22
[3,]   15   22   29
> 
> str( svd(m) )
List of 3
 $ d: num [1:2] 7.35 1
 $ u: num [1:3, 1:2] 0.393 0.561 0.729 -0.824 -0.137 ...
 $ v: num [1:2, 1:2] 0.275 0.962 0.962 -0.275
> str( lapply(eigen(m3), zapsmall))
List of 2
 $ values : num [1:3] 54 1 0
 $ vectors: num [1:3, 1:3] -0.393 -0.561 -0.729 0.824 0.137 ...
> 
> ### outer()  used to work thanks to  as.array() -- up to R 2.2.1
> ##  no longer, because the definition of outer has changed  -- FIXME?
> ## Whould work by providing an as.vector(.) method
> ##  *and*  is.array(.) \-> TRUE  which may be too strong
> ##--> For %o%: "need" to make  outer(.,.) an S3 generic
> ##    *and* provide Matrix S3 methods
> ## stopifnot(identical(outer(m, m2),
> ##                    outer(as(m,"matrix"), as(m2,"matrix"))),
> ##          identical(outer(m3, m2),
> ##                    outer(as(m3,"matrix"), as(m2,"matrix"))))
> 
> 
> cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
Time elapsed:  1.18 0.15 1.28 NA NA 
> 
> proc.time()
   user  system elapsed 
   1.18    0.15    1.28