R Under development (unstable) (2023-11-05 r85474 ucrt) -- "Unsuffered Consequences"
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> ### Testing the group methods --- some also happens in ./Class+Meth.R
>
> ## for R_DEFAULT_PACKAGES=NULL :
> library(stats)
> library(utils)
>
> library(Matrix)
> source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
Loading required package: tools
> assertErrV <- function(e) tools::assertError(e, verbose=TRUE)
>
> cat("doExtras:",doExtras,"\n")
doExtras: FALSE
> options(nwarnings = 1e4)
>
> set.seed(2001)
>
> mm <- Matrix(rnorm(50 * 7), ncol = 7)
> xpx <- crossprod(mm)# -> "factors" in mm !
> round(xpx, 3) # works via "Math2"
7 x 7 Matrix of class "dsyMatrix"
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 47.565 -6.382 -4.728 -9.123 16.727 1.727 2.572
[2,] -6.382 54.324 -1.016 1.032 -7.856 -0.907 -0.923
[3,] -4.728 -1.016 46.545 4.594 -2.694 -13.324 -4.899
[4,] -9.123 1.032 4.594 47.742 -3.846 -9.994 -0.052
[5,] 16.727 -7.856 -2.694 -3.846 49.438 8.762 0.372
[6,] 1.727 -0.907 -13.324 -9.994 8.762 50.182 -1.418
[7,] 2.572 -0.923 -4.899 -0.052 0.372 -1.418 44.602
>
> y <- rnorm(nrow(mm))
> xpy <- crossprod(mm, y)
> res <- solve(xpx, xpy)
> signif(res, 4) # 7 x 1 Matrix
7 x 1 Matrix of class "dgeMatrix"
[,1]
[1,] 0.05242
[2,] -0.17070
[3,] 0.09749
[4,] -0.02275
[5,] 0.11190
[6,] 0.13720
[7,] -0.04519
>
> stopifnot(all(signif(res) == signif(res, 6)),
+ all(round (xpx) == round (xpx, 0)))
>
> ## exp(): component wise
> signif(dd <- (expm(xpx) - exp(xpx)) / 1e34, 3)# 7 x 7
7 x 7 Matrix of class "dsyMatrix"
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 4.780 -2.800 -3.200 -3.690 5.100 4.300 0.723
[2,] -2.800 1.640 1.880 2.160 -2.990 -2.520 -0.424
[3,] -3.200 1.880 2.140 2.470 -3.420 -2.880 -0.484
[4,] -3.690 2.160 2.470 2.850 -3.940 -3.320 -0.558
[5,] 5.100 -2.990 -3.420 -3.940 5.450 4.590 0.772
[6,] 4.300 -2.520 -2.880 -3.320 4.590 3.870 0.651
[7,] 0.723 -0.424 -0.484 -0.558 0.772 0.651 0.109
>
> validObject(xpx)
[1] TRUE
> validObject(xpy)
[1] TRUE
> validObject(dd)
[1] TRUE
>
> ## "Math" also, for log() and [l]gamma() which need special treatment
> stopifnot(exprs = {
+ identical(exp(res)@x, exp(res@x))
+ identical(log(abs(res))@x, log(abs((res@x))))
+ identical(lgamma(res)@x, lgamma(res@x))
+ })
>
> ## "Arith" / "Ops"
> M <- Matrix(1:12, 4,3)
> m <- cbind(4:1)
> stopifnot(exprs = {
+ identical(M*m, M*c(m)) # M*m failed in Matrix_1.3-3 pre-release:
+ identical(m*M, c(m)*M)
+ ## M*m: Error in eval(....) : object 'x1' not found
+ isValid(M1 <- M[, 1, drop=FALSE], "dgeMatrix")
+ identical(M*M1, M*M1[,1]) # M*M1 failed ..
+ identical(M-M1, M-M1[,1])
+ identical(M/M1, M/M1[,1])
+ identical(M1*M, M1[,1]*M)
+ identical(M1-M, M1[,1]-M)
+ identical(M1/M, M1[,1]/M)
+ })
>
>
>
> ###--- sparse matrices ---------
>
> mC <- Matrix(c(0, 0, 2:0), 3, 5)
> sm <- sin(mC)
> stopifnot(class(sm) == class(mC), class(mC) == class(mC^2),
+ dim(sm) == dim(mC),
+ class(0 + 100*mC) == class(mC),
+ all.equal(0.1 * ((0 + 100*mC)/10), mC),
+ all.equal(sqrt(mC ^ 2), mC),
+ identical(mC^2, mC * mC),
+ identical(mC*2, mC + mC)
+ )
>
> x <- Matrix(rbind(0,cbind(0, 0:3,0,0,-1:2,0),0))
> x # sparse
6 x 6 sparse Matrix of class "dgCMatrix"
[1,] . . . . . .
[2,] . . . . -1 .
[3,] . 1 . . . .
[4,] . 2 . . 1 .
[5,] . 3 . . 2 .
[6,] . . . . . .
> (x2 <- x + 10*t(x))
6 x 6 sparse Matrix of class "dgCMatrix"
[1,] . . . . . .
[2,] . . 10 20 29 .
[3,] . 1 . . . .
[4,] . 2 . . 1 .
[5,] . -7 . 10 22 .
[6,] . . . . . .
> stopifnot(is(x2, "sparseMatrix"),
+ identical(x2, t(x*10 + t(x))),
+ identical(x, as((x + 10) - 10, "CsparseMatrix")))
>
> (px <- Matrix(x^x - 1))#-> sparse again
6 x 6 sparse Matrix of class "dgCMatrix"
[1,] . . . . . .
[2,] . . . . -2 .
[3,] . . . . . .
[4,] . 3 . . . .
[5,] . 26 . . 3 .
[6,] . . . . . .
> stopifnot(px@i == c(3,4,1,4),
+ px@x == c(3,26,-2,3))
>
> ## From: "Florent D." .. Thu, 23 Feb 2012 -- bug report
> ##---> MM: Make a regression test:
> tst <- function(n, i = 1) {
+ stopifnot(i >= 1, n >= i)
+ D <- .sparseDiagonal(n)
+ ee <- numeric(n) ; ee[i] <- 1
+ stopifnot(all(D - ee == diag(n) - ee),
+ all(D * ee == diag(n) * ee),
+ all(ee - D == ee - diag(n)),
+ {C <- (ee / D == ee / diag(n)); all(is.na(C) | C)},
+ TRUE)
+ }
> nn <- if(doExtras) 27 else 7
> tmp <- sapply(1:nn, tst) # failed in Matrix 1.0-4
> i <- sapply(1:nn, function(i) sample(i,1))
> tmp <- mapply(tst, n= 1:nn, i= i)# failed too
>
> (lsy <- new("lsyMatrix", Dim = c(2L,2L), x=c(TRUE,FALSE,TRUE,TRUE)))
2 x 2 Matrix of class "lsyMatrix"
[,1] [,2]
[1,] TRUE TRUE
[2,] TRUE TRUE
> nsy <- as(lsy, "nMatrix")
> (t1 <- new("ltrMatrix", Dim = c(1L,1L), x = TRUE))
1 x 1 Matrix of class "ltrMatrix"
[,1]
[1,] TRUE
> (t2 <- new("ltrMatrix", Dim = c(2L,2L), x = rep(TRUE,4)))
2 x 2 Matrix of class "ltrMatrix"
[,1] [,2]
[1,] TRUE TRUE
[2,] . TRUE
> stopifnot(all(lsy), # failed in Matrix 1.0-4
+ all(nsy), # dito
+ all(t1), # "
+ ## ok previously (all following):
+ !all(t2),
+ all(sqrt(lsy) == 1))
> dsy <- lsy+1
>
> D3 <- Diagonal(x=4:2); L7 <- Diagonal(7) > 0
> validObject(xpp <- pack(round(xpx,2)))
[1] TRUE
> lsp <- xpp > 0
> (dsyU <- .diag2dense(D3, ".", "s"))
3 x 3 Matrix of class "dsyMatrix"
[,1] [,2] [,3]
[1,] 4 0 0
[2,] 0 3 0
[3,] 0 0 2
> lsyU <- .diag2dense(Diagonal(5) > 0, ".", "s")
> str(lsyU)
Formal class 'lsyMatrix' [package "Matrix"] with 5 slots
..@ Dim : int [1:2] 5 5
..@ Dimnames:List of 2
.. ..$ : NULL
.. ..$ : NULL
..@ x : logi [1:25] TRUE FALSE FALSE FALSE FALSE FALSE ...
..@ uplo : chr "U"
..@ factors : list()
> stopifnot({
+ isValid(dsyU, "dsyMatrix") && dsyU@uplo == "U"
+ isValid(dsyL <- t(dsyU), "dsyMatrix") && dsyL@uplo == "L"
+ isValid(dspU <- pack(dsyU), "dspMatrix") && dspU@uplo == "U"
+ isValid(dspL <- pack(dsyL), "dspMatrix") && dspL@uplo == "L"
+ identical(dspU, t(dspL))
+ isValid(lsyU, "lsyMatrix") && lsyU@uplo == "U"
+ isValid(lsyL <- t(lsyU), "lsyMatrix") && lsyL@uplo == "L"
+ isValid(lspU <- pack(lsyU), "lspMatrix") && lspU@uplo == "U"
+ isValid(lspL <- pack(lsyL), "lspMatrix") && lspL@uplo == "L"
+ identical(lspL, t(lspU))
+ ##
+ ## log(x, ) -- was mostly *wrong* upto 2019-10 [Matrix <= 1.2-17]
+ all.equal(log(abs(dsy), 2), log2(abs(dsy)))
+ all.equal(log(abs(dsyL),2), log2(abs(dsyL)))
+ all.equal(log(abs(dspU),2), log2(abs(dspU)))
+ all.equal(log(abs(dspL),2), log2(abs(dspL)))
+ ## These always worked, as {0,1} -> {-Inf,0} independent of 'base':
+ all.equal(log(abs(lsy), 2), log2(abs(lsy)))
+ all.equal(log(abs(lsyL),2), log2(abs(lsyL)))
+ all.equal(log(abs(lspU),2), log2(abs(lspU)))
+ all.equal(log(abs(lspL),2), log2(abs(lspL)))
+ ##
+ all.equal(log(abs(res), 2), log2(abs(res)))
+ all.equal(log(abs(xpy), 2), log2(abs(xpy)))
+ all.equal(log(abs(xpp), 2), log2(abs(xpp)))
+ all.equal(log(abs( D3), 2), log2(abs( D3)))
+ all.equal(log(abs( L7), 2), log2(abs( L7)))
+ })
> showProc.time()
Time (user system elapsed): 0.31 0.01 0.33
>
> ## is.finite() -- notably for symmetric packed / uplo="L" with NA :
> spU <- new("dspMatrix", Dim = c(3L, 3L), x = c(0, NA, 0, NA, NA, 0), uplo = "U")
> sU <- new("dsyMatrix", Dim = c(3L, 3L), x = c(1, NA, NA, NA, 1, NA, 8, 2, 1), uplo = "U")
> sL <- t(sU)
> spL <- t(spU)
> trU <- triu(spU)
> trL <- tril(spL)
> stopifnot(exprs = {
+ spL@uplo == "L"
+ trU@uplo == "U"
+ trL@uplo == "L"
+ identical(trU, triu(spL))
+ identical(trL, tril(spU))
+ })
> isU <- is.finite(sU)
> isL <- is.finite(sL)
> stopifnot(exprs = {
+ identical(isU, t(isL))
+ all(isU == isL)
+ which(!isU, arr.ind = TRUE) == c(2:1, 1:2)
+ })
> isFu <- is.finite(spU)
> isFl <- is.finite(spL)
> isFtu <- is.finite(trU)
> isFtl <- is.finite(trL)
> stopifnot(exprs = {
+ all(isFu == diag(TRUE, 3))
+ all(isFu == isFl) # has failed till 2022-06-11
+ isTriangular(isFtu)
+ isTriangular(isFtl)
+ identical(rep(TRUE, 6), pack(tril(isFtu))@x)
+ identical(rep(TRUE, 6), pack(triu(isFtl))@x)
+ })
>
> showProc.time()
Time (user system elapsed): 0.02 0 0.02
> set.seed(111)
> local({
+ for(i in 1:(if(doExtras) 20 else 5)) {
+ M <- rspMat(n=1000, 200, density = 1/20)
+ v <- rnorm(ncol(M))
+ m <- as(M,"matrix")
+ stopifnot(all(t(M)/v == t(m)/v))
+ cat(".")
+ }});cat("\n")
.....
>
> ## Now just once, with a large such matrix:
> local({
+ n <- 100000; m <- 30000
+ AA <- rspMat(n, m, density = 1/20000)
+ v <- rnorm(m)
+ st <- system.time({
+ BB <- t(AA)/v # should happen *fast*
+ stopifnot(dim(BB) == c(m,n), is(BB, "sparseMatrix"))
+ })
+ str(BB)
+ print(st)
+ if(Sys.info()[["sysname"]] == "Linux") {
+ mips <- try(as.numeric(sub(".*: *", '',
+ grep("bogomips", readLines("/proc/cpuinfo"),
+ ignore.case=TRUE, # e.g. ARM : "BogoMIPS"
+ value=TRUE)[[1]])))
+ print(mips)
+ if(is.numeric(mips) && all(mips) > 0 && doExtras)
+ # doExtras: valgrind (2023-07-26) gave large 'st[1]'
+ stopifnot(st[1] < 1000/mips)# ensure there was no gross inefficiency
+ }
+ })
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
..@ i : int [1:150000] 12313 12670 16811 12507 25011 25802 6142 1708 8669 17869 ...
..@ p : int [1:100001] 0 3 6 7 8 8 12 13 13 13 ...
..@ Dim : int [1:2] 30000 100000
..@ Dimnames:List of 2
.. ..$ : NULL
.. ..$ : NULL
..@ x : num [1:150000] -139671 -13383 -43683 181413 -654341 ...
..@ factors : list()
user system elapsed
0.02 0.00 0.01
>
>
> ###----- Compare methods ---> logical Matrices ------------
> l3 <- upper.tri(matrix(, 3, 3))
> (ll3 <- Matrix(l3))
3 x 3 sparse Matrix of class "ltCMatrix"
[1,] . | |
[2,] . . |
[3,] . . .
> dt3 <- (99* Diagonal(3) + (10 * ll3 + Diagonal(3)))/10
> (dsc <- crossprod(ll3))
3 x 3 sparse Matrix of class "dsCMatrix"
[1,] . . .
[2,] . 1 1
[3,] . 1 2
> stopifnot(identical(ll3, t(t(ll3))),
+ identical(dsc, t(t(dsc))))
> stopifnotValid(ll3, "ltCMatrix")
> stopifnotValid(dsc, "dsCMatrix")
> stopifnotValid(dsc + 3 * Diagonal(nrow(dsc)), "dsCMatrix")
> stopifnotValid(dt3, "triangularMatrix") # remained triangular
> stopifnotValid(dt3 > 0, "triangularMatrix")# ditto
>
>
> (lm1 <- dsc >= 1) # now ok
3 x 3 sparse Matrix of class "lsCMatrix"
[1,] . . .
[2,] . | |
[3,] . | |
> (lm2 <- dsc == 1) # now ok
3 x 3 sparse Matrix of class "lsCMatrix"
[1,] . . .
[2,] . | |
[3,] . | :
> nm1 <- as(lm1, "nMatrix")
> (nm2 <- as(lm2, "nMatrix"))
3 x 3 sparse Matrix of class "nsCMatrix"
[1,] . . .
[2,] . | |
[3,] . | |
>
> stopifnot(validObject(lm1), validObject(lm2),
+ validObject(nm1), validObject(nm2),
+ identical(dsc, dsc * as(lm1, "dMatrix")))
>
> crossprod(lm1) # lm1: "lsC*"
3 x 3 sparse Matrix of class "dsCMatrix"
[1,] . . .
[2,] . 2 2
[3,] . 2 2
> cnm1 <- crossprod(nm1, boolArith = FALSE)
> stopifnot(is(cnm1, "symmetricMatrix"), ## whereas the %*% is not:
+ Q.eq(cnm1, nm1 %*% nm1))
> dn1 <- as(nm1, "denseMatrix")
> stopifnot(all(dn1 == nm1))
>
> dsc[2,3] <- NA ## now has an NA (and no longer is symmetric)
> ## ----- and "everything" is different
> ## also add "non-structural 0":
> dsc@x[1] <- 0
> dsc
3 x 3 sparse Matrix of class "dgCMatrix"
[1,] . . .
[2,] . 0 NA
[3,] . 1 2
> dsc/ 5
3 x 3 sparse Matrix of class "dgCMatrix"
[1,] . . .
[2,] . 0.0 NA
[3,] . 0.2 0.4
> dsc + dsc
3 x 3 sparse Matrix of class "dgCMatrix"
[1,] . . .
[2,] . 0 NA
[3,] . 2 4
> dsc - dsc
3 x 3 sparse Matrix of class "dgCMatrix"
[1,] . . .
[2,] . 0 NA
[3,] . 0 0
> dsc + 1 # -> no longer sparse
3 x 3 Matrix of class "dgeMatrix"
[,1] [,2] [,3]
[1,] 1 1 1
[2,] 1 1 NA
[3,] 1 2 3
> Tsc <- as(dsc, "TsparseMatrix")
> dsc. <- drop0(dsc)
> stopifnot(Q.eq(dsc., Matrix((dsc + 1) - 1)),
+ identical(as(-Tsc,"CsparseMatrix"), (-1) * Tsc),
+ identical(-dsc., (-1) * dsc.),
+ identical3(-Diagonal(3), Diagonal(3, -1), (-1) * Diagonal(3)),
+ Q.eq(dsc., Matrix((Tsc + 1) -1)), # ok (exact arithmetic)
+ Q.eq(0 != dsc, dsc != Matrix(0, 3, 3)),
+ Q.eq(0 != dsc, dsc != c(0,0)) # with a warning ("not multiple ..")
+ )
Warning message:
In Matrix(e2, nrow = d[1], ncol = d[2]) :
data length [2] is not a sub-multiple or multiple of the number of rows [3]
> str(lm1 <- dsc >= 1) # now ok (NA in proper place, however:
Formal class 'lgCMatrix' [package "Matrix"] with 6 slots
..@ i : int [1:4] 1 2 1 2
..@ p : int [1:4] 0 0 2 4
..@ Dim : int [1:2] 3 3
..@ Dimnames:List of 2
.. ..$ : NULL
.. ..$ : NULL
..@ x : logi [1:4] FALSE TRUE NA TRUE
..@ factors : list()
> lm1 ## NA used to print as ' ' , now 'N'
3 x 3 sparse Matrix of class "lgCMatrix"
[1,] . . .
[2,] . : N
[3,] . | |
> (lm2 <- dsc == 1)# ditto
3 x 3 sparse Matrix of class "lgCMatrix"
[1,] . . .
[2,] . : N
[3,] . | :
> stopifnot(identical(crossprod(lm1),# "lgC": here works!
+ crossprod(as(lm1, "dMatrix"))),
+ identical(lm2, lm1 & lm2),
+ identical(lm1, lm1 | lm2))
>
> ddsc <- kronecker(Diagonal(7), dsc)
> isValid(ddv <- rowSums(ddsc, sparseResult=TRUE), "sparseVector")
[1] TRUE
> sv <- colSums(kC <- kronecker(mC,kronecker(mC,mC)), sparseResult=TRUE)
> EQ <- ddv == rowSums(ddsc)
> na.ddv <- is.na(ddv)
> sM <- Matrix(pmax(0, round(rnorm(50*15, -1.5), 2)), 50,15)
> stopifnot(sv == colSums(kC), is.na(as.vector(ddv)) == na.ddv,
+ isValid(sM/(-7:7), "CsparseMatrix"),
+ all(EQ | na.ddv))
>
> ## Subclasses (!)
> setClass("m.spV", contains = "dsparseVector")
> (m.ddv <- as(ddv, "m.spV"))
sparse vector (nnz/length = 14/21) of class "m.spV"
[1] . NA 3 . NA 3 . NA 3 . NA 3 . NA 3 . NA 3 . NA 3
> stopifnot(all.equal(m.ddv, ddv, check.class = FALSE))# failed
> setClass("m.dgC", contains = "dgCMatrix")
> (m.mC <- as(mC, "m.dgC"))
3 x 5 sparse Matrix of class "m.dgC"
[1,] . 1 . . 2
[2,] . . 2 . 1
[3,] 2 . 1 . .
> stopifnot(all(m.mC == mC))
> ## 2-level inheritance (R-forge Matrix bug #6185)
> ## https://r-forge.r-project.org/tracker/index.php?func=detail&aid=6185&group_id=61&atid=294
> setClass("Z", representation(zz = "list"))
> setClass("C", contains = c("Z", "dgCMatrix"))
> setClass("C2", contains = "C")
> setClass("C3", contains = "C2")
> (cc <- as(mC, "C"))
3 x 5 sparse Matrix of class "C"
[1,] . 1 . . 2
[2,] . . 2 . 1
[3,] 2 . 1 . .
> c2 <- as(mC, "C2")
> c3 <- as(mC, "C3")
> # as(*, "matrix") of these __fail__ in R < 3.5.0
> # before R_check_class_and_super() became better :
> print(c2)
3 x 5 sparse Matrix of class "C2"
[1,] . 1 . . 2
[2,] . . 2 . 1
[3,] 2 . 1 . .
> print(c3)
3 x 5 sparse Matrix of class "C3"
[1,] . 1 . . 2
[2,] . . 2 . 1
[3,] 2 . 1 . .
> ## ==> Error in asMethod(object) : invalid class of object to as_cholmod_sparse
> stopifnot(identical(cc > 0, mC > 0 -> m.gt.0), ## cc > 0 - gave error in Matrix <= 1.2-11
+ identical(c2 > 0, m.gt.0),
+ identical(c3 > 0, m.gt.0))
>
> ## Just for print "show":
> z <- round(rnorm(77), 2)
> z[sample(77,10)] <- NA
> (D <- Matrix(z, 7)) # dense
7 x 11 Matrix of class "dgeMatrix"
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] -0.86 -0.09 1.17 NA NA 1.25 0.62 -1.63 -1.60 1.49 -1.60
[2,] -1.74 0.34 0.56 1.00 NA 0.33 1.13 0.58 0.01 -0.69 -0.66
[3,] NA 1.47 0.45 -1.35 -1.39 -0.54 -1.59 -1.72 -0.99 -1.09 -0.22
[4,] 1.46 -0.67 -0.73 -0.34 NA NA 1.24 0.54 -0.68 NA 2.23
[5,] -1.35 -0.50 -0.49 -0.50 -0.56 0.42 NA 0.37 0.81 -0.63 -0.90
[6,] 1.27 NA 2.82 1.91 NA -2.83 0.84 0.93 -0.73 -0.65 0.09
[7,] 0.44 2.38 -0.47 -0.16 -1.15 0.25 -0.31 -0.37 2.31 -1.44 0.25
> z[sample(77,15)] <- 0
> (D <- Matrix(z, 7)) # sparse
7 x 11 Matrix of class "dgeMatrix"
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] -0.86 -0.09 1.17 0.00 NA 0.00 0.62 -1.63 -1.60 1.49 0.00
[2,] 0.00 0.00 0.00 1.00 NA 0.33 1.13 0.58 0.01 0.00 -0.66
[3,] NA 0.00 0.45 -1.35 -1.39 -0.54 -1.59 -1.72 0.00 -1.09 -0.22
[4,] 1.46 -0.67 -0.73 -0.34 NA 0.00 1.24 0.54 -0.68 NA 2.23
[5,] -1.35 -0.50 -0.49 -0.50 -0.56 0.42 NA 0.37 0.81 0.00 0.00
[6,] 0.00 NA 2.82 1.91 0.00 -2.83 0.84 0.93 -0.73 0.00 0.09
[7,] 0.44 2.38 -0.47 -0.16 -1.15 0.25 -0.31 -0.37 2.31 -1.44 0.25
> abs(D) >= 0.5 # logical sparse
7 x 11 Matrix of class "lgeMatrix"
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] TRUE FALSE TRUE FALSE NA FALSE TRUE TRUE TRUE TRUE FALSE
[2,] FALSE FALSE FALSE TRUE NA FALSE TRUE TRUE FALSE FALSE TRUE
[3,] NA FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE TRUE FALSE
[4,] TRUE TRUE TRUE FALSE NA FALSE TRUE TRUE TRUE NA TRUE
[5,] TRUE TRUE FALSE TRUE TRUE FALSE NA FALSE TRUE FALSE FALSE
[6,] FALSE NA TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE
[7,] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE
>
> ## For the checks below, remove some and add a few more objects:
> rm(list= ls(pattern="^.[mMC]?$"))
> T3 <- Diagonal(3) > 0; stopifnot(T3@diag == "U") # "uni-diagonal"
> validObject(dtp <- pack(as(dt3, "denseMatrix")))
[1] TRUE
> stopifnot(exprs = {
+ isValid(lsC <- as(lsp, "CsparseMatrix"), "lsCMatrix")
+ ## 0-extent matrices {fixes in Feb.2019}:
+ isValid(L00 <- L7[FALSE,FALSE], "ldiMatrix")
+ isValid(x60 <- x2[,FALSE], "dgCMatrix")
+ identical(t(x60), x06 <- x2[FALSE,])
+ isValid(x00 <- x06[,FALSE], "dgCMatrix")
+ isValid(sv0 <- as(x06, "sparseVector"), "dsparseVector")
+ })
>
> showProc.time()
Time (user system elapsed): 0.53 0.07 0.59
>
> ### Consider "all" Matrix classes
> cl <- sapply(ls(), function(.) class(get(.)))
> Mcl <- cl[vapply(cl, extends, "Matrix", FUN.VALUE=NA) |
+ vapply(cl, extends, "sparseVector", FUN.VALUE=NA)]
> table(Mcl)
, , L7 = ldiMatrix, M1 = dgeMatrix, T3 = ldiMatrix, Tsc = dgTMatrix, c2 = C2, c3 = C3, cc = C, cnm1 = dsCMatrix, dd = dsyMatrix, ddsc = dgCMatrix, ddv = dsparseVector, dn1 = nsyMatrix, dsc = dgCMatrix, dsc. = dgCMatrix, dspL = dspMatrix, dspU = dspMatrix, dsy = dsyMatrix, dsyL = dsyMatrix, dsyU = dsyMatrix, dt3 = dtCMatrix, dtp = dtpMatrix, isFl = nspMatrix, isFtl = ngeMatrix, isFtu = ngeMatrix, isFu = nspMatrix, isL = nsyMatrix, isU = nsyMatrix, ll3 = ltCMatrix, lm1 = lgCMatrix, lm2 = lgCMatrix, lsC = lsCMatrix, lsp = lspMatrix, lspL = lspMatrix, lspU = lspMatrix, lsy = lsyMatrix, lsyL = lsyMatrix, lsyU = lsyMatrix, m.ddv = m.spV, m.gt.0 = lgCMatrix, m.mC = m.dgC, na.ddv = nsparseVector, nm1 = nsCMatrix, nm2 = nsCMatrix, nsy = nsyMatrix, px = dgCMatrix, res = dgeMatrix, sL = dsyMatrix, sU = dsyMatrix, spL = dspMatrix, spU = dspMatrix, sv = dsparseVector, sv0 = dsparseVector, t1 = ltrMatrix, t2 = ltrMatrix, trL = dtpMatrix, trU = dtpMatrix, x00 = dgCMatrix, x06 = dgCMatrix, x2 = dgCMatrix, x60 = dgCMatrix, xpp = dspMatrix, xpx = dpoMatrix, xpy = dgeMatrix
L00
D3 ldiMatrix
ddiMatrix 1
> ## choose *one* of each class:
> ## M.objs <- names(Mcl[!duplicated(Mcl)])
> ## choose all
> M.objs <- names(Mcl) # == the ls() from above
> Mat.objs <- M.objs[vapply(M.objs, function(nm) is(get(nm), "Matrix"), NA)]
> MatDims <- t(vapply(Mat.objs, function(nm) dim(get(nm)), 0:1))
> ## Nice summary info :
> noquote(cbind(Mcl[Mat.objs], format(MatDims)))
[,1] [,2] [,3]
D3 "ddiMatrix" " 3" " 3"
L00 "ldiMatrix" " 0" " 0"
L7 "ldiMatrix" " 7" " 7"
M1 "dgeMatrix" " 4" " 1"
T3 "ldiMatrix" " 3" " 3"
Tsc "dgTMatrix" " 3" " 3"
c2 "C2" " 3" " 5"
c3 "C3" " 3" " 5"
cc "C" " 3" " 5"
cnm1 "dsCMatrix" " 3" " 3"
dd "dsyMatrix" " 7" " 7"
ddsc "dgCMatrix" "21" "21"
dn1 "nsyMatrix" " 3" " 3"
dsc "dgCMatrix" " 3" " 3"
dsc. "dgCMatrix" " 3" " 3"
dspL "dspMatrix" " 3" " 3"
dspU "dspMatrix" " 3" " 3"
dsy "dsyMatrix" " 2" " 2"
dsyL "dsyMatrix" " 3" " 3"
dsyU "dsyMatrix" " 3" " 3"
dt3 "dtCMatrix" " 3" " 3"
dtp "dtpMatrix" " 3" " 3"
isFl "nspMatrix" " 3" " 3"
isFtl "ngeMatrix" " 3" " 3"
isFtu "ngeMatrix" " 3" " 3"
isFu "nspMatrix" " 3" " 3"
isL "nsyMatrix" " 3" " 3"
isU "nsyMatrix" " 3" " 3"
ll3 "ltCMatrix" " 3" " 3"
lm1 "lgCMatrix" " 3" " 3"
lm2 "lgCMatrix" " 3" " 3"
lsC "lsCMatrix" " 7" " 7"
lsp "lspMatrix" " 7" " 7"
lspL "lspMatrix" " 5" " 5"
lspU "lspMatrix" " 5" " 5"
lsy "lsyMatrix" " 2" " 2"
lsyL "lsyMatrix" " 5" " 5"
lsyU "lsyMatrix" " 5" " 5"
m.gt.0 "lgCMatrix" " 3" " 5"
m.mC "m.dgC" " 3" " 5"
nm1 "nsCMatrix" " 3" " 3"
nm2 "nsCMatrix" " 3" " 3"
nsy "nsyMatrix" " 2" " 2"
px "dgCMatrix" " 6" " 6"
res "dgeMatrix" " 7" " 1"
sL "dsyMatrix" " 3" " 3"
sU "dsyMatrix" " 3" " 3"
spL "dspMatrix" " 3" " 3"
spU "dspMatrix" " 3" " 3"
t1 "ltrMatrix" " 1" " 1"
t2 "ltrMatrix" " 2" " 2"
trL "dtpMatrix" " 3" " 3"
trU "dtpMatrix" " 3" " 3"
x00 "dgCMatrix" " 0" " 0"
x06 "dgCMatrix" " 0" " 6"
x2 "dgCMatrix" " 6" " 6"
x60 "dgCMatrix" " 6" " 0"
xpp "dspMatrix" " 7" " 7"
xpx "dpoMatrix" " 7" " 7"
xpy "dgeMatrix" " 7" " 1"
>
> ## dtCMatrix, uplo="L" :
> (CtL <- t(as(Diagonal(x=4:2), "CsparseMatrix")))
3 x 3 sparse Matrix of class "dtCMatrix"
[1,] 4 . .
[2,] . 3 .
[3,] . . 2
> m2 <- cbind(c(0, NA, NA),
+ c(0, 0, NA), 0)
> op <- options(Matrix.verbose = 2)
> r <- CtL > m2 # failed in Matrix <= 1.4-1, with
Compare -- "dtCMatrix" > "dtCMatrix" :
> ## Compare -- "dtCMatrix" > "dtCMatrix" :
> stopifnot(identical(is.na(m2), unname(as.matrix(is.na(r)))), diag(r), isDiagonal(triu(r)))
> M <- new("dtCMatrix", i = c(0L, 0:1, 0:2), p = c(0:1, 3L, 6L),
+ x = c(10,1, 10,1, 1,10), Dim = c(3L, 3L), uplo = "U")
> m2 <- matrix(c(0, NA, NA, 0, 0, NA, 0, 0, 0), 3)
> r <- M & m2 # failed in Matrix <= 1.4-1
> assert.EQ.mat(M | m2 -> ro,
+ as.mat(M)| m2, tol=0)
> D4 <- Diagonal(x=0+ 4:2)
> rd <- D4 | m2 # gave invalid class "ltTMatrix" object: uplo='U' must not have sparse entries below the diagonal
> M2 <- Matrix(m2); T2 <- Matrix:::.diag2T.smart(D4, M2, kind="l")
> stopifnot(exprs = {
+ all(!r)
+ ## fix in .do.Logic.lsparse() {needed uplo="L"}
+ identical(rd, T2 | M2)
+ identical(rd, as(T2, "CsparseMatrix") | as(M2, "lMatrix"))
+ })
>
> options(op)
>
> if(doExtras || interactive()) { # save testing time
+
+ ### Systematically look at all "Ops" group generics for "all" Matrix classes
+ ### -------------- Main issue: Detect infinite recursion problems
+
+ mDims <- MatDims %*% (d.sig <- c(1, 1000)) # "dim-signature" to match against
+ m2num <- function(m) { if(is.integer(m)) storage.mode(m) <- "double" ; m }
+ M.knd <- Matrix:::.M.kind
+ cat("Checking all Ops group generics for a set of arguments:\n",
+ "-------------------------------------------------------\n", sep='')
+ op <- options(warn = 2)#, error=recover)
+ for(gr in getGroupMembers("Ops")) {
+ cat(gr,"\n",paste(rep.int("=",nchar(gr)),collapse=""),"\n", sep='')
+ v0 <- if(gr == "Arith") numeric() else logical()
+ for(f in getGroupMembers(gr)) {
+ line <- strrep("-", nchar(f) + 2)
+ cat(sprintf("%s\n%s :\n%s\n", line, dQuote(f), line))
+ for(nm in M.objs) {
+ if(doExtras) cat(" '",nm,"' ", sep="")
+ M <- get(nm, inherits=FALSE)
+ n.m <- NROW(M)
+ cat("o")
+ for(x in list(TRUE, -3.2, 0L, seq_len(n.m))) {
+ cat(".")
+ validObject(r1 <- do.call(f, list(M,x)))
+ validObject(r2 <- do.call(f, list(x,M)))
+ stopifnot(dim(r1) == dim(M), dim(r2) == dim(M),
+ allow.logical0 = TRUE)
+ }
+ ## M o 0-length === M :
+ validObject(M0. <- do.call(f, list(M, numeric())))
+ validObject(.M0 <- do.call(f, list(numeric(), M)))
+ if(length(M)) # o <0-length v> == 0-length v
+ stopifnot(identical(M0., v0), identical(.M0, v0))
+ else if(is(M, "Matrix"))
+ stopifnot(identical(M0., as(M, if(gr == "Arith") "dMatrix" else "lMatrix")),
+ identical(M0., .M0))
+ else # if(is(M, "sparseVector")) of length 0
+ stopifnot(identical(M0., v0), identical(.M0, v0))
+ ## M o
+ x <- numeric(n.m)
+ if(length(x)) x[c(1,length(x))] <- 1:2
+ sv <- as(x, "sparseVector")
+ cat("s.")
+ validObject(r3 <- do.call(f, list(M, sv)))
+ stopifnot(identical(dim(r3), dim(M)))
+ if(doExtras && is(M, "Matrix")) { ## M o
+ d <- dim(M)
+ ds <- sum(d * d.sig) # signature .. match with all other sigs
+ match. <- ds == mDims # (matches at least itself)
+ cat("\nM o M:")
+ for(oM in Mat.objs[match.]) {
+ M2 <- get(oM)
+ ## R4 := M f M2
+ validObject(R4 <- do.call(f, list(M, M2)))
+ cat(".")
+ for(M. in list(as.mat(M), M)) { ## two cases ..
+ r4 <- m2num(as.mat(do.call(f, list(M., as.mat(M2)))))
+ cat(",")
+ if(!identical(r4, as.mat(R4))) {
+ cat(sprintf("\n %s %s %s gave not identical r4 & R4:\n",
+ nm, f, oM)); print(r4); print(R4)
+ C1 <- (eq <- R4 == r4) | (N4 <- as.logical((nr4 <- is.na(eq)) & !is.finite(R4)))
+ if(isTRUE(all(C1)) || isTRUE(all.equal(as.mat(R4), r4,
+ tolerance = 1e-14)))
+ cat(sprintf(
+ " --> %s %s %s (ok): only difference is %s (matrix) and %s (Matrix)\n",
+ M.knd(M), f, M.knd(M2)
+ , paste(vapply(unique(r4[N4]), format, ""), collapse="/")
+ , paste(vapply(unique(R4[N4]), format, ""), collapse="/")
+ ))
+ else if(isTRUE(all(eq | (nr4 & Matrix:::is0(R4)))))
+ cat(" --> 'ok': only difference is 'NA' (matrix) and 0 (Matrix)\n")
+ else stop("R4 & r4 differ \"too much\"")
+ }
+ }
+ cat("i")
+ }
+ }
+ }
+ cat("\n")
+ }
+ }
+ if(length(warnings())) print(summary(warnings()))
+ showProc.time()
+ options(op) # reset 'warn'
+ } # doExtras
>
> ###---- Now checking 0-length / 0-dim cases <==> to R >= 3.4.0 !
>
> ## arithmetic, logic, and comparison (relop) for 0-extent arrays
> (m <- Matrix(cbind(a=1[0], b=2[0])))
0 x 2 Matrix of class "dgeMatrix"
a b
> Lm <- as(m, "lMatrix")
> ## Im <- as(m, "iMatrix")
> stopifnot(
+ identical(m, m + 1), identical(m, m + 1[0]),
+ identical(m, m + NULL),## now (2016-09-27) ok
+ identical(m, Lm+ 1L) ,
+ identical(m, m+2:3), ## gave error "length does not match dimension"
+ identical(Lm, m & 1),
+ identical(Lm, m | 2:3),## had Warning "In .... : data length exceeds size of matrix"
+ identical(Lm, m & TRUE[0]),
+ identical(Lm, m | FALSE[0]),
+ identical(Lm, m > NULL),
+ identical(Lm, m > 1),
+ identical(Lm, m > .1[0]),## was losing dimnames
+ identical(Lm, m > NULL), ## was not-yet-implemented
+ identical(Lm, m <= 2:3) ## had "wrong" warning
+ )
> mm <- m[,c(1:2,2:1,2)]
> assertErrV(m + mm) # ... non-conformable arrays
Asserted error: number of rows are not compatible for +
> assertErrV(m | mm) # ... non-conformable arrays
Asserted error: non-conformable matrix dimensions in m | mm
> ## Matrix: ok ; R : ok, in R >= 3.4.0
> assertErrV(m == mm)
Asserted error: non-conformable matrix dimensions in m == mm
> ## in R <= 3.3.x, relop returned logical(0) and m + 2:3 returned numeric(0)
> ##
> ## arithmetic, logic, and comparison (relop) -- inconsistency for 1x1 array o = 2>:
> ## FIXME: desired errors are _not_ thrown for ddiMatrix (when doDiag=TRUE)
> (m1 <- Matrix(1, 1L, 1L, dimnames = list("Ro", "col"), doDiag = FALSE))
1 x 1 Matrix of class "dtrMatrix"
col
Ro 1
> ## col
> ## Ro 1
> ## Before Sep.2016, here, Matrix was the *CONTRARY* to R:
> assertErrV(m1 + 1:2)## M.: "correct" ERROR // R 3.4.0: "deprecated" warning (--> will be error)
Asserted error: dim [product 1] do not match the length of object [2]
> assertErrV(m1 & 1:2)## gave 1 x 1 [TRUE] -- now Error, as R
Asserted error: dim [product 1] do not match the length of object [2]
> assertErrV(m1 <= 1:2)## gave 1 x 1 [TRUE] -- now Error, as R
Asserted error: dim [product 1] do not match the length of object [2]
> assertErrV(m1 & 1:2)## gave 1 x 1 [TRUE] -- now Error, as R
Asserted error: dim [product 1] do not match the length of object [2]
> assertErrV(m1 <= 1:2)## gave 1 x 1 [TRUE] -- now Error, as R
Asserted error: dim [product 1] do not match the length of object [2]
> ##
> ## arrays combined with NULL works now
> stopifnot(identical(Matrix(3,1,1) + NULL, 3[0]))
> stopifnot(identical(Matrix(3,1,1) > NULL, T[0]))
> stopifnot(identical(Matrix(3,1,1) & NULL, T[0]))
> ## in R >= 3.4.0: logical(0) # with *no* warning and that's correct!
>
> if(doExtras || interactive()) { # save testing time
+ mStop <- function(...) stop(..., call. = FALSE)
+ ##
+ cat("Checking the Math (+ Math2) group generics for a set of arguments:\n",
+ "------------ ==== ------------------------------------------------\n", sep='')
+ doStop <- function() mStop("**Math: ", f,"(<",class(M),">) of 'wrong' class ", dQuote(class(R)))
+ mM <- getGroupMembers("Math")
+ mM2 <- getGroupMembers("Math2")
+ (mVec <- grep("^cum", mM, value=TRUE)) ## <<- are special: return *vector* for matrix input
+ for(f in c(mM, mM2)) {
+ cat(sprintf("%-9s :\n %-7s\n", paste0('"',f,'"'), paste(rep("-", nchar(f)), collapse="")))
+ givesVec <- f %in% mVec
+ fn <- get(f)
+ if(f %in% mM2) { fn0 <- fn ; fn <- function(x) fn0(x, digits=3) }
+ for(nm in M.objs) {
+ M <- get(nm, inherits=FALSE)
+ is.m <- length(dim(M)) == 2
+ cat(" '",nm,"':", if(is.m) "m" else "v", sep="")
+ R <- fn(M)
+ r <- fn(m <- if(is.m) as.mat(M) else as.vector(M))
+ stopifnot(identical(dim(R), dim(r)))
+ if(givesVec || !is.m) {
+ assert.EQ(R, r, check.class = FALSE)
+ } else { ## (almost always:) matrix result
+ assert.EQ.mat(R, r, check.class = FALSE)
+ ## check preservation of properties, notably super class
+ if(prod(dim(M)) > 1 && is(M, "diagonalMatrix" ) && isDiagonal(R) && !is(R, "diagonalMatrix" )) doStop()
+ if(prod(dim(M)) > 1 && is(M, "triangularMatrix") && (iT <- isTriangular(R)) && attr(iT, "kind") == M@uplo &&
+ !is(R, "triangularMatrix")) doStop()
+ }
+ }
+ cat("\n")
+ }
+ showProc.time()
+
+ ##
+ cat("Checking the Summary group generics for a set of arguments:\n",
+ "------------ ======= ------------------------------------------------\n", sep='')
+ for(f in getGroupMembers("Summary")) {
+ cat(sprintf("%-9s :\n %-7s\n", paste0('"',f,'"'), paste(rep("-", nchar(f)), collapse="")))
+ givesVec <- f %in% mVec
+ fn <- get(f)
+ if(f %in% mM2) { fn0 <- fn ; fn <- function(x) fn0(x, digits=3) }
+ for(nm in M.objs) {
+ M <- get(nm, inherits=FALSE)
+ is.m <- length(dim(M)) == 2
+ cat(" '",nm,"':", if(is.m) "m" else "v", sep="")
+ R <- fn(M)
+ r <- fn(m <- if(is.m) as.mat(M) else as.vector(M))
+ stopifnot(identical(dim(R), dim(r)))
+ assert.EQ(R, r)
+ }
+ cat("\n")
+ if(length(warnings())) print(summary(warnings()))
+ }
+ } # doExtras
>
> ##