R Under development (unstable) (2023-11-05 r85474 ucrt) -- "Unsuffered Consequences"
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> ####--------- Test interfaces to other non-standard Packages ---------------
> 
> ## for R_DEFAULT_PACKAGES=NULL :
> library(grDevices)
> library(stats)
> library(utils)
> 
> library(Matrix)
> source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
Loading required package: tools
> MatrixRversion <- pkgRversion("Matrix")
> 
> 
> ###-- 1)  'graph' (from Bioconductor) ---------------------------
> ###-- ==  =======                     ---------------------------
> 
> if(requireNamespace("graph")) {
+ 
+     if(packageVersion("graph") <= "1.10.2") {
+ 
+     ## graph 1.10.x for x <= 2 had too many problems  as(<graph>, "matrix")
+     cat("Version of 'graph' is too old --- no tests done here!\n")
+ 
+     } else if(pkgRversion("graph") != MatrixRversion) {
+ 
+     cat(sprintf("The R version (%s) of 'graph' installation differs from the Matrix one (%s)\n",
+                 pkgRversion("graph"), MatrixRversion))
+ 
+     } else { ## do things
+ 
+     if(doPdf <- !dev.interactive(orNone = TRUE))
+         pdf("other-pkgs-graph.pdf")
+ 
+     ## 0) Simplest non-trivial graph: has no weights:
+     g0 <- graph::graphNEL(paste(1:2), edgeL=list("1"="2"), "directed")
+     m0 <- as(g0, "Matrix")
+     stopifnot(is(m0,"ngCMatrix"), dim(m0) == c(2,2), which(m0) == 3)
+     g. <- as(m0, "graph") ## failed in Matrix <= 1.1-0
+     m. <- as(g., "Matrix")
+     stopifnot( identical(m., m0) ) ## but (g0, g.) differ: the latter has '1' weights
+ 
+     ## 1) undirected
+ 
+     V <- LETTERS[1:4]
+     edL <- vector("list", length=4)
+     names(edL) <- V
+     ## 1a) unweighted
+     for(i in 1:4)
+         edL[[i]] <- list(edges = 5-i)
+     gR <- new("graphNEL", nodes=V, edgeL=edL)
+     str(graph::edges(gR))
+     sm.g <- as(gR, "sparseMatrix")
+     str(sm.g) ## dgC: TODO: want 'ds.' (symmetric)
+     validObject(sm.g)
+     show( sm.g )## (incl colnames !)
+ 
+     ## 1b) weighted
+     set.seed(123)
+     for(i in 1:4)
+         edL[[i]] <- list(edges = 5-i, weights=runif(1))
+     gRw <- new("graphNEL", nodes=V, edgeL=edL)
+     str(graph::edgeWeights(gRw))
+     sm.gw <- as(gRw, "sparseMatrix")
+     str(sm.gw) ## *numeric* dgCMatrix
+     validObject(sm.gw)
+     show( sm.gw )## U[0,1] numbers in anti-diagonal
+ 
+     ## 2) directed
+     gU <- gR; graph::edgemode(gU) <- "directed"
+     sgU <- as(gU, "sparseMatrix")
+     str(sgU) ## 'dgC'
+     validObject(sgU)
+     show( sgU )
+ 
+     ## Reverse :  sparseMatrix -> graph
+     sm.g[1,2] <- TRUE
+     gmg  <-  as(sm.g, "graph")
+     validObject(gmg2 <-  as(sm.g, "graphNEL"))
+     gmgw <-  as(sm.gw, "graph")
+     validObject(gmgw2 <- as(sm.gw, "graphNEL"))
+     gmgU <-  as(sgU, "graph")
+     validObject(gmgU2 <- as(sgU, "graphNEL"))
+     stopifnot(identical(gmg, gmg2),
+               identical(gmgw, gmgw2),
+               identical(gmgU, gmgU2))
+ 
+     data(CAex, package = "Matrix")
+     cc <- crossprod(CAex)
+     ## work around bug in 'graph': diagonal must be empty:
+     diag(cc) <- 0; cc <- drop0(cc)
+     image(cc)
+     gg <- as(cc, "graph")
+ 
+     ## Don't run on CRAN and don't trigger 'R CMD check' :
+     if(doExtras && match.fun("requireNamespace")("Rgraphviz"))
+         get("plot", asNamespace("Rgraphviz"), mode = "function")(gg, "circo")
+ 
+     stopifnot(all.equal(graph::edgeMatrix(gg),
+                         rbind(from = c(rep(1:24, each=2), 25:48),
+                               to   = c(rbind(25:48,49:72), 49:72))))
+ 
+     if(doPdf)
+         dev.off()
+ 
+     } # {else}
+ 
+ } # end{graph}
Loading required namespace: graph
Failed with error:  'there is no package called 'graph''
> 
> 
> ###-- 2)  'SparseM' ---------------------------------------------
> ###-- ==  ========= ---------------------------------------------
> 
> if(requireNamespace("SparseM")) {
+ 
+     if(pkgRversion("SparseM") != MatrixRversion) {
+ 
+     cat(sprintf("The R version (%s) of 'SparseM' installation differs from the Matrix one (%s)\n",
+                 pkgRversion("SparseM"), MatrixRversion))
+ 
+     } else { ## do things
+ 
+ 	set.seed(1)
+ 	a <- round(rnorm(5*4), 2)
+ 	a[abs(a) < 0.7] <- 0
+ 	A <- matrix(a,5,4)
+ 	print(M <- Matrix(A))
+ 	stopifnot(
+             validObject(A.csr <- SparseM::as.matrix.csr(A)),
+             validObject(At.csr <- SparseM::as.matrix.csr(t(A))),
+             validObject(A.csc <- SparseM::as.matrix.csc(A)),
+             identical(At.csr, t(A.csr)),
+             identical(A, as.matrix(A.csr)),
+             identical(A.csr, as(M, "matrix.csr")),
+             identical(A.csc, as(M, "matrix.csc")),
+             identical3(M, as(A.csr, "CsparseMatrix"), as(A.csr, "dgCMatrix")),
+             identical(t(M), as(At.csr, "CsparseMatrix"))
+             )
+ 
+ 	## More tests, notably for triplets
+ 	A.coo <- SparseM::as.matrix.coo(A)
+ 	str(T  <- as(M, "TsparseMatrix")) # has 'j' sorted
+ 	str(T. <- as(A.coo, "TsparseMatrix")) # has 'i' sorted
+ 
+ 	T3 <- as(as(T, "matrix.coo"), "Matrix") # dgT
+ 	M3 <- as(A.csr,               "Matrix") # dgC
+ 	M4 <- as(A.csc,               "Matrix") # dgC
+ 	M5 <- as(as(M, "matrix.coo"), "Matrix") # dgT
+     stopifnot(identical4(asUniqueT(T ), asUniqueT(T.),
+                          asUniqueT(T3), asUniqueT(M5)),
+               identical3(M, M3, M4))
+ 
+     } # {else}
+ 
+ } # end{SparseM}
Loading required namespace: SparseM
Failed with error:  'there is no package called 'SparseM''
> 
> proc.time()
   user  system elapsed 
   1.14    0.17    1.29