Running 'Matrix-ex.R' [175s]
Running the tests in 'tests/Matrix-ex.R' failed.
Complete output:
  > ###################################################
  > ### chunk number 1: preliminaries
  > ###################################################
  > 
  > library(classGraph)
  
  Attaching package: 'classGraph'
  
  The following object is masked from 'package:graphics':
  
      plot
  
  The following object is masked from 'package:base':
  
      plot
  
  > 
  > stopifnot(require("Matrix"),
  +           require("graph"))
  Loading required package: Matrix
  Loading required package: graph
  Loading required package: BiocGenerics
  
  Attaching package: 'BiocGenerics'
  
  The following objects are masked from 'package:stats':
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from 'package:base':
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
      union, unique, unsplit, which.max, which.min
  
  > 
  > allCl <- getClasses("package:Matrix")
  > ## Those called "...Matrix" :
  > M.Cl <- grep("Matrix$",allCl, value = TRUE)
  > 
  > str(M3cl <- grep("^...Matrix$",M.Cl, value = TRUE))
   chr [1:50] "lgeMatrix" "dtrMatrix" "dgRMatrix" "lspMatrix" "lsTMatrix" ...
  > 
  > M3cl <- M3cl[M3cl != "corMatrix"] # corMatrix not desired in following
  > 
  > 
  > 
  > 
  > 
  > ###################################################
  > ### chunk number 2: tree-Matrix
  > ###################################################
  > trMatrix <- classTree("Matrix") ; trMatrix
  A graphNEL graph with directed edges
  Number of Nodes = 74 
  Number of Edges = 166 
  > ## 2005-08: 58 nodes with 109 edges
  > ## 2007-01: 74 nodes with 151 edges
  > par(lwd = 0.3)# no effect --- learn to use Rgraphviz!!
  > plotRag(mRagraph(trMatrix), subArgs=.optRagargs(adj = 0.5))
  > 
  > 
  > ###################################################
  > ### chunk number 3: sTree-M1
  > ###################################################
  > allN <- nodes(trMatrix)
  > "%w/o%" <- function(x,y) x[!x %in% y] #--  x without y
  > 
  > hier1 <- paste(c("diagonal", "triangular", "symmetric", "general", "comp"),
  +                "Matrix", sep = '') # composites can be factorized:  ^^^^
  > 
  > ## dropping 1st ``dim'' hierarchy -- much less edges:
  > (trM1 <- subGraph(allN %w/o% hier1, trMatrix))
  A graphNEL graph with directed edges
  Number of Nodes = 70 
  Number of Edges = 117 
  > plotRag(mRagraph(trM1), subArgs=.optRagargs(adj = 0.5))
  > 
  > 
  > ###################################################
  > ### chunk number 4: sTree-top12
  > ###################################################
  > defMatrix <- getClassDef("Matrix")
  > ## Distances of subclasses:
  > table(subDist <- sapply(defMatrix@subclasses, slot, "distance"))
  
   1  2  3  4 
  10 16 48  2 
  > sub12 <- defMatrix@subclasses[subDist <= 2] # but not unique!
  > trM_top12 <- subGraph(c("Matrix", unique(names(sub12))), trMatrix)
  > plotRag(mRagraph(trM_top12)) ## first and second level virtual classes
  > 
  > 
  > ###################################################
  > ### chunk number 5: sTree-sparse
  > ###################################################
  > trSpMatrix <- classTree("sparseMatrix")
  > trSpMatrix
  A graphNEL graph with directed edges
  Number of Nodes = 40 
  Number of Edges = 66 
  > plotRag(mRagraph(trSpMatrix, "dot"),
  +         subArgs= .optRagargs(side = 3, adj = 1, line = 0),
  +         main = "'sparseMatrix' classes -- sub graph")
  > 
  > 
  > ###################################################
  > ### chunk number 6: sTree-sp-neato
  > ###################################################
  > ## now this *does* look kind of neat:
  > plotRag(mRagraph(trSpMatrix, "neato"),
  +         subArgs= .optRagargs(side = 3, adj = 1, line = 0),
  +         main = "'sparseMatrix' classes -- in \"neato\" layout")
  > ## all three others do not
  > 
  > 
  > 
  > proc.time()
     user  system elapsed 
     2.96    0.28    3.23