Running 'apply.R'
  Comparing 'apply.Rout' to 'apply.Rout.save' ... OK
  Running 'distance.R'
  Comparing 'distance.Rout' to 'distance.Rout.save' ... OK
  Running 'distcalls.R'
Running the tests in 'tests/distcalls.R' failed.
Complete output:
  > #################################
  > ## Test for dist calls
  > ##################################
  > 
  > library(proxy)
  
  Attaching package: 'proxy'
  
  The following objects are masked from 'package:stats':
  
      as.dist, dist
  
  The following object is masked from 'package:base':
  
      as.matrix
  
  > 
  > set.seed(20140107)
  > 
  > ## get all measures
  > proxies = pr_DB$get_entry_names()
  > 
  > ## remove special cases
  > proxies = setdiff(proxies, c("Mahalanobis", "Minkowski", "Stiles", "Levenshtein", "fJaccard"))
  > 
  > ## create test data
  > x = matrix(1:100, 10)
  > 
  > ## test function: checks if dist(x) == dist(x,x) for all measures,
  > ## and if diag(dist(x, x)) == diag(x, x, pairwise = TRUE)
  > prtest <- function(...) {
  +     CD <- dist(x, x, ...)
  +     all(as.matrix(dist(x, ...)) == CD) &&
  +       all(diag(CD) == dist(x, x, pairwise = TRUE, ...))
  + }
  > 
  > ## loop over all measures (except special cases)
  > for (i in proxies)
  +     {cat(i); prtest(i); cat(": OK.\n")}
  Jaccard: OK.
  Kulczynski1: OK.
  Kulczynski2: OK.
  Mountford: OK.
  Fager: OK.
  Russel: OK.
  simple matching: OK.
  Hamman: OK.
  Faith: OK.
  Tanimoto: OK.
  Dice: OK.
  Phi: OK.
  Michael: OK.
  Mozley: OK.
  Yule: OK.
  Yule2: OK.
  Ochiai: OK.
  Simpson: OK.
  Braun-Blanquet: OK.
  cosine: OK.
  eJaccard: OK.
  eDice: OK.
  correlation: OK.
  Chi-squared: OK.
  Phi-squared: OK.
  Tschuprow: OK.
  Cramer: OK.
  Pearson: OK.
  Gower: OK.
  Euclidean: OK.
  Bhjattacharyya: OK.
  Manhattan: OK.
  supremum: OK.
  Canberra: OK.
  Wave: OK.
  divergence: OK.
  Kullback: OK.
  Bray: OK.
  Soergel: OK.
  Podani: OK.
  Chord: OK.
  Geodesic: OK.
  Whittaker: OK.
  Hellinger: OK.
  > 
  > ## Minkowski
  > for (j in c(0.5, 1, 2, 3, Inf))
  +     {cat("Minkowski: p =", j); prtest("Minkowski", p = j); cat(": OK.\n")}
  Minkowski: p = 0.5: OK.
  Minkowski: p = 1: OK.
  Minkowski: p = 2: OK.
  Minkowski: p = 3: OK.
  Minkowski: p = Inf: OK.
  > 
  > ## Mahalanobis (need non-singular matrix)
  > x = as.matrix(iris[1:50,-5])
  > prtest("Mahalanobis")
  [1] TRUE
  > 
  > ## fJaccard (needs values in unit interval)
  > x = as.matrix(1:100/100, 10)
  > prtest("fJaccard")
  [1] TRUE
  > 
  > ## produce binary matrix
  > x = matrix(rbinom(100,1,0.7), 10)
  > 
  > ## Stiles (gives a lot of warnings due to log)
  > tmp = dist(x, "Stiles")
  There were 27 warnings (use warnings() to see them)
  > tmp = dist(x, x, "Stiles")
  There were 50 or more warnings (use warnings() to see the first 50)
  > 
  > ## try again (almost) all measures, this time with binary data to check
  > ## conversions
  > for (i in proxies)
  +     {cat(i); prtest(i); cat(": OK.\n")}
  Jaccard: OK.
  Kulczynski1: OK.
  Kulczynski2: OK.
  Mountford: OK.
  Fager: OK.
  Russel: OK.
  simple matching: OK.
  Hamman: OK.
  Faith: OK.
  Tanimoto: OK.
  Dice: OK.
  Phi: OK.
  Michael: OK.
  Mozley: OK.
  Yule: OK.
  Yule2: OK.
  Ochiai: OK.
  Simpson: OK.
  Braun-Blanquet: OK.
  cosine: OK.
  eJaccard: OK.
  eDice: OK.
  correlation: OK.
  Chi-squared: OK.
  Phi-squared: OK.
  Tschuprow: OK.
  Cramer: OK.
  Pearson: OK.
  Gower: OK.
  Euclidean: OK.
  Bhjattacharyya: OK.
  Manhattan: OK.
  supremum: OK.
  Canberra: OK.
  Wave: OK.
  divergence: OK.
  Kullback: OK.
  Bray: OK.
  Soergel: OK.
  Podani: OK.
  Chord: OK.
  Geodesic: OK.
  Whittaker: OK.
  Hellinger: OK.
  > ## Minkowski
  > for (j in c(0.5, 1, 2, 3, Inf))
  +     {cat("Minkowski: p =", j); prtest("Minkowski", p = j); cat(": OK.\n")}
  Minkowski: p = 0.5: OK.
  Minkowski: p = 1: OK.
  Minkowski: p = 2: OK.
  Minkowski: p = 3: OK.
  Minkowski: p = Inf: OK.
  > 
  > ## Levenshtein distance
  > s <- c("A", "quick", "brown", "fox", "jumps", "over", "the", "lazy", "dog")
  > all(as.matrix(dist(s, "Levenshtein")) == dist(s, s, "Levenshtein"))
  Error in pr_Levenshtein_prefun(c("A", "quick", "brown", "fox", "jumps",  : 
    Need package 'cba'!
  Calls: as.matrix ... <Anonymous> -> dist -> do.call -> pr_Levenshtein_prefun
  Execution halted