• using R version 2.10.0 Under development (unstable) (2009-07-01 r48886)
• using session charset: UTF-8
• checking for file 'BiodiversityR/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'BiodiversityR' version '1.2'
• checking package name space information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking for executable files ... OK
• checking whether package 'BiodiversityR' can be installed ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... NOTE
  Non-standard license specification:
  GPL v2
  Standardizable: TRUE
  Standardized license specification:
  GPL-2
• checking top-level files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the name space can be loaded with stated dependencies ... OK
• checking for unstated dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... NOTE
  import.from.Access: no visible global function definition for
  ‘odbcConnectAccess’
  import.from.Excel: no visible global function definition for
  ‘odbcConnectExcel’
• checking Rd files ... OK
• checking Rd files against version 2 parser ... WARNING
  Warning: ./man/rankabundance.Rd:50: Unnecessary braces at ‘{rankabuncomp}’
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking data for non-ASCII characters ... OK
• checking examples ... ERROR
  Running examples in 'BiodiversityR-Ex.R' failed.
  The error most likely occurred in:
  
  > ### * caprescale
  >
  > flush(stderr()); flush(stdout())
  >
  > ### Name: caprescale
  > ### Title: Rescaling of Capscale Results to Reflect Total Sums of Squares
  > ### Of Distance Matrix
  > ### Aliases: caprescale
  > ### Keywords: multivariate
  >
  > ### ** Examples
  >
  > library(vegan)
  > library(MASS)
  > data(dune)
  > data(dune.env)
  > Distmatrix.1 <- vegdist(dune,method='bray')
  > Ordination.model1 <- cmdscale(Distmatrix.1, k=19, eig=TRUE, add=FALSE)
  Warning in cmdscale(Distmatrix.1, k = 19, eig = TRUE, add = FALSE) :
  some of the first 19 eigenvalues are < 0
  Warning in sqrt(ev) : NaNs produced
  > # Sum of positive eigenvalues
  > sum(Ordination.model1$eig[1:14])
  [1] 4.593947
  > # [1] 4.593946896588808
  > Distmatrix.2 <- as.matrix(vegdist(Ordination.model1$points[,1:14],method='euc'))
  > totalsumsquares1 <- sum(Distmatrix.2^2)/(2*20)
  > # Sum of distances among sites in principal coordinates analysis on axes
  > # corresponding to positive eigenvalues
  > totalsumsquares1
  [1] 4.593947
  > # [1] 4.593946896588808
  > Ordination.model2 <- capscale(dune ~ Management,dune.env,dist='bray', add=FALSE)
  > # Total sums of squares of the distance-based redundancy analysis
  > Ordination.model2$tot.chi/19
  [1] 0.2262643
  > # [1] 4.593946896588808
  > Ordination.model3 <- caprescale(Ordination.model2, verbose=TRUE)
  SSTot obtained from all eigenvalues: 0.2262643
  SSTot reflected by distances among site scores on all axes: 0.3056471
  SSExpl obtained from eigenvalues of constrained axes: 0.0789546
  SSExpl reflected by distances among fitted site scores on constrained axes (scaling 1): 0.0789546
  SSRes obtained from eigenvalues of unconstrained axes: 0.1473097
  Error in as.matrix(x) : subscript out of bounds
  Calls: caprescale -> as.matrix -> vegdist -> nrow -> as.matrix
  Execution halted