• using R version 2.10.0 Patched (2009-11-18 r50482)
• using session charset: ASCII
• checking for file 'networksis/DESCRIPTION' ... OK
• this is package 'networksis' version '1.0'
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking for executable files ... OK
• checking whether package 'networksis' can be installed ... WARNING
  Found the following significant warnings:
  Warning: ./man/simulate_sis.Rd:61: unknown macro '\times'
  See http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/networksis-00install.html for details.
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• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking index information ... OK
• checking package subdirectories ... WARNING
  Invalid citation information in 'inst/CITATION':
  'networksis' is part of the statnet suite of packages.
  Please read the license using license.statnet("networksis")
  
  If you are using the 'networksis' package for research that will be published,
  we request that you acknowledge this with the following citation:
  
  Mark S. Handcock, David R. Hunter, Carter T. Butts, Steven M. Goodreau,
  and Martina Morris (2003) statnet: Software Tools for the Statistical
  Modeling of Network Data. Version 2.0,
  URL http://statnetproject.org.
  
  A BibTeX entry for LaTeX users is
  
  @Manual{,
  title = {statnet: Software Tools for the Statistical Modeling of Network Data},
  author = {Mark S. Handcock and David R. Hunter and Carter T. Butts and Steven M. Goodreau and Martina Morris},
  year = {2003},
  note = {Version 2.0},
  address = {Seattle, WA},
  url = {http://statnetproject.org},
  }
• checking R files for non-ASCII characters ... OK
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• checking whether the package can be loaded ... OK
• checking whether the package 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 ... OK
• checking Rd files ... WARNING
  prepare_Rd: simulate_sis.Rd:61: unknown macro '\times'
• checking Rd metadata ... OK
• checking Rd cross-references ... WARNING
  Missing link(s) in documentation object './man/networksis-package.Rd':
  '[statnet]{statnet}'
  
  See the information in section 'Cross-references' of the 'Writing R
  Extensions' manual.
  
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• checking for portable use of $BLAS_LIBS ... OK
• checking examples ... ERROR
  Running examples in 'networksis-Ex.R' failed.
  The error most likely occurred in:
  
  > ### * finch
  >
  > flush(stderr()); flush(stdout())
  >
  > ### Name: finch
  > ### Title: Co-location of Darwin's Finches as a bipartite graph
  > ### Aliases: finch
  > ### Keywords: datasets
  >
  > ### ** Examples
  > ## Darwin's finches example ##
  > data(finch)
  > as.sociomatrix(finch)
  A B C D E F G H I J K L M N O P Q
  Large ground finch 0 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1
  Medium ground finch 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 0 0
  Small ground finch 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 0
  Sharp-beaked ground finch 0 0 1 1 1 0 0 1 0 1 0 1 1 0 1 1 1
  Cactus ground finch 1 1 1 0 1 1 1 1 1 1 0 1 0 1 1 0 0
  Large cactus ground finch 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0
  Large tree finch 0 0 1 1 1 1 1 1 1 0 0 1 0 1 1 0 0
  Medium tree finch 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
  Small tree finch 0 0 1 1 1 1 1 1 1 1 0 1 0 0 1 0 0
  Vegetarian finch 0 0 1 1 1 1 1 1 1 1 0 1 0 1 1 0 0
  Woodpecker finch 0 0 1 1 1 0 1 1 0 1 0 0 0 0 0 0 0
  Mangrove finch 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
  Warbler finch 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
  > plot(finch,vertex.col=c(rep(2,13),rep(3,17)),vertex.cex=2.5,displaylabels=FALSE)
  > ## Consider the graph statistic \bar{s}^2 (Roberts and Stone, 1990) ##
  > prob.vec<-rep(0,500)
  > s.bar.squared.vec<-rep(0,500)
  > for(i in 1:500)
  + {
  + sim<-simulate(finch, nsim=1)
  + ## Extract new bipartite graph ##
  + new.graph<-as.matrix.network(sim)
  + ## Calculate custom graph statistic ##
  + s.bar.squared<-(sum((new.graph%*%t(new.graph))^2)-
  + sum(diag((new.graph%*%t(new.graph))^2)))/(13*12)
  + s.bar.squared.vec[i]<-s.bar.squared
  + ## Graph probability ##
  + prob.vec[i]<-exp(sim %n% "log.prob")
  + }
  > ## Plot the null distribution of \bar{s}^2 ##
  > nbreaks<-75
  > w<-(1/prob.vec)/(sum(1/prob.vec))
  > intervals<-cut(s.bar.squared.vec, nbreaks, include.lowest=TRUE)
  > weights<-sapply(split(w, f=intervals), sum)
  > x<-seq(min(s.bar.squared.vec), max(s.bar.squared.vec), length.out=nbreaks)
  > plot(x,weights, type="h", xlab="", ylab="Probability Density", lwd=2)
  > abline(v=53.115)
  > ## Consider graph statistics "coincidences(x)", which measure ##
  > ## the number of finches sharing x islands ##
  > sim<-simulate_sis(finch~coincidences(0:17), nsim=1000)
  Error in vector("double", length) : invalid 'length' argument
  Calls: simulate_sis -> networksis.slave -> double -> vector
  Execution halted
• elapsed time (check, wall clock): 0:29