• using R Under development (unstable) (2012-05-22 r59396)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘Bergm/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘Bergm’ version ‘2.3’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package ‘Bergm’ can be installed ... [10s/28s] OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... OK
• 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 package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking examples ... ERROR
  Running examples in ‘Bergm-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: bergm
  > ### Title: Bayesian exponential random graph models
  > ### Aliases: bergm
  >
  > ### ** Examples
  >
  > # load the Florentine marriage network
  > # included with the ergm package
  >
  > data(florentine)
  >
  > # Estimation of a 3-dimensional model
  > # measuring the propensity to form 2- and 3- stars.
  > # Population MCMC with ADS approach is used
  > # (this will take about 1 minute)
  >
  > flo <- bergm(flomarriage ~ edges + kstar(2:3),
  + burn.in=500,
  + aux.iters=3000,
  + main.iters=1500)
  >
  > # MCMC diagnostics
  >
  > bergm.output(flo)
  
  MCMC results for Model: y ~ edges + kstar(2:3)
  
  Posterior mean:
  theta1 (edges) theta2 (kstar2) theta3 (kstar3)
  Chain 1 -1.45516753 0.05601207 -0.09948583
  Chain 2 -1.80107424 0.17037442 -0.13843813
  Chain 3 -1.90914500 0.30069678 -0.24903487
  Chain 4 -1.72474534 0.16917262 -0.15070356
  Chain 5 -2.17012297 0.31565370 -0.20857494
  Chain 6 -2.03766714 0.27148108 -0.18918887
  
  Posterior sd:
  theta1 (edges) theta2 (kstar2) theta3 (kstar3)
  Chain 1 1.3270347 0.4390601 0.1961118
  Chain 2 1.4354476 0.4960586 0.2139340
  Chain 3 1.4894847 0.5820546 0.2787265
  Chain 4 1.1932793 0.4358149 0.2033169
  Chain 5 1.1216898 0.3825460 0.1895444
  Chain 6 1.1468433 0.4401119 0.2053061
  
  Acceptance rate:
  Chain 1 0.3286667
  Chain 2 0.3100000
  Chain 3 0.3393333
  Chain 4 0.3133333
  Chain 5 0.3206667
  Chain 6 0.3100000
  
  
  Overall posterior density estimate:
  theta1 (edges) theta2 (kstar2) theta3 (kstar3)
  Post. mean -1.849654 0.2138984 -0.1725710
  Post. sd 1.313207 0.4755551 0.2219537
  
  Overall acceptance rate: 0.320333333333333
  
  
  >
  > # Bayesian goodness-of-fit test
  >
  > bgof(flo,
  + n.sim=100,
  + n.deg=10,
  + n.dist=9,
  + n.esp=6)
  Error in .Internal(update.formula(as.formula(object), as.formula(new))) :
  no internal function "update.formula"
  Calls: bgof ... simulate.formula -> ergm.update.formula -> as.formula
  Execution halted